# Copyright (C) 2013 by Zheng Ruan (zruan1991@gmail.com) # This code is part of the Biopython distribution and governed by its # license. Please see the LICENSE file that should have been included # as part of this package. """Unit tests for CodonAligner and Bio.Align.analysis.""" import unittest try: import numpy as np except ImportError: from Bio import MissingPythonDependencyError raise MissingPythonDependencyError( "Install numpy if you want to use Bio.Align." ) from None from Bio import Align from Bio import SeqIO from Bio.Align import Alignment from Bio.Align import CodonAligner from Bio.Align.analysis import calculate_dn_ds from Bio.Align.analysis import calculate_dn_ds_matrix from Bio.Align.analysis import mktest from Bio.Data import CodonTable from Bio.Seq import Seq from Bio.SeqRecord import SeqRecord class TestBasic(unittest.TestCase): def test_aligner(self): aligner = CodonAligner() self.assertEqual( str(aligner), """\ Codon aligner with parameters wildcard: 'X' match_score: 1.0 mismatch_score: 0.0 frameshift_minus_two_score: -3.0 frameshift_minus_one_score: -3.0 frameshift_plus_one_score: -3.0 frameshift_plus_two_score: -3.0 """, ) aligner.wildcard = "Y" aligner.match_score = 2.0 aligner.mismatch_score = -1.0 aligner.frameshift_score = -5.0 aligner.frameshift_two_score = -2.0 aligner.frameshift_minus_score = -4.0 self.assertEqual( str(aligner), """\ Codon aligner with parameters wildcard: 'Y' match_score: 2.0 mismatch_score: -1.0 frameshift_minus_two_score: -4.0 frameshift_minus_one_score: -4.0 frameshift_plus_one_score: -5.0 frameshift_plus_two_score: -2.0 """, ) self.assertEqual(aligner.wildcard, "Y") self.assertAlmostEqual(aligner.match_score, 2.0) self.assertAlmostEqual(aligner.mismatch_score, -1.0) self.assertAlmostEqual(aligner.frameshift_minus_two_score, -4.0) self.assertAlmostEqual(aligner.frameshift_minus_one_score, -4.0) self.assertAlmostEqual(aligner.frameshift_plus_one_score, -5.0) self.assertAlmostEqual(aligner.frameshift_plus_two_score, -2.0) def test_alignments(self): aligner = CodonAligner() aligner.frameshift_score = -1.0 dna = SeqRecord(Seq("TTTAAAAAAAAATTT"), id="dna") pro = SeqRecord(Seq("FKKKF"), id="pro") alignments = aligner.align(pro, dna) self.assertEqual(len(alignments), 1) self.assertAlmostEqual(alignments.score, 5.0) alignment = alignments[0] self.assertEqual( str(alignment), """\ pro 0 F K K K F 5 dna 0 TTTAAAAAAAAATTT 15 """, ) dna = SeqRecord(Seq("TTTAAAAAAAATTT"), id="dna") score = aligner.score(pro, dna) self.assertAlmostEqual(score, 4.0) alignments = aligner.align(pro, dna) self.assertEqual(len(alignments), 2) self.assertAlmostEqual(alignments.score, 4.0) alignment = alignments[0] self.assertEqual( str(alignment), """\ pro 0 F K K 3 dna 0 TTTAAAAAA 9 pro 3 K F 5 dna 8 AAATTT 14 """, ) alignment = alignments[1] self.assertEqual( str(alignment), """\ pro 0 F K 2 dna 0 TTTAAA 6 pro 2 K K F 5 dna 5 AAAAAATTT 14 """, ) dna = SeqRecord(Seq("TTTAAAAAAATTT"), id="dna") score = aligner.score(pro, dna) self.assertAlmostEqual(score, 4.0) alignments = aligner.align(pro, dna) self.assertEqual(len(alignments), 2) self.assertAlmostEqual(alignments.score, 4.0) alignment = alignments[0] self.assertEqual( str(alignment), """\ pro 0 F K K 3 dna 0 TTTAAAAAA 9 pro 3 K F 5 dna 7 AAATTT 13 """, ) alignment = alignments[1] self.assertEqual( str(alignment), """\ pro 0 F K 2 dna 0 TTTAAA 6 pro 2 K K F 5 dna 4 AAAAAATTT 13 """, ) dna = SeqRecord(Seq("TTTAAAAAATTT"), id="dna") score = aligner.score(pro, dna) self.assertAlmostEqual(score, 3.0) alignments = aligner.align(pro, dna) self.assertEqual(len(alignments), 2) self.assertAlmostEqual(alignments.score, 3.0) alignment = alignments[0] self.assertEqual( str(alignment), """\ pro 0 F K 2 dna 0 TTTAAA 6 pro 2 K 3 dna 5 AAA 8 pro 3 K F 5 dna 6 AAATTT 12 """, ) alignment = alignments[1] self.assertEqual( str(alignment), """\ pro 0 F K 2 dna 0 TTTAAA 6 pro 2 K 3 dna 4 AAA 7 pro 3 K F 5 dna 6 AAATTT 12 """, ) dna = SeqRecord(Seq("TTTAAAAATTT"), id="dna") score = aligner.score(pro, dna) self.assertAlmostEqual(score, 3.0) alignments = aligner.align(pro, dna) self.assertEqual(len(alignments), 1) self.assertAlmostEqual(alignments.score, 3.0) alignment = alignments[0] self.assertEqual( str(alignment), """\ pro 0 F K 2 dna 0 TTTAAA 6 pro 2 K 3 dna 4 AAA 7 pro 3 K F 5 dna 5 AAATTT 11 """, ) dna = SeqRecord(Seq("TTTAAAAAAAAAATTT"), id="dna") alignments = aligner.align(pro, dna) self.assertEqual(len(alignments), 6) self.assertAlmostEqual(alignments.score, 4.0) alignment = alignments[0] self.assertEqual( str(alignment), """\ pro 0 F K K K F 5 dna 0 TTTAAAAAAAAAATT 15 """, ) alignment = alignments[1] self.assertEqual( str(alignment), """\ pro 0 F K K K F 5 dna 1 TTAAAAAAAAAATTT 16 """, ) alignment = alignments[2] self.assertEqual( str(alignment), """\ pro 0 F -K K K F 5 dna 0 TTTAAAAAAAAAATTT 16 """, ) alignment = alignments[3] self.assertEqual( str(alignment), """\ pro 0 F K -K K F 5 dna 0 TTTAAAAAAAAAATTT 16 """, ) alignment = alignments[4] self.assertEqual( str(alignment), """\ pro 0 F K K -K F 5 dna 0 TTTAAAAAAAAAATTT 16 """, ) alignment = alignments[5] self.assertEqual( str(alignment), """\ pro 0 F K K K -F 5 dna 0 TTTAAAAAAAAAATTT 16 """, ) dna = SeqRecord(Seq("TTTAAAAAAAAAAATTT"), id="dna") alignments = aligner.align(pro, dna) self.assertEqual(len(alignments), 6) self.assertAlmostEqual(alignments.score, 4.0) alignment = alignments[0] self.assertEqual( str(alignment), """\ pro 0 F K K K F 5 dna 0 TTTAAAAAAAAAAAT 15 """, ) alignment = alignments[1] self.assertEqual( str(alignment), """\ pro 0 F K K K F 5 dna 2 TAAAAAAAAAAATTT 17 """, ) alignment = alignments[2] self.assertEqual( str(alignment), """\ pro 0 F --K K K F 5 dna 0 TTTAAAAAAAAAAATTT 17 """, ) alignment = alignments[3] self.assertEqual( str(alignment), """\ pro 0 F K --K K F 5 dna 0 TTTAAAAAAAAAAATTT 17 """, ) alignment = alignments[4] self.assertEqual( str(alignment), """\ pro 0 F K K --K F 5 dna 0 TTTAAAAAAAAAAATTT 17 """, ) alignment = alignments[5] self.assertEqual( str(alignment), """\ pro 0 F K K K --F 5 dna 0 TTTAAAAAAAAAAATTT 17 """, ) dna = SeqRecord(Seq("TTTAAAAAAAAAAAATTT"), id="dna") alignments = aligner.align(pro, dna) self.assertEqual(len(alignments), 2) self.assertAlmostEqual(alignments.score, 4.0) alignment = alignments[0] self.assertEqual( str(alignment), """\ pro 0 F K K K F 5 dna 0 TTTAAAAAAAAAAAA 15 """, ) alignment = alignments[1] self.assertEqual( str(alignment), """\ pro 0 F K K K F 5 dna 3 AAAAAAAAAAAATTT 18 """, ) class TestBuildAndIO(unittest.TestCase): def test1(self): aligner = CodonAligner() nucleotide_records = SeqIO.parse("codonalign/nucl1.fa", "fasta") protein_alignment = Align.read("codonalign/pro1.aln", "clustal") self.assertEqual(len(protein_alignment.sequences), 3) codon_alignments = [] nucleotide_record = next(nucleotide_records) protein_record = protein_alignment.sequences[0] self.assertEqual(nucleotide_record.id, protein_record.id) alignments = aligner.align(protein_record, nucleotide_record) self.assertEqual(len(alignments), 1) alignment = next(alignments) codon_alignments.append(alignment) self.assertTrue( np.array_equal(alignment.coordinates, np.array([[0, 183], [0, 549]])) ) self.assertEqual( str(alignment), """\ isotig697 0 R G D Q R S N F Q L S P S T M Q I S T G isotig697 0 AGAGGCGATCAACGCAGCAACTTCCAGCTGTCTCCCTCCACCATGCAGATCTCCACAGGG isotig697 20 L L C L L L V A T G F T S Q V L A H P G isotig697 60 CTTCTGTGCcTGCTGCTTGTGGCCACTGGCTTCACTTCCCAGGTGCTGGCTCACCCAGGC isotig697 40 S I P S T Y C F V M T S K K I P K S L L isotig697 120 TCTATCCCATCTACCTaCTGCTTTGTTATGACCAGTAAGAaGATCCCCAAATCACTACTG isotig697 60 K S Y K R I S N S R C T L K A I L F K T isotig697 180 AaGAGCTACAAAaGAATCTCCAACAGCAGATGCACCcTGAAAGCCATACTCTTCAAGACC isotig697 80 K S G K E I C A D P K K K W V Q D A T K isotig697 240 AAGTCGGGCAAAGAGATCTGTGCTGACCCCAAGAAGAAGTGGGTCcAGGATGCCACAAAG isotig697 100 H L D Q I L Q T P K P T I P S F E T H P isotig697 300 CACCTGGACCAAATCCTTCAAACTCCAAAACCGACAATCCCCTCTTTTGAGACTCACCCA isotig697 120 E T K K C F I H S P F L R R A P R S T Q isotig697 360 GAGACTAAGAAATGCTTCATTCATTCTCCATTCCTAAGACGTGCTCCAAGGTCAACTCAG isotig697 140 H H S P R T W L H L V M D R T E S H Y V isotig697 420 CACCATTCCCCAAGGACTTGGCTTCATTTAGTTATGGATAGAACTGAAAGTCATTATGTT isotig697 160 Q N K P D L K R L C N F L N M Q N L K R isotig697 480 CAGAATAAGCCAGACTTGAAGAGGTTGTGTAATTTCTTGAATATGCAAAATCTTAAAAGG isotig697 180 G A C 183 isotig697 540 GGGGCATGC 549 """, ) nucleotide_record = next(nucleotide_records) protein_record = protein_alignment.sequences[1] self.assertEqual(nucleotide_record.id, protein_record.id) alignments = aligner.align(protein_record, nucleotide_record) self.assertEqual(len(alignments), 1) alignment = next(alignments) codon_alignments.append(alignment) self.assertTrue( np.array_equal(alignment.coordinates, np.array([[0, 65], [0, 195]])) ) self.assertEqual( str(alignment), """\ ENSG00000 0 M K V S A A L L C L L L I A A T F I P Q ENSG00000 0 ATGAAAGTCTCTGCCGCCCTTCTGTGCCTGCTGCTCATAGCAGCCACCTTCATTCCCCAA ENSG00000 20 G L A Q P D A I N A P V T C C Y N F T N ENSG00000 60 GGGCTCGCTCAGCCAGATGCAATCAATGCCCCAGTCACCTGCTGTTATAACTTCACCAAT ENSG00000 40 R K I S V Q R L A S Y R R I T S S K C P ENSG00000 120 AGGAAGATCTCAGTGCAGAGGCTCGCGAGCTATAGAAGAATCACCAGCAGCAAGTGTCCC ENSG00000 60 K E A V M 65 ENSG00000 180 AAAGAAGCTGTGATG 195 """, ) nucleotide_record = next(nucleotide_records) protein_record = protein_alignment.sequences[2] self.assertEqual(nucleotide_record.id, protein_record.id) alignments = aligner.align(protein_record, nucleotide_record) self.assertEqual(len(alignments), 1) alignment = next(alignments) codon_alignments.append(alignment) self.assertTrue( np.array_equal(alignment.coordinates, np.array([[0, 99], [9, 306]])) ) self.assertEqual( str(alignment), """\ ENSG00000 0 M K V S A A L L C L L L I A A T F I P Q ENSG00000 9 ATGAAAGTCTCTGCCGCCCTTCTGTGCCTGCTGCTCATAGCAGCCACCTTCATTCCCCAA ENSG00000 20 G L A Q P D A I N A P V T C C Y N F T N ENSG00000 69 GGGCTCGCTCAGCCAGATGCAATCAATGCCCCAGTCACCTGCTGTTATAACTTCACCAAT ENSG00000 40 R K I S V Q R L A S Y R R I T S S K C P ENSG00000 129 AGGAAGATCTCAGTGCAGAGGCTCGCGAGCTATAGAAGAATCACCAGCAGCAAGTGTCCC ENSG00000 60 K E A V I F K T I V A K E I C A D P K Q ENSG00000 189 AAAGAAGCTGTGATCTTCAAGACCATTGTGGCCAAGGAGATCTGTGCTGACCCCAAGCAG ENSG00000 80 K W V Q D S M D H L D K Q T Q T P K T ENSG00000 249 AAGTGGGTTCAGGATTCCATGGACCACCTGGACAAGCAAACCCAAACTCCGAAGACT ENSG00000 99 ENSG00000 306 """, ) alignment = protein_alignment.mapall(codon_alignments) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[0, 42, 126, 126, 231, 333, 549], [0, 0, 84, 90, 195, 195, 195], [9, 9, 93, 99, 204, 306, 306]]) # fmt: on ) ) self.assertEqual( format(alignment, "clustal"), """\ isotig69710 AGAGGCGATCAACGCAGCAACTTCCAGCTGTCTCCCTCCACCATGCAGAT ENSG00000108691:ENST0000058090 ------------------------------------------ATGAAAGT ENSG00000108691:ENST0000022583 ------------------------------------------ATGAAAGT isotig69710 CTCCACAGGGCTTCTGTGCcTGCTGCTTGTGGCCACTGGCTTCACTTCCC ENSG00000108691:ENST0000058090 CTCTGCCGCCCTTCTGTGCCTGCTGCTCATAGCAGCCACCTTCATTCCCC ENSG00000108691:ENST0000022583 CTCTGCCGCCCTTCTGTGCCTGCTGCTCATAGCAGCCACCTTCATTCCCC isotig69710 AGGTGCTGGCTCACCCAGGCTCTATC------CCATCTACCTaCTGCTTT ENSG00000108691:ENST0000058090 AAGGGCTCGCTCAGCCAGATGCAATCAATGCCCCAGTCACCTGCTGTTAT ENSG00000108691:ENST0000022583 AAGGGCTCGCTCAGCCAGATGCAATCAATGCCCCAGTCACCTGCTGTTAT isotig69710 GTTATGACCAGTAAGAaGATCCCCAAATCACTACTGAaGAGCTACAAAaG ENSG00000108691:ENST0000058090 AACTTCACCAATAGGAAGATCTCAGTGCAGAGGCTCGCGAGCTATAGAAG ENSG00000108691:ENST0000022583 AACTTCACCAATAGGAAGATCTCAGTGCAGAGGCTCGCGAGCTATAGAAG isotig69710 AATCTCCAACAGCAGATGCACCcTGAAAGCCATACTCTTCAAGACCAAGT ENSG00000108691:ENST0000058090 AATCACCAGCAGCAAGTGTCCCAAAGAAGCTGTGATG------------- ENSG00000108691:ENST0000022583 AATCACCAGCAGCAAGTGTCCCAAAGAAGCTGTGATCTTCAAGACCATTG isotig69710 CGGGCAAAGAGATCTGTGCTGACCCCAAGAAGAAGTGGGTCcAGGATGCC ENSG00000108691:ENST0000058090 -------------------------------------------------- ENSG00000108691:ENST0000022583 TGGCCAAGGAGATCTGTGCTGACCCCAAGCAGAAGTGGGTTCAGGATTCC isotig69710 ACAAAGCACCTGGACCAAATCCTTCAAACTCCAAAACCGACAATCCCCTC ENSG00000108691:ENST0000058090 -------------------------------------------------- ENSG00000108691:ENST0000022583 ATGGACCACCTGGACAAGCAAACCCAAACTCCGAAGACT----------- isotig69710 TTTTGAGACTCACCCAGAGACTAAGAAATGCTTCATTCATTCTCCATTCC ENSG00000108691:ENST0000058090 -------------------------------------------------- ENSG00000108691:ENST0000022583 -------------------------------------------------- isotig69710 TAAGACGTGCTCCAAGGTCAACTCAGCACCATTCCCCAAGGACTTGGCTT ENSG00000108691:ENST0000058090 -------------------------------------------------- ENSG00000108691:ENST0000022583 -------------------------------------------------- isotig69710 CATTTAGTTATGGATAGAACTGAAAGTCATTATGTTCAGAATAAGCCAGA ENSG00000108691:ENST0000058090 -------------------------------------------------- ENSG00000108691:ENST0000022583 -------------------------------------------------- isotig69710 CTTGAAGAGGTTGTGTAATTTCTTGAATATGCAAAATCTTAAAAGGGGGG ENSG00000108691:ENST0000058090 -------------------------------------------------- ENSG00000108691:ENST0000022583 -------------------------------------------------- isotig69710 CATGC ENSG00000108691:ENST0000058090 ----- ENSG00000108691:ENST0000022583 ----- """, ) def test2(self): aligner = CodonAligner() nucleotide_records = SeqIO.parse("codonalign/nucl2.fa", "fasta") protein_alignment = Align.read("codonalign/pro2.aln", "clustal") self.assertEqual(len(protein_alignment.sequences), 3) codon_alignments = [] nucleotide_record = next(nucleotide_records) protein_record = protein_alignment.sequences[0] self.assertEqual(nucleotide_record.id, protein_record.id) alignments = aligner.align(protein_record, nucleotide_record) self.assertEqual(len(alignments), 1) alignment = next(alignments) codon_alignments.append(alignment) self.assertTrue( np.array_equal(alignment.coordinates, np.array([[0, 1094], [0, 3282]])) ) self.assertEqual( str(alignment), """\ isotig351 0 E R Q G R W C V P G E A V E A R V S R S isotig351 0 GAAAGGCAGGGTCGctGGTGCGTGCCCGGCGAGGCTGTGGAGGCCcgTGTGTCTAGAAGC isotig351 20 C V R E M A E P G R R R G P R S R G G G isotig351 60 TGTGTGAGAGAGATGGCGGAACCCGGGAGGAGACGGGGTCCGAGGTCCCGCGGTGGCGGC isotig351 40 A G R G A R R A R V A R G R R P R A P Q isotig351 120 GCCGGCCGAGGCgCTCGAAGAGCCCGGGTCGCCCGTGGCCGGCGTCCTCGCGCCCCGCAG isotig351 60 S L S R L I P D T V L V D L V S D S D E isotig351 180 TCTCTGTCCCGGCTCATTCCAGACACGGTGCTTGTGGACTTGGTCAGTGACAGCGACGAG isotig351 80 E I L E V V A D P V E A P A A R A P A P isotig351 240 GAGATCCTGGAAGTCGTCGCGGACCCGGTAGAAGCGCCCGCCGCCCGGGCcCCcGCGCCG isotig351 100 A A H G Q D S D S D S A G A D E G P A G isotig351 300 GCCGCACATGGGCAGGACAGCGACAGCGACAGTGCAGGGGCGgACGAGGGGCCTGCAGGA isotig351 120 A P Q T L V R R R R R R L L D P G E A P isotig351 360 GCCCCTCAGACCTTGGTCCGGCGGCGGCGCCGGCGGCTGCTGGATCCCGGCGAGGCACCG isotig351 140 V V P V Y S G K V Q S S L N L I P D N S isotig351 420 GTGGTTCCTGTGTACTCCGGGAAGGTACAAAGCAGCCTCAACCTCATCCCAGATAATTCA isotig351 160 S L L K L C P S E P E D E A D V T D C G isotig351 480 TCCCTCTTGAAACTTTGCCCCTCAGAGCCTGAAGATGAGGCAGATGTGACAGATTGTGGC isotig351 180 S P P P E D A L I P G S P W K K K L R N isotig351 540 AGTCCTCCTCCTGAGGATGCCCTAATTCCAGGTTCTCCCTGGAAGAAGAAGCTGAGGAAT isotig351 200 K H E K E E M K M E E F P D Q D I S P L isotig351 600 AAGCATGAAAAaGAAGAGATGAAGATGGAAGAGTTtCCGGACCAGGACATCTCTCCTTTG isotig351 220 P R P S S R N K S R K H T E A L Q K L R isotig351 660 CCCCGACCTTCATCAAGAAaCAAAAGCAGAAAGCATACCGAGGCACTCCAGAAGTTGAGG isotig351 240 E V N K R L Q D L R S C L S P K Q H Q S isotig351 720 GAAGTGAACAAGCGCCTCCAAGATCTCCGATCCTGCCTGAGCCCCAAGCAGCACCAGAGT isotig351 260 P A L Q N P D D E V V L V D G P V L S Q isotig351 780 CCAGCCCTTCAGAACCCAGATGATGAGGTGGTCCTCGTGGACGGGCCTGtCTTGTCACAG isotig351 280 S P R L F T L K I R C R A D L V R L P V isotig351 840 AGCCCGAGACTCTTCACCCTCAAGATCCGGTGCCGGGCTGACCTAGTCAGATTGCCCGTC isotig351 300 M T S E P L Q N V V D Y M A N H L G V S isotig351 900 ATGACATCGGAACCCCTTCAGAATGTGGTGGATTACATGGCCAATCATCTTGGGGTGTCT isotig351 320 P S R I L L L F G E T E L S P T A T P R isotig351 960 CCAAGCAGGATTCTTTTACTCTTTGGAGAGACAGAACTGTCCCCTACTGCCACCCCTAGG isotig351 340 T L K L G V A D I I D C V V L T S S S E isotig351 1020 ACCCTAAAGCTTGGTGTGGCTGACATCATTGATTGTGTGGTGCTGACAAGTTCTTCAGAG isotig351 360 A T E T T Q Q L C L R V Q G K E K H Q M isotig351 1080 GCCACAGAGACAACCCAGCAGCTCTGCCTCCGGGTGCAGGGGAAGGAGAAGCACCAGATG isotig351 380 L E I S L S P D S P L E V L M A H Y E E isotig351 1140 TTGGAGATCTCACTCTCTCCTGACTCtCCTCTTGAGGTCCTCATGGCGCACTATGAGGAG isotig351 400 A M G L S G H K L S F F F D G T K L S G isotig351 1200 GCCATGGGACTCTCCGGACACAAGCTCTCCTTCTTCTTCGATGGGACAAAGCTGTCGGGC isotig351 420 K E L P A D L G M E S G D L I E V W G S isotig351 1260 AAGGAGCTGCCAGCTGATCTGGGCATGGAATCCGGGGATCTCATTGAAGTTTGGGGCAGC isotig351 440 F L L L F G C R A K T W G Q Q L P L L L isotig351 1320 TTCCTCCTCCTGTTTGGATGCAGAGCCAAGACTTGGGGACAACAGCTCCCACTTTtATTA isotig351 460 L F F A P G L T E T E L E L V Y L F P A isotig351 1380 TTATTTTTtGCCCcAGGGCTAACAGAAACCGAATTAGAACTCGTTTATTTATTTCCGGCA isotig351 480 L G I E P R A V H M L R M C E V E V K P isotig351 1440 CTGGGGATTGAACCCAGGGCTGTGCATATGCTAAGGATGTGTGAAGTTGAGGTAAAaCCA isotig351 500 R H D L C P V S L T V V S S G L I G N C isotig351 1500 AGGCATGACCTTTGCCcTGTCTCGTTGACCGTAGTCTCAAGCGGTCTGATTGGTAATTGT isotig351 520 V T V A A L G G L W L C V L V L C T A A isotig351 1560 GTGACTGTGGCTGCCCTGGGTGgCCTGTGGCTGTGTGTGTTGGTGCTGTGTACAGCAGCT isotig351 540 P G A W R R G I G F P T I S F S S A Q M isotig351 1620 CCTGGGGCATGGAGAAGGGGTATTGGCTTCCCTACCATTTCGTTCAGTAGTGCACAAATG isotig351 560 S L A F G C P G L F M P H W G P T G I L isotig351 1680 AGCCTTGCATTTGGGTGCCCAGGCTTGTTTATGCCACATTGGGGACCAACAGGGATTTTA isotig351 580 I L I W G L R C R Y L P W W G S V A G K isotig351 1740 ATTCTCATTTGGGGGCTGAGATGCAGGTACCTTCCCTGGTGGGGATCGGTTGCAGGGAAA isotig351 600 T S N D I Y A E A E D V D S G F L K A N isotig351 1800 ACAAGCAATGACATCTATGCTGAAGCTGAGGACGTAGACAGTGGGTTTTTAAAGGCTAAC isotig351 620 R S G V F S P G H P L S Q D S A S I W Y isotig351 1860 AGGAGTGGTGTCTTCAGCCCTGGGCATCCACTCTCCCAGGACTCGGCCAGCATCTGGTAC isotig351 640 I L P G M H I P H L S T C S C V C L L F isotig351 1920 ATACTTCCTGGCATGCACATCCCACATCTGAGCACATGCAGCTGTGTTTGTTTACTCTTC isotig351 660 R P P A L S C Q H P L G I F V S E C L Y isotig351 1980 cGTCCTCCCGCCCTCTCCTGTCAGCACCCACTTGGTATATTTGTATCTGAATGTCTTTAT isotig351 680 K M I F M C V I L V Y V H G T V Q T F C isotig351 2040 AAGATGATTTTCATGTGTGTGATTTTAGTGTATGTACATGGTACTGTGCAAACATTCTGT isotig351 700 L H S V V T G P C H L L D L L L F R S A isotig351 2100 CTTCACTCAGTGGTGACAGGCCCATGTCACCTTCTAGATCTGTTGTTGTTCCGATCTGCT isotig351 720 V A A P W H M I L L T H C L N W R D T V isotig351 2160 GTGGCTGCCCCATGGCATATGATATTACTCACACATTGCCTTAATTGGAGGGATACCGTC isotig351 740 A S S E P N S R P Q Q T S F C V F P S G isotig351 2220 GCCAGCTCCGAACCAAATTCCAGACCACAGCAAACATCTTTTTGTGTGTTCCCTTCTGGG isotig351 760 P G V I V W H T C P G W D C G L R R F I isotig351 2280 CCAGGGGTAATTGTCTGGCATACTTGCCCAGGATGGGACTgTGGGTTACGCAGGTTCATT isotig351 780 S L V F L G F S S E C G L L F L E L L F isotig351 2340 TcTCTGGTTTTTCTAGGgTTTTCTTCAGAATGTGGACTGCTTTTCTTGGAGCTTCTcTTT isotig351 800 P S L D Q Y L V L L Y F L I C Q S T V Y isotig351 2400 CCTTcTCTTGACCAGTATTTAGTGTTGttgTACTTTCTGATTTGCCAGTCTACTGTGTAT isotig351 820 K A L H I L I S F I P P F L I N V H L L isotig351 2460 AAAGCACTGCATATCTTAATATCCTTTATCCCACCATTTCTTATCAATGTCCACCTTCTG isotig351 840 V F L C L L V F L G F L L C V F S V R S isotig351 2520 GTTTTTCTTTGTCTGCTTGTTTTCTTGGGCTTCCTTTTGTGTGTTTTTtCTGTGAGGAGT isotig351 860 C L C S R Q L Q I T F R I A L C V P R G isotig351 2580 TGCTTGTGTTCTaGgCAATTGCAAATAACCTTCAGAATAGCACTTTGTGTACCCAGGGGG isotig351 880 I F T K Q T F L T L M Q T A G F C K G F isotig351 2640 ATTTTCACCAAACAGACATTCTTAACTTTAATGCAGACAGCTGGCTTTTGTAAAGGGTTT isotig351 900 F V L C F F F F C F C F C F L R E N E K isotig351 2700 TTTGTTTTGTGTTTtTTTTTtttttGCTTTTGTTTTtGcTTTTTAAGGGAAAATGAGAAA isotig351 920 E L P E W Q G F R G V S G L L L L D L T isotig351 2760 GAACTTCCAGAATGGCAGGGGTTCCGGGGAGTCTCAGGATTGCTACTTTTGGATCTCACT isotig351 940 S E T F I V F C L A S F L F F C F Y L S isotig351 2820 AGTGAAACTTTCATTGTCTTCTGTCTTGCTAGTTTTTTGTTCTTTTGTTTTTATCTCTCA isotig351 960 Y D H M R I E F L I C C G V D T D C S E isotig351 2880 TATGACCACATGAGAATAGAGTTCCTGATCTGCTGTGGTGTGGATaCTGACTGTTCTGAa isotig351 980 L S T L L L T G Y S T V L V P D Y C M L isotig351 2940 CTTTCCACTCTGCTTCTCACTGGTTACAGCACTGTACTGGTTCCTGACTATTGTATGTtA isotig351 1000 R L N H L K C T F V W E S K F Y C V L I isotig351 3000 CGTCTAAACCATCTGAAATGCACCTTTGTGTGGGAGAGCAAATTTTATTGTGTTTTAATT isotig351 1020 I M S Q F S K L C L L K N Y V V L S Q E isotig351 3060 ATAATGAGCCAGTTTTCtAAGCTTTGTCTaCTAAAAAATTATGTAGTCCTTTCACAAGAA isotig351 1040 V C Q L L K N F F C E N M L Y L I L I F isotig351 3120 GTATGTCAACTTCTtAAAAATTTTTTTtGtGAGAATATGTTATACCTTATTTTAATATTT isotig351 1060 K N S M T Y S F Q V S Q L L Y D N I T H isotig351 3180 AAAAATTCCATGACATATAGCTTCCAGGTTTCTCAGCTCTTGTATGACAATATCACACAT isotig351 1080 Y Y Y V F N L S Q R E M P L 1094 isotig351 3240 TaCTATTATGTATTCAATCTCAGCCAAAGGGAGATGCCTTTA 3282 """, ) nucleotide_record = next(nucleotide_records) protein_record = protein_alignment.sequences[1] self.assertEqual(nucleotide_record.id, protein_record.id) alignments = aligner.align(protein_record, nucleotide_record) self.assertEqual(len(alignments), 1) alignment = next(alignments) codon_alignments.append(alignment) self.assertTrue( np.array_equal(alignment.coordinates, np.array([[0, 1104], [0, 3312]])) ) self.assertEqual( str(alignment), """\ isotig351 0 E R Q G R W C V P G E A V E A R V S R S isotig351 0 GAAAGGCAGGGTCGctGGTGCGTGCCCGGCGAGGCTGTGGAGGCCcgTGTGTCTAGAAGC isotig351 20 C V R E M A E P G R R R G P R S R G G G isotig351 60 TGTGTGAGAGAGATGGCGGAACCCGGGAGGAGACGGGGTCCGAGGTCCCGCGGTGGCGGC isotig351 40 A G R G A R R A R V A R G R R P R A P Q isotig351 120 GCCGGCCGAGGCgCTCGAAGAGCCCGGGTCGCCCGTGGCCGGCGTCCTCGCGCCCCGCAG isotig351 60 S L S R L I P D T V L V D L V S D S D E isotig351 180 TCTCTGTCCCGGCTCATTCCAGACACGGTGCTTGTGGACTTGGTCAGTGACAGCGACGAG isotig351 80 E I L E V V A D P V E A P A A R A P A P isotig351 240 GAGATCCTGGAAGTCGTCGCGGACCCGGTAGAAGCGCCCGCCGCCCGGGCcCCcGCGCCG isotig351 100 A A H G Q D S D S D S A G A D E G P A G isotig351 300 GCCGCACATGGGCAGGACAGCGACAGCGACAGTGCAGGGGCGgACGAGGGGCCTGCAGGA isotig351 120 A P Q T L V R R R R R R L L D P G E A P isotig351 360 GCCCCTCAGACCTTGGTCCGGCGGCGGCGCCGGCGGCTGCTGGATCCCGGCGAGGCACCG isotig351 140 V V P V Y S G K V Q S S L N L I P D N S isotig351 420 GTGGTTCCTGTGTACTCCGGGAAGGTACAAAGCAGCCTCAACCTCATCCCAGATAATTCA isotig351 160 S L L K L C P S E P E D E A D V T D C G isotig351 480 TCCCTCTTGAAACTTTGCCCCTCAGAGCCTGAAGATGAGGCAGATGTGACAGATTGTGGC isotig351 180 S P P P E D A L I P G S P W K K K L R N isotig351 540 AGTCCTCCTCCTGAGGATGCCCTAATTCCAGGTTCTCCCTGGAAGAAGAAGCTGAGGAAT isotig351 200 K H E K E E M K M E E F P D Q D I S P L isotig351 600 AAGCATGAAAAaGAAGAGATGAAGATGGAAGAGTTtCCGGACCAGGACATCTCTCCTTTG isotig351 220 P R P S S R N K S R K H T E A L Q K L R isotig351 660 CCCCGACCTTCATCAAGAAaCAAAAGCAGAAAGCATACCGAGGCACTCCAGAAGTTGAGG isotig351 240 E V N K R L Q D L R S C L S P K Q H Q S isotig351 720 GAAGTGAACAAGCGCCTCCAAGATCTCCGATCCTGCCTGAGCCCCAAGCAGCACCAGAGT isotig351 260 P A L Q N P D D E V V L V D G P V L S Q isotig351 780 CCAGCCCTTCAGAACCCAGATGATGAGGTGGTCCTCGTGGACGGGCCTGtCTTGTCACAG isotig351 280 S P R L F T L K I R C R A D L V R L P V isotig351 840 AGCCCGAGACTCTTCACCCTCAAGATCCGGTGCCGGGCTGACCTAGTCAGATTGCCCGTC isotig351 300 M T S E P L Q N V V D Y M A N H L G V S isotig351 900 ATGACATCGGAACCCCTTCAGAATGTGGTGGATTACATGGCCAATCATCTTGGGGTGTCT isotig351 320 P S R I L L L F G E T E L S P T A T P R isotig351 960 CCAAGCAGGATTCTTTTACTCTTTGGAGAGACAGAACTGTCCCCTACTGCCACCCCTAGG isotig351 340 T L K L G V A D I I D C V V L T S S S E isotig351 1020 ACCCTAAAGCTTGGTGTGGCTGACATCATTGATTGTGTGGTGCTGACAAGTTCTTCAGAG isotig351 360 A T E T T Q Q L C L R V Q G K E K H Q M isotig351 1080 GCCACAGAGACAACCCAGCAGCTCTGCCTCCGGGTGCAGGGGAAGGAGAAGCACCAGATG isotig351 380 L E I S L S P D S P L E V L M A H Y E E isotig351 1140 TTGGAGATCTCACTCTCTCCTGACTCgCCTCTTGAGGTCCTCATGGCGCACTATGAGGAG isotig351 400 A M G L S G H K L S F F F D G T K L S G isotig351 1200 GCCATGGGACTCTCCGGACACAAGCTCTCCTTCTTCTTCGATGGGACAAAGCTGTCGGGC isotig351 420 K E L P A D L G M E S G D L I E V W G S isotig351 1260 AAGGAACTGCCAGCTGATCTGGGCATGGAATCCGGGGATCTCATTGAAGTTTGGGGCAGC isotig351 440 F L L L F G C R A K T W G Q Q L P L L L isotig351 1320 TTCCTCCTCCTGTTTGGATGCAGAGCCAAGACTTGGGGACAACAGCTCCCACTTTTATTA isotig351 460 L F F A P G L T E T E L E L V Y L F P A isotig351 1380 TTATTTTTTGCCCCAGGGCTAACAGAAACCGAATTAGAACTCGTTTATTTATTTCCGGCA isotig351 480 L G I E P W A V H M L R M C E V E V K P isotig351 1440 CTGGGGATTGAACCCTGGGCTGTGCATATGCTAAGGATGTGTGAAGTTGAGGTAAAACCA isotig351 500 R H D L C P V S L T D W L C D C G C P G isotig351 1500 AGGCATGACCTTTGCCCTGTCTCGTTGACCGATTGGTTGTGTGACTGTGGCTGCCCTGGG isotig351 520 W P V A V C V G A V D S S S W G M E K G isotig351 1560 TGGCCTGTGGCTGTGTGTGTTGGTGCTGTGGACAGCAGCTCCTGGGGCATGGAGAAGGGG isotig351 540 Y W L P Y H F V Q C T N E P C I W V P R isotig351 1620 TATTGGCTTCCCTACCATTTCGTTCAGTGCACAAATGAGCCTTGCATTTGGGTGCCCAGG isotig351 560 L V I Y A T L G T N R D F N S H L G A E isotig351 1680 CTTGTGATTTATGCCACATTGGGGACCAACAGGGATTTTAATTCTCATTTGGGGGCTGAG isotig351 580 M Q V P S L V G I V G C R E I N K Q H L isotig351 1740 ATGCAGGTACCTTCCCTGGTGGGGATAGTCGGTTGCAGGGAAATAAACAAGCAACATCTA isotig351 600 C S G L G R Q W V I F K G Q E W C L Q P isotig351 1800 TGCAGCGGACTAGGTAGACAGTGGGTAATTTTTAAAGGCCAGGAGTGGTGTCTTCAGCCC isotig351 620 W A S T L P G L G Q H L V H T S W H A H isotig351 1860 TGGGCATCCACTCTCCCAGGACTCGGCCAGCATCTGGTACATACTTCCTGGCATGCACAT isotig351 640 L A T S E H M Q L L S L M F T L V P S S isotig351 1920 CTAGCCACATCTGAGCACATGCAGCTGTTGAGTTTGATGTTTACTCTAGTTCcGTCCTCC isotig351 660 R P L L S A P T W Y I C I M S L D D F L isotig351 1980 CGCCCTCTCCTGTCAGCACCCACTTGGTATATTTGTATCATGTCTTTAGATGATTTTCTG isotig351 680 N V C D F S V C T W Y C A I D I L S S L isotig351 2040 AATGTGTGTGATTTTAGTGTATGTACATGGTACTGTGCAATAGACATTCTGTCTTCACTC isotig351 700 S V S D R L A M L A P S R S V V V P I C isotig351 2100 AGTGTGAGTGACAGGCTAGCCATGTTAGCACCTTCTAGATCTGTTGTTGTTCCGATCTGC isotig351 720 C G C P I V A L D D I T H T L P L E G Y isotig351 2160 TGTGGCTGCCCCATAGTGGCATTAGATGATATTACTCACACATTGCCTTTGGAGGGATAC isotig351 740 L S R Q L L G T K F Q T T A N I F L C V isotig351 2220 CTGAGTCGCCAGCTCCTAGGAACCAAATTCCAGACCACAGCAAACATCTTTTTGTGTGTT isotig351 760 P F W A R V G N C L A Y L P R M G L W V isotig351 2280 CCCTTCTGGGCCAGGGTAGGTAATTGTCTGGCATACTTGCCCAGGATGGGACTgTGGGTT isotig351 780 T Q V H F S G F S R V F F R M W T A F L isotig351 2340 ACGCAGGTTCATTTcTCTGGTTTTTCTAGGgTTTTCTTCAGAATGTGGACTGCTTTTCTT isotig351 800 G A S L S F S P V F S V V V L S D L P V isotig351 2400 GGAGCTTCTcTTTCCTTcTCTCCAGTATTTAGTGTTGttgTACTTTCTGATTTGCCAGTC isotig351 820 Y C V S T A Y L N I L Y L T T I S Y Q C isotig351 2460 TACTGTGTAAGCACTGCATATCTTAATATCCTTTATCTGACCACCATTTCTTATCAATGT isotig351 840 P P S G F S L L A A C F L V R L P F V C isotig351 2520 CCACCTTCTGGTTTTTCTTTGTTAGCTGCTTGTTTTCTTGTGAGGCTTCCTTTTGTGTGT isotig351 860 F F C E E L L V F A I A N N L Q N S T L isotig351 2580 TTTTtCTGTGAGGAGTTGCTTGTGTTCgCAATTGCAAATAACCTTCAGAATAGCACTTTG isotig351 880 C T Q G D F H Q T D I L N F N A D S W L isotig351 2640 TGTACCCAGGGGGATTTTCACCAAACAGACATTCTTAACTTTAATGCAGACAGCTGGCTT isotig351 900 L L E R V F C F V F F F F L L L F L L F isotig351 2700 TTGTTAGAAAGGGTTTTTTGTTTTGTGTTTtTTTTTtttttGCTTTTGTTTTtGcTTTTT isotig351 920 K G K E R T S R M A G V L A G S L R I A isotig351 2760 AAGGGAAAAGAAAGAACTTCCAGAATGGCAGGGGTTCTAGCGGGGAGTCTCAGGATTGCT isotig351 940 T F G S L N L R N F H C L L L A C F F V isotig351 2820 ACTTTTGGATCTCTAAACTTAAGAAACTTTCATTGTCTTCTGTTAGCTTGCTTTTTTGTT isotig351 960 L L F L S L I L R P L N E N R V L T D L isotig351 2880 CTTTTGTTTTTATCTCTCATATTGAGACCACTAAATGAGAATAGAGTTCTAACTGATCTG isotig351 980 L W C G Y L F T F H S A S H W L Q L D C isotig351 2940 CTGTGGTGTGGATaCCTGTTCaCTTTCCACTCTGCTTCTCACTGGTTACAGCTAGACTGT isotig351 1000 T G S L L Y V T S K P S E M H L C V G E isotig351 3000 ACTGGTTCCCTATTGTATGTtACGTCTAAACCATCTGAAATGCACCTTTGTGTGGGAGAG isotig351 1020 Q I L L C F N Y N E P V F A L S T K K L isotig351 3060 CAAATTTTATTGTGTTTTAATTATAATGAGCCAGTTTTCGCTTTGTCTaCTAAAAAATTA isotig351 1040 I C S L T F T R S M S T S K F F L E Y V isotig351 3120 ATATGTAGTCTGACTTTCACAAGAAGTATGTCAACTTCTAAATTTTTTTtGGAATATGTT isotig351 1060 I P L N F N I K F H D I V L P G F S A L isotig351 3180 ATACCTTTGAATTTTAATATTAAATTCCATGACATAGTACTTCCAGGTTTCTCAGCTCTT isotig351 1080 V Q L M N L N T L L L C I Q S Q P I K G isotig351 3240 GTACAATTAATGAATCTGAACACATTaCTATTATGTATTCAATCTCAGCCAATAAAGGGA isotig351 1100 D A F N 1104 isotig351 3300 GATGCCTTTAAC 3312 """, ) nucleotide_record = next(nucleotide_records) protein_record = protein_alignment.sequences[2] self.assertEqual(nucleotide_record.id, protein_record.id) alignments = aligner.align(protein_record, nucleotide_record) self.assertEqual(len(alignments), 1) alignment = next(alignments) codon_alignments.append(alignment) self.assertTrue( np.array_equal(alignment.coordinates, np.array([[0, 419], [0, 1257]])) ) self.assertEqual( str(alignment), """\ ENSG00000 0 M A E P V G K R G R W S G G S G A G R G ENSG00000 0 ATGGCGGAGCCTGTGGGGAAGCGGGGCCGCTGGTCCGGAGGTAGCGGTGCCGGCCGAGGG ENSG00000 20 G R G G W G G R G R R P R A Q R S P S R ENSG00000 60 GGTCGGGGCGGCTGGGGCGGTCGGGGCCGGCGTCCTCGGGCCCAGCGGTCTCCATCCCGG ENSG00000 40 G T L D V V S V D L V T D S D E E I L E ENSG00000 120 GGCACGCTGGACGTAGTGTCTGTGGACTTGGTCACCGACAGCGATGAGGAAATTCTGGAG ENSG00000 60 V A T A R G A A D E V E V E P P E P P G ENSG00000 180 GTCGCCACCGCTCGCGGTGCCGCGGACGAGGTTGAGGTGGAGCCCCCGGAGCCCCCGGGG ENSG00000 80 P V A S R D N S N S D S E G E D R R P A ENSG00000 240 CCGGTCGCGTCCCGGGATAACAGCAACAGTGACAGCGAAGGGGAGGACAGGCGGCCCGCA ENSG00000 100 G P P R E P V R R R R R L V L D P G E A ENSG00000 300 GGACCCCCGCGGGAGCCGGTCAGGCGGCGGCGGCGGCTGGTGCTGGATCCGGGGGAGGCG ENSG00000 120 P L V P V Y S G K V K S S L R L I P D D ENSG00000 360 CCGCTGGTTCCGGTGTACTCGGGGAAGGTTAAAAGCAGCCTTCGCCTTATCCCAGATGAT ENSG00000 140 L S L L K L Y P P G D E E E A E L A D S ENSG00000 420 CTATCCCTCCTGAAACTCTACCCTCCAGGGGATGAGGAAGAGGCAGAGCTGGCAGATTCG ENSG00000 160 S G L Y H E G S P S P G S P W K T K L R ENSG00000 480 AGTGGTCTCTACCATGAGGGCTCCCCATCACCAGGCTCTCCCTGGAAGACAAAGCTGAGG ENSG00000 180 T K D K E E K K K T E F L D L D N S P L ENSG00000 540 ACTAAGGATAAAGAAGAGAAGAAAAAGACAGAGTTTCTGGATCTGGACAACTCTCCTCTG ENSG00000 200 S P P S P R T K S R T H T R A L K K L S ENSG00000 600 TCCCCACCTTCACCAAGGACCAAAAGCAGAACGCATACTCGGGCACTCAAGAAGTTAAGT ENSG00000 220 E V N K R L Q D L R S C L S P K P P Q G ENSG00000 660 GAGGTGAACAAGCGCCTCCAGGATCTCCGTTCCTGTCTGAGCCCCAAGCCACCTCAGGGT ENSG00000 240 Q E Q Q G Q E D E V V L V E G P T L P E ENSG00000 720 CAAGAGCAACAGGGCCAAGAGGATGAAGTGGTCTTGGTGGAAGGGCCCACCCTCCCAGAG ENSG00000 260 T P R L F P L K I R C R A D L V R L P L ENSG00000 780 ACCCCCCGACTCTTCCCACTCAAAATCCGTTGCCGGGCTGACCTGGTCAGATTGCCCCTC ENSG00000 280 R M S E P L Q S V V D H M A T H L G V S ENSG00000 840 AGGATGTCGGAGCCCCTGCAGAGTGTGGTGGACCACATGGCCACCCACCTTGGGGTGTCC ENSG00000 300 P S R I L L L F G E T E L S P T A T P R ENSG00000 900 CCAAGCAGGATCCTTTTGCTTTTTGGAGAGACAGAGCTATCACCTACTGCCACTCCCAGG ENSG00000 320 T L K L G V A D I I D C V V L T S S P E ENSG00000 960 ACCCTAAAGCTCGGAGTGGCTGACATCATTGACTGTGTGGTACTAACAAGTTCTCCAGAG ENSG00000 340 A T E T S Q Q L Q L R V Q G K E K H Q T ENSG00000 1020 GCCACAGAGACGTCCCAACAGCTCCAGCTCCGGGTGCAGGGAAAGGAGAAACACCAGACA ENSG00000 360 L E V S L S R D S P L K T L M S H Y E E ENSG00000 1080 CTGGAAGTCTCACTGTCTCGAGATTCCCCTCTAAAGACCCTCATGTCCCACTATGAGGAG ENSG00000 380 A M G L S G R K L S F F F D G T K L S G ENSG00000 1140 GCCATGGGACTGTCGGGACGGAAGCTCTCCTTCTTCTTTGATGGGACAAAGCTTTCAGGC ENSG00000 400 R E L P A D L G M E S G D L I E V W G ENSG00000 1200 AGGGAGCTGCCAGCTGACCTGGGCATGGAATCTGGGGACCTCATTGAGGTCTGGGGC ENSG00000 419 ENSG00000 1257 """, ) alignment = protein_alignment.mapall(codon_alignments) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 72, 255, 255, 603, 606, 1317, 1530, 1530, 1737, 1737, 1902, 1902, 1926, 1926, 2031, 2088, 2343, 2346, 2418, 2442, 2556, 2562, 2763, 2784, 2853, 2859, 3165, 3165, 3282, 3282], [ 0, 72, 255, 255, 603, 606, 1317, 1530, 1569, 1776, 1821, 1986, 1992, 2016, 2031, 2136, 2136, 2391, 2391, 2463, 2463, 2577, 2577, 2778, 2778, 2847, 2847, 3153, 3162, 3279, 3312], [ 0, 0, 183, 198, 546, 546, 1257, 1257, 1257, 1257, 1257, 1257, 1257, 1257, 1257, 1257, 1257, 1257, 1257, 1257, 1257, 1257, 1257, 1257, 1257, 1257, 1257, 1257, 1257, 1257, 1257]]) # fmt: on ) ) self.assertEqual( format(alignment, "clustal"), """\ isotig35100 GAAAGGCAGGGTCGctGGTGCGTGCCCGGCGAGGCTGTGGAGGCCcgTGT isotig35101 GAAAGGCAGGGTCGctGGTGCGTGCCCGGCGAGGCTGTGGAGGCCcgTGT ENSG00000176953:ENST0000032080 -------------------------------------------------- isotig35100 GTCTAGAAGCTGTGTGAGAGAGATGGCGGAACCCGGGAGGAGACGGGGTC isotig35101 GTCTAGAAGCTGTGTGAGAGAGATGGCGGAACCCGGGAGGAGACGGGGTC ENSG00000176953:ENST0000032080 ----------------------ATGGCGGAGCCTGTGGGGAAGCGGGGCC isotig35100 CGAGGTCCCGCGGTGGCGGCGCCGGCCGAGGCgCTCGAAGAGCCCGGGTC isotig35101 CGAGGTCCCGCGGTGGCGGCGCCGGCCGAGGCgCTCGAAGAGCCCGGGTC ENSG00000176953:ENST0000032080 GCTGGTCCGGAGGTAGCGGTGCCGGCCGAGGGGGTCGGGGCGGCTGGGGC isotig35100 GCCCGTGGCCGGCGTCCTCGCGCCCCGCAGTCTCTGTCCCGGCTCATTCC isotig35101 GCCCGTGGCCGGCGTCCTCGCGCCCCGCAGTCTCTGTCCCGGCTCATTCC ENSG00000176953:ENST0000032080 GGTCGGGGCCGGCGTCCTCGGGCCCAGCGGTCTCCATCCCGGGGCACGCT isotig35100 AGACACGGTGCTTGTGGACTTGGTCAGTGACAGCGACGAGGAGATCCTGG isotig35101 AGACACGGTGCTTGTGGACTTGGTCAGTGACAGCGACGAGGAGATCCTGG ENSG00000176953:ENST0000032080 GGACGTAGTGTCTGTGGACTTGGTCACCGACAGCGATGAGGAAATTCTGG isotig35100 AAGTC---------------GTCGCGGACCCGGTAGAAGCGCCCGCCGCC isotig35101 AAGTC---------------GTCGCGGACCCGGTAGAAGCGCCCGCCGCC ENSG00000176953:ENST0000032080 AGGTCGCCACCGCTCGCGGTGCCGCGGACGAGGTTGAGGTGGAGCCCCCG isotig35100 CGGGCcCCcGCGCCGGCCGCACATGGGCAGGACAGCGACAGCGACAGTGC isotig35101 CGGGCcCCcGCGCCGGCCGCACATGGGCAGGACAGCGACAGCGACAGTGC ENSG00000176953:ENST0000032080 GAGCCCCCGGGGCCGGTCGCGTCCCGGGATAACAGCAACAGTGACAGCGA isotig35100 AGGGGCGgACGAGGGGCCTGCAGGAGCCCCTCAGACCTTGGTCCGGCGGC isotig35101 AGGGGCGgACGAGGGGCCTGCAGGAGCCCCTCAGACCTTGGTCCGGCGGC ENSG00000176953:ENST0000032080 AGGGGAGGACAGGCGGCCCGCAGGACCCCCGCGGGAGCCGGTCAGGCGGC isotig35100 GGCGCCGGCGGCTGCTGGATCCCGGCGAGGCACCGGTGGTTCCTGTGTAC isotig35101 GGCGCCGGCGGCTGCTGGATCCCGGCGAGGCACCGGTGGTTCCTGTGTAC ENSG00000176953:ENST0000032080 GGCGGCGGCTGGTGCTGGATCCGGGGGAGGCGCCGCTGGTTCCGGTGTAC isotig35100 TCCGGGAAGGTACAAAGCAGCCTCAACCTCATCCCAGATAATTCATCCCT isotig35101 TCCGGGAAGGTACAAAGCAGCCTCAACCTCATCCCAGATAATTCATCCCT ENSG00000176953:ENST0000032080 TCGGGGAAGGTTAAAAGCAGCCTTCGCCTTATCCCAGATGATCTATCCCT isotig35100 CTTGAAACTTTGCCCCTCAGAGCCTGAAGATGAGGCAGATGTGACAGATT isotig35101 CTTGAAACTTTGCCCCTCAGAGCCTGAAGATGAGGCAGATGTGACAGATT ENSG00000176953:ENST0000032080 CCTGAAACTCTACCCTCCAGGGGATGAGGAAGAGGCAGAGCTGGCAGATT isotig35100 GTGGCAGTCCTCCTCCTGAGGATGCCCTAATTCCAGGTTCTCCCTGGAAG isotig35101 GTGGCAGTCCTCCTCCTGAGGATGCCCTAATTCCAGGTTCTCCCTGGAAG ENSG00000176953:ENST0000032080 CGAGTGGTCTCTACCATGAGGGCTCCCCATCACCAGGCTCTCCCTGGAAG isotig35100 AAGAAGCTGAGGAATAAGCATGAAAAaGAAGAGATGAAGATGGAAGAGTT isotig35101 AAGAAGCTGAGGAATAAGCATGAAAAaGAAGAGATGAAGATGGAAGAGTT ENSG00000176953:ENST0000032080 ACAAAGCTGAGGACTAAG---GATAAAGAAGAGAAGAAAAAGACAGAGTT isotig35100 tCCGGACCAGGACATCTCTCCTTTGCCCCGACCTTCATCAAGAAaCAAAA isotig35101 tCCGGACCAGGACATCTCTCCTTTGCCCCGACCTTCATCAAGAAaCAAAA ENSG00000176953:ENST0000032080 TCTGGATCTGGACAACTCTCCTCTGTCCCCACCTTCACCAAGGACCAAAA isotig35100 GCAGAAAGCATACCGAGGCACTCCAGAAGTTGAGGGAAGTGAACAAGCGC isotig35101 GCAGAAAGCATACCGAGGCACTCCAGAAGTTGAGGGAAGTGAACAAGCGC ENSG00000176953:ENST0000032080 GCAGAACGCATACTCGGGCACTCAAGAAGTTAAGTGAGGTGAACAAGCGC isotig35100 CTCCAAGATCTCCGATCCTGCCTGAGCCCCAAGCAGCACCAGAGTCCAGC isotig35101 CTCCAAGATCTCCGATCCTGCCTGAGCCCCAAGCAGCACCAGAGTCCAGC ENSG00000176953:ENST0000032080 CTCCAGGATCTCCGTTCCTGTCTGAGCCCCAAGCCACCTCAGGGTCAAGA isotig35100 CCTTCAGAACCCAGATGATGAGGTGGTCCTCGTGGACGGGCCTGtCTTGT isotig35101 CCTTCAGAACCCAGATGATGAGGTGGTCCTCGTGGACGGGCCTGtCTTGT ENSG00000176953:ENST0000032080 GCAACAGGGCCAAGAGGATGAAGTGGTCTTGGTGGAAGGGCCCACCCTCC isotig35100 CACAGAGCCCGAGACTCTTCACCCTCAAGATCCGGTGCCGGGCTGACCTA isotig35101 CACAGAGCCCGAGACTCTTCACCCTCAAGATCCGGTGCCGGGCTGACCTA ENSG00000176953:ENST0000032080 CAGAGACCCCCCGACTCTTCCCACTCAAAATCCGTTGCCGGGCTGACCTG isotig35100 GTCAGATTGCCCGTCATGACATCGGAACCCCTTCAGAATGTGGTGGATTA isotig35101 GTCAGATTGCCCGTCATGACATCGGAACCCCTTCAGAATGTGGTGGATTA ENSG00000176953:ENST0000032080 GTCAGATTGCCCCTCAGGATGTCGGAGCCCCTGCAGAGTGTGGTGGACCA isotig35100 CATGGCCAATCATCTTGGGGTGTCTCCAAGCAGGATTCTTTTACTCTTTG isotig35101 CATGGCCAATCATCTTGGGGTGTCTCCAAGCAGGATTCTTTTACTCTTTG ENSG00000176953:ENST0000032080 CATGGCCACCCACCTTGGGGTGTCCCCAAGCAGGATCCTTTTGCTTTTTG isotig35100 GAGAGACAGAACTGTCCCCTACTGCCACCCCTAGGACCCTAAAGCTTGGT isotig35101 GAGAGACAGAACTGTCCCCTACTGCCACCCCTAGGACCCTAAAGCTTGGT ENSG00000176953:ENST0000032080 GAGAGACAGAGCTATCACCTACTGCCACTCCCAGGACCCTAAAGCTCGGA isotig35100 GTGGCTGACATCATTGATTGTGTGGTGCTGACAAGTTCTTCAGAGGCCAC isotig35101 GTGGCTGACATCATTGATTGTGTGGTGCTGACAAGTTCTTCAGAGGCCAC ENSG00000176953:ENST0000032080 GTGGCTGACATCATTGACTGTGTGGTACTAACAAGTTCTCCAGAGGCCAC isotig35100 AGAGACAACCCAGCAGCTCTGCCTCCGGGTGCAGGGGAAGGAGAAGCACC isotig35101 AGAGACAACCCAGCAGCTCTGCCTCCGGGTGCAGGGGAAGGAGAAGCACC ENSG00000176953:ENST0000032080 AGAGACGTCCCAACAGCTCCAGCTCCGGGTGCAGGGAAAGGAGAAACACC isotig35100 AGATGTTGGAGATCTCACTCTCTCCTGACTCtCCTCTTGAGGTCCTCATG isotig35101 AGATGTTGGAGATCTCACTCTCTCCTGACTCgCCTCTTGAGGTCCTCATG ENSG00000176953:ENST0000032080 AGACACTGGAAGTCTCACTGTCTCGAGATTCCCCTCTAAAGACCCTCATG isotig35100 GCGCACTATGAGGAGGCCATGGGACTCTCCGGACACAAGCTCTCCTTCTT isotig35101 GCGCACTATGAGGAGGCCATGGGACTCTCCGGACACAAGCTCTCCTTCTT ENSG00000176953:ENST0000032080 TCCCACTATGAGGAGGCCATGGGACTGTCGGGACGGAAGCTCTCCTTCTT isotig35100 CTTCGATGGGACAAAGCTGTCGGGCAAGGAGCTGCCAGCTGATCTGGGCA isotig35101 CTTCGATGGGACAAAGCTGTCGGGCAAGGAACTGCCAGCTGATCTGGGCA ENSG00000176953:ENST0000032080 CTTTGATGGGACAAAGCTTTCAGGCAGGGAGCTGCCAGCTGACCTGGGCA isotig35100 TGGAATCCGGGGATCTCATTGAAGTTTGGGGCAGCTTCCTCCTCCTGTTT isotig35101 TGGAATCCGGGGATCTCATTGAAGTTTGGGGCAGCTTCCTCCTCCTGTTT ENSG00000176953:ENST0000032080 TGGAATCTGGGGACCTCATTGAGGTCTGGGGC------------------ isotig35100 GGATGCAGAGCCAAGACTTGGGGACAACAGCTCCCACTTTtATTATTATT isotig35101 GGATGCAGAGCCAAGACTTGGGGACAACAGCTCCCACTTTTATTATTATT ENSG00000176953:ENST0000032080 -------------------------------------------------- isotig35100 TTTtGCCCcAGGGCTAACAGAAACCGAATTAGAACTCGTTTATTTATTTC isotig35101 TTTTGCCCCAGGGCTAACAGAAACCGAATTAGAACTCGTTTATTTATTTC ENSG00000176953:ENST0000032080 -------------------------------------------------- isotig35100 CGGCACTGGGGATTGAACCCAGGGCTGTGCATATGCTAAGGATGTGTGAA isotig35101 CGGCACTGGGGATTGAACCCTGGGCTGTGCATATGCTAAGGATGTGTGAA ENSG00000176953:ENST0000032080 -------------------------------------------------- isotig35100 GTTGAGGTAAAaCCAAGGCATGACCTTTGCCcTGTCTCGTTGACC----- isotig35101 GTTGAGGTAAAACCAAGGCATGACCTTTGCCCTGTCTCGTTGACCGATTG ENSG00000176953:ENST0000032080 -------------------------------------------------- isotig35100 ----------------------------------GTAGTCTCAAGCGGTC isotig35101 GTTGTGTGACTGTGGCTGCCCTGGGTGGCCTGTGGCTGTGTGTGTTGGTG ENSG00000176953:ENST0000032080 -------------------------------------------------- isotig35100 TGATTGGTAATTGTGTGACTGTGGCTGCCCTGGGTGgCCTGTGGCTGTGT isotig35101 CTGTGGACAGCAGCTCCTGGGGCATGGAGAAGGGGTATTGGCTTCCCTAC ENSG00000176953:ENST0000032080 -------------------------------------------------- isotig35100 GTGTTGGTGCTGTGTACAGCAGCTCCTGGGGCATGGAGAAGGGGTATTGG isotig35101 CATTTCGTTCAGTGCACAAATGAGCCTTGCATTTGGGTGCCCAGGCTTGT ENSG00000176953:ENST0000032080 -------------------------------------------------- isotig35100 CTTCCCTACCATTTCGTTCAGTAGTGCACAAATGAGCCTTGCATTTGGGT isotig35101 GATTTATGCCACATTGGGGACCAACAGGGATTTTAATTCTCATTTGGGGG ENSG00000176953:ENST0000032080 -------------------------------------------------- isotig35100 GCCCAGGCTTGTTTATGCCACATTGGGGACCAACAGGGATT--------- isotig35101 CTGAGATGCAGGTACCTTCCCTGGTGGGGATAGTCGGTTGCAGGGAAATA ENSG00000176953:ENST0000032080 -------------------------------------------------- isotig35100 ------------------------------------TTAATTCTCATTTG isotig35101 AACAAGCAACATCTATGCAGCGGACTAGGTAGACAGTGGGTAATTTTTAA ENSG00000176953:ENST0000032080 -------------------------------------------------- isotig35100 GGGGCTGAGATGCAGGTACCTTCCCTGGTGGGGATCGGTTGCAGGGAAAA isotig35101 AGGCCAGGAGTGGTGTCTTCAGCCCTGGGCATCCACTCTCCCAGGACTCG ENSG00000176953:ENST0000032080 -------------------------------------------------- isotig35100 CAAGCAATGACATCTATGCTGAAGCTGAGGACGTAGACAGTGGGTTTTTA isotig35101 GCCAGCATCTGGTACATACTTCCTGGCATGCACATCTAGCCACATCTGAG ENSG00000176953:ENST0000032080 -------------------------------------------------- isotig35100 AAGGCTAACAGGAGTGGTGTCTTCAGCCCTGGGCATCCACTCTCCCAGGA isotig35101 CACATGCAGCTGTTGAGTTTGATGTTTACTCTAGTTCcGTCCTCCCGCCC ENSG00000176953:ENST0000032080 -------------------------------------------------- isotig35100 C------TCGGCCAGCATCTGGTACATACTT---------------CCTG isotig35101 TCTCCTGTCAGCACCCACTTGGTATATTTGTATCATGTCTTTAGATGATT ENSG00000176953:ENST0000032080 -------------------------------------------------- isotig35100 GCATGCACATCCCACATCTGAGCACATGCAGCTGTGTTTGTTTACTCTTC isotig35101 TTCTGAATGTGTGTGATTTTAGTGTATGTACATGGTACTGTGCAATAGAC ENSG00000176953:ENST0000032080 -------------------------------------------------- isotig35100 cGTCCTCCCGCCCTCTCCTGTCAGCACCCACTTGGTATATTTGTATCTGA isotig35101 ATTCTGTCTTCACTCAGTGTGAGTGACAGGCTAGCCATGTTAGCACCTTC ENSG00000176953:ENST0000032080 -------------------------------------------------- isotig35100 ATGTCTTTATAAGATGATTTTCATGTGTGTGATTTTAGTGTATGTACATG isotig35101 T------------------------------------------------- ENSG00000176953:ENST0000032080 -------------------------------------------------- isotig35100 GTACTGTGCAAACATTCTGTCTTCACTCAGTGGTGACAGGCCCATGTCAC isotig35101 --------AGATCTGTTGTTGTTCCGATCTGCTGTGGCTGCCCCATAGTG ENSG00000176953:ENST0000032080 -------------------------------------------------- isotig35100 CTTCTAGATCTGTTGTTGTTCCGATCTGCTGTGGCTGCCCCATGGCATAT isotig35101 GCATTAGATGATATTACTCACACATTGCCTTTGGAGGGATACCTGAGTCG ENSG00000176953:ENST0000032080 -------------------------------------------------- isotig35100 GATATTACTCACACATTGCCTTAATTGGAGGGATACCGTCGCCAGCTCCG isotig35101 CCAGCTCCTAGGAACCAAATTCCAGACCACAGCAAACATCTTTTTGTGTG ENSG00000176953:ENST0000032080 -------------------------------------------------- isotig35100 AACCAAATTCCAGACCACAGCAAACATCTTTTTGTGTGTTCCCTTCTGGG isotig35101 TTCCCTTCTGGGCCAGGGTAGGTAATTGTCTGGCATACTTGCCCAGGATG ENSG00000176953:ENST0000032080 -------------------------------------------------- isotig35100 CCAGGGGTAATTGTCTGGCATACTTGCCCAGGATGGGACTgTGGGTTACG isotig35101 GGACTgTGGGTTACGCAGGTTCATTTcTCTGGTTTTTCTAGGgTTTTCTT ENSG00000176953:ENST0000032080 -------------------------------------------------- isotig35100 CAGGTTCATTTcTCTGGTTTTTCTAGGgTTTTCTTCAGAATGTGGACTGC isotig35101 CAGAATGTGGACT---GCTTTTCTTGGAGCTTCTcTTTCCTTcTCTCCAG ENSG00000176953:ENST0000032080 -------------------------------------------------- isotig35100 TTTTCTTGGAGCTTCTcTTTCCTTcTCTTGACCAGTATTTAGTGTTGttg isotig35101 TATTTAGTGTTGttgTACTTTCTGATTTGCCAGTCTAC------------ ENSG00000176953:ENST0000032080 -------------------------------------------------- isotig35100 TACTTTCTGATTTGCCAGTCTACTGTGTATAAAGCACTGCATATCTTAAT isotig35101 ------------TGTGTAAGCACTGCATATCTTAATATCCTTTATCTGAC ENSG00000176953:ENST0000032080 -------------------------------------------------- isotig35100 ATCCTTTATCCCACCATTTCTTATCAATGTCCACCTTCTGGTTTTTCTTT isotig35101 CACCATTTCTTATCAATGTCCACCTTCTGGTTTTTCTTTGTTAGCTGCTT ENSG00000176953:ENST0000032080 -------------------------------------------------- isotig35100 GTCTGCTTGTTTTCTTGGGCTTCCTTTTGTGTGTTTTTtCTGTGAGGAGT isotig35101 GTTTTCTTGTGAGGCTTCCTTTTGTG------TGTTTTTtCTGTGAGGAG ENSG00000176953:ENST0000032080 -------------------------------------------------- isotig35100 TGCTTGTGTTCTaGgCAATTGCAAATAACCTTCAGAATAGCACTTTGTGT isotig35101 TTGCTTGTGTTCgCAATTGCAAATAACCTTCAGAATAGCACTTTGTGTAC ENSG00000176953:ENST0000032080 -------------------------------------------------- isotig35100 ACCCAGGGGGATTTTCACCAAACAGACATTCTTAACTTTAATGCAGACAG isotig35101 CCAGGGGGATTTTCACCAAACAGACATTCTTAACTTTAATGCAGACAGCT ENSG00000176953:ENST0000032080 -------------------------------------------------- isotig35100 CTGGCTTTTGTAAAGGGTTTTTTGTTTTGTGTTTtTTTTTtttttGCTTT isotig35101 GGCTTTTGTTAGAAAGGGTTTTTTGTTTTGTGTTTtTTTTTtttttGCTT ENSG00000176953:ENST0000032080 -------------------------------------------------- isotig35100 TGTTTTtGcTTTTTAAGGGAAAATGAGAAAGAACTTCCAGAATGGCAGGG isotig35101 TTGTTTTtGcTTTTTAAGGGAAAAGAAAGAACT----------------- ENSG00000176953:ENST0000032080 -------------------------------------------------- isotig35100 GTTCCGGGGAGTCTCAGGATTGCTACTTTTGGATCTCACTAGTGAAACTT isotig35101 ----TCCAGAATGGCAGGGGTTCTAGCGGGGAGTCTCAGGATTGCTACTT ENSG00000176953:ENST0000032080 -------------------------------------------------- isotig35100 TCATTGTCTTCTGTCTTGCTAGTTTTTTGTTCTTTTGTTTTTATCTCTCA isotig35101 TTGGATCTCTAAACTTAAGAAAC------TTTCATTGTCTTCTGTTAGCT ENSG00000176953:ENST0000032080 -------------------------------------------------- isotig35100 TATGACCACATGAGAATAGAGTTCCTGATCTGCTGTGGTGTGGATaCTGA isotig35101 TGCTTTTTTGTTCTTTTGTTTTTATCTCTCATATTGAGACCACTAAATGA ENSG00000176953:ENST0000032080 -------------------------------------------------- isotig35100 CTGTTCTGAaCTTTCCACTCTGCTTCTCACTGGTTACAGCACTGTACTGG isotig35101 GAATAGAGTTCTAACTGATCTGCTGTGGTGTGGATaCCTGTTCaCTTTCC ENSG00000176953:ENST0000032080 -------------------------------------------------- isotig35100 TTCCTGACTATTGTATGTtACGTCTAAACCATCTGAAATGCACCTTTGTG isotig35101 ACTCTGCTTCTCACTGGTTACAGCTAGACTGTACTGGTTCCCTATTGTAT ENSG00000176953:ENST0000032080 -------------------------------------------------- isotig35100 TGGGAGAGCAAATTTTATTGTGTTTTAATTATAATGAGCCAGTTTTCtAA isotig35101 GTtACGTCTAAACCATCTGAAATGCACCTTTGTGTGGGAGAGCAAATTTT ENSG00000176953:ENST0000032080 -------------------------------------------------- isotig35100 GCTTTGTCTaCTAAAAAATTATGTAGTCCTTTCACAAGAAGTATGTCAAC isotig35101 ATTGTGTTTTAATTATAATGAGCCAGTTTTCGCTTTGTCTaCTAAAAAAT ENSG00000176953:ENST0000032080 -------------------------------------------------- isotig35100 TTCTtAAAAATTTTTTTtGtGAGAATATGTTATAC---------CTTATT isotig35101 TAATATGTAGTCTGACTTTCACAAGAAGTATGTCAACTTCTAAATTTTTT ENSG00000176953:ENST0000032080 -------------------------------------------------- isotig35100 TTAATATTTAAAAATTCCATGACATATAGCTTCCAGGTTTCTCAGCTCTT isotig35101 TtGGAATATGTTATACCTTTGAATTTTAATATTAAATTCCATGACATAGT ENSG00000176953:ENST0000032080 -------------------------------------------------- isotig35100 GTATGACAATATCACACATTaCTATTATGTATTCAATCTCAGCCAAAGGG isotig35101 ACTTCCAGGTTTCTCAGCTCTTGTACAATTAATGAATCTGAACACATTaC ENSG00000176953:ENST0000032080 -------------------------------------------------- isotig35100 AGATGCCTTTA--------------------------------- isotig35101 TATTATGTATTCAATCTCAGCCAATAAAGGGAGATGCCTTTAAC ENSG00000176953:ENST0000032080 -------------------------------------------- """, ) def test3(self): aligner = CodonAligner() nucleotide_records = SeqIO.index("codonalign/nucl3.fa", "fasta") protein_alignment = Align.read("codonalign/pro3.aln", "clustal") self.assertEqual(len(protein_alignment.sequences), 10) codon_alignments = [] protein_record = protein_alignment.sequences[0] nucleotide_record = nucleotide_records[protein_record.id] self.assertEqual(nucleotide_record.id, protein_record.id) alignments = aligner.align(protein_record, nucleotide_record) self.assertEqual(len(alignments), 1) alignment = next(alignments) codon_alignments.append(alignment) self.assertTrue( np.array_equal(alignment.coordinates, np.array([[0, 847], [0, 2541]])) ) self.assertEqual( str(alignment), """\ ENSG00000 0 M S L W G L V S K M P P E K V Q R L Y V ENSG00000 0 ATGTCTCTGTGGGGTCTGGTCTCCAAGATGCCCCCAGAAAAAGTGCAGCGGCTCTATGTC ENSG00000 20 D F P Q H L R H L L G D W L E S Q P W E ENSG00000 60 GACTTTCCCCAACACCTGCGGCATCTTCTGGGTGACTGGCTGGAGAGCCAGCCCTGGGAG ENSG00000 40 F L V G S D A F C C N L A S A L L S D T ENSG00000 120 TTCCTGGTCGGCTCCGACGCCTTCTGCTGCAACTTGGCTAGTGCCCTACTTTCAGACACT ENSG00000 60 V Q H L Q A S V G E Q G E G S T I L Q H ENSG00000 180 GTCCAGCACCTTCAGGCCTCGGTGGGAGAGCAGGGGGAGGGGAGCACCATCTTGCAACAC ENSG00000 80 I S T L E S I Y Q R D P L K L V A T F R ENSG00000 240 ATCAGCACCCTTGAGAGCATATATCAGAGGGACCCCCTGAAGCTGGTGGCCACTTTCAGA ENSG00000 100 Q I L Q G E K K A V M E Q F R H L P M P ENSG00000 300 CAAATACTTCAAGGAGAGAAAAAAGCTGTTATGGAACAGTTCCGCCACTTGCCAATGCCT ENSG00000 120 F H W K Q E E L K F K T G L R R L Q H R ENSG00000 360 TTCCACTGGAAGCAGGAAGAACTCAAGTTTAAGACAGGCTTGCGGAGGCTGCAGCACCGA ENSG00000 140 V G E I H L L R E A L Q K G A E A G Q V ENSG00000 420 GTAGGGGAGATCCACCTTCTCCGAGAAGCCCTGCAGAAGGGGGCTGAGGCTGGCCAAGTG ENSG00000 160 S L H S L I E T P A N G T G P S E A L A ENSG00000 480 TCTCTGCACAGCTTGATAGAAACTCCTGCTAATGGGACTGGGCCAAGTGAGGCCCTGGCC ENSG00000 180 M L L Q E T T G E L E A A K A L V L K R ENSG00000 540 ATGCTACTGCAGGAGACCACTGGAGAGCTAGAGGCAGCCAAAGCCCTAGTGCTGAAGAGG ENSG00000 200 I Q I W K R Q Q Q L A G N G A P F E E S ENSG00000 600 ATCCAGATTTGGAAACGGCAGCAGCAGCTGGCAGGGAATGGCGCACCGTTTGAGGAGAGC ENSG00000 220 L A P L Q E R C E S L V D I Y S Q L Q Q ENSG00000 660 CTGGCCCCACTCCAGGAGAGGTGTGAAAGCCTGGTGGACATTTATTCCCAGCTACAGCAG ENSG00000 240 E V G A A G G E L E P K T R A S L T G R ENSG00000 720 GAGGTAGGGGCGGCTGGTGGGGAGCTTGAGCCCAAGACCCGGGCATCGCTGACTGGCCGG ENSG00000 260 L D E V L R T L V T S C F L V E K Q P P ENSG00000 780 CTGGATGAAGTCCTGAGAACCCTCGTCACCAGTTGCTTCCTGGTGGAGAAGCAGCCCCCC ENSG00000 280 Q V L K T Q T K F Q A G V R F L L G L R ENSG00000 840 CAGGTACTGAAGACTCAGACCAAGTTCCAGGCTGGAGTTCGATTCCTGTTGGGCTTGAGG ENSG00000 300 F L G A P A K P P L V R A D M V T E K Q ENSG00000 900 TTCCTGGGGGCCCCAGCCAAGCCTCCGCTGGTCAGGGCCGACATGGTGACAGAGAAGCAG ENSG00000 320 A R E L S V P Q G P G A G A E S T G E I ENSG00000 960 GCGCGGGAGCTGAGTGTGCCTCAGGGTCCTGGGGCTGGAGCAGAAAGCACTGGAGAAATC ENSG00000 340 I N N T V P L E N S I P G N C C S A L F ENSG00000 1020 ATCAACAACACTGTGCCCTTGGAGAACAGCATTCCTGGGAACTGCTGCTCTGCCCTGTTC ENSG00000 360 K N L L L K K I K R C E R K G T E S V T ENSG00000 1080 AAGAACCTGCTTCTCAAGAAGATCAAGCGGTGTGAGCGGAAGGGCACTGAGTCTGTCACA ENSG00000 380 E E K C A V L F S A S F T L G P G K L P ENSG00000 1140 GAGGAGAAGTGCGCTGTGCTCTTCTCTGCCAGCTTCACACTTGGCCCCGGCAAACTCCCC ENSG00000 400 I Q L Q A L S L P L V V I V H G N Q D N ENSG00000 1200 ATCCAGCTCCAGGCCCTGTCTCTGCCCCTGGTGGTCATCGTCCATGGCAACCAAGACAAC ENSG00000 420 N A K A T I L W D N A F S E M D R V P F ENSG00000 1260 AATGCCAAAGCCACTATCCTGTGGGACAATGCCTTCTCTGAGATGGACCGCGTGCCCTTT ENSG00000 440 V V A E R V P W E K M C E T L N L K F M ENSG00000 1320 GTGGTGGCTGAGCGGGTGCCCTGGGAGAAGATGTGTGAAACTCTGAACCTGAAGTTCATG ENSG00000 460 A E V G T N R G L L P E H F L F L A Q K ENSG00000 1380 GCTGAGGTGGGGACCAACCGGGGGCTGCTCCCAGAGCACTTCCTCTTCCTGGCCCAGAAG ENSG00000 480 I F N D N S L S M E A F Q H R S V S W S ENSG00000 1440 ATCTTCAATGACAACAGCCTCAGTATGGAGGCCTTCCAGCACCGTTCTGTGTCCTGGTCG ENSG00000 500 Q F N K E I L L G R G F T F W Q W F D G ENSG00000 1500 CAGTTCAACAAGGAGATCCTGCTGGGCCGTGGCTTCACCTTTTGGCAGTGGTTTGATGGT ENSG00000 520 V L D L T K R C L R S Y W S D R L I I G ENSG00000 1560 GTCCTGGACCTCACCAAACGCTGTCTCCGGAGCTACTGGTCTGACCGGCTGATCATTGGC ENSG00000 540 F I S K Q Y V T S L L L N E P D G T F L ENSG00000 1620 TTCATCAGCAAACAGTACGTTACTAGCCTTCTTCTCAATGAGCCCGACGGAACCTTTCTC ENSG00000 560 L R F S D S E I G G I T I A H V I R G Q ENSG00000 1680 CTCCGCTTCAGCGACTCAGAGATTGGGGGCATCACCATTGCCCATGTCATCCGGGGCCAG ENSG00000 580 D G S P Q I E N I Q P F S A K D L S I R ENSG00000 1740 GATGGCTCTCCACAGATAGAGAACATCCAGCCATTCTCTGCCAAAGACCTGTCCATTCGC ENSG00000 600 S L G D R I R D L A Q L K N L Y P K K P ENSG00000 1800 TCACTGGGGGACCGAATCCGGGATCTTGCTCAGCTCAAAAATCTCTATCCCAAGAAGCCC ENSG00000 620 K D E A F R S H Y K P E Q M G K D G R G ENSG00000 1860 AAGGATGAGGCTTTCCGGAGCCACTACAAGCCTGAACAGATGGGTAAGGATGGCAGGGGT ENSG00000 640 Y V P A T I K M T V E R D Q P L P T P E ENSG00000 1920 TATGTCCCAGCTACCATCAAGATGACCGTGGAAAGGGACCAACCACTTCCTACCCCAGAG ENSG00000 660 L Q M P T M V P S Y D L G M A P D S S M ENSG00000 1980 CTCCAGATGCCTACCATGGTGCCTTCTTATGACCTTGGAATGGCCCCTGATTCCTCCATG ENSG00000 680 S M Q L G P D M V P Q V Y P P H S H S I ENSG00000 2040 AGCATGCAGCTTGGCCCAGATATGGTGCCCCAGGTGTACCCACCACACTCTCACTCCATC ENSG00000 700 P P Y Q G L S P E E S V N V L S A F Q E ENSG00000 2100 CCCCCGTATCAAGGCCTCTCCCCAGAAGAATCAGTCAACGTGTTGTCAGCCTTCCAGGAG ENSG00000 720 P H L Q M P P S L G Q M S L P F D Q P H ENSG00000 2160 CCTCACCTGCAGATGCCCCCCAGCCTGGGCCAGATGAGCCTGCCCTTTGACCAGCCTCAC ENSG00000 740 P Q G L L P C Q P Q E H A V S S P D P L ENSG00000 2220 CCCCAGGGCCTGCTGCCGTGCCAGCCTCAGGAGCATGCTGTGTCCAGCCCTGACCCCCTG ENSG00000 760 L C S D V T M V E D S C L S Q P V T A F ENSG00000 2280 CTCTGCTCAGATGTGACCATGGTGGAAGACAGCTGCCTGAGCCAGCCAGTGACAGCGTTT ENSG00000 780 P Q G T W I G E D I F P P L L P P T E Q ENSG00000 2340 CCTCAGGGCACTTGGATTGGTGAAGACATATTCCCTCCTCTGCTGCCTCCCACTGAACAG ENSG00000 800 D L T K L L L E G Q G E S G G G S L G A ENSG00000 2400 GACCTCACTAAGCTTCTCCTGGAGGGGCAAGGGGAGTCGGGGGGAGGGTCCTTGGGGGCA ENSG00000 820 Q P L L Q P S H Y G Q S G I S M S H M D ENSG00000 2460 CAGCCCCTCCTGCAGCCCTCCCACTATGGGCAATCTGGGATCTCAATGTCCCACATGGAC ENSG00000 840 L R A N P S W 847 ENSG00000 2520 CTAAGGGCCAACCCCAGTTGG 2541 """, ) protein_record = protein_alignment.sequences[1] nucleotide_record = nucleotide_records[protein_record.id] self.assertEqual(nucleotide_record.id, protein_record.id) alignments = aligner.align(protein_record, nucleotide_record) self.assertEqual(len(alignments), 1) alignment = next(alignments) codon_alignments.append(alignment) self.assertTrue( np.array_equal(alignment.coordinates, np.array([[0, 847], [0, 2541]])) ) self.assertEqual( str(alignment), """\ ENSG00000 0 M S L W G L V S K M P P E K V Q R L Y V ENSG00000 0 ATGTCTCTGTGGGGTCTGGTCTCCAAGATGCCCCCAGAAAAAGTGCAGCGGCTCTATGTC ENSG00000 20 D F P Q H L R H L L G D W L E S Q P W E ENSG00000 60 GACTTTCCCCAACACCTGCGGCATCTTCTGGGTGACTGGCTGGAGAGCCAGCCCTGGGAG ENSG00000 40 F L V G S D A F C C N L A S A L L S D T ENSG00000 120 TTCCTGGTCGGCTCCGACGCCTTCTGCTGCAACTTGGCTAGTGCCCTACTTTCAGACACT ENSG00000 60 V Q H L Q A S V G E Q G E G S T I L Q H ENSG00000 180 GTCCAGCACCTTCAGGCCTCGGTGGGAGAGCAGGGGGAGGGGAGCACCATCTTGCAACAC ENSG00000 80 I S T L E S I Y Q R D P L K L V A T F R ENSG00000 240 ATCAGCACCCTTGAGAGCATATATCAGAGGGACCCCCTGAAGCTGGTGGCCACTTTCAGA ENSG00000 100 Q I L Q G E K K A V M E Q F R H L P M P ENSG00000 300 CAAATACTTCAAGGAGAGAAAAAAGCTGTTATGGAACAGTTCCGCCACTTGCCAATGCCT ENSG00000 120 F H W K Q E E L K F K T G L R R L Q H R ENSG00000 360 TTCCACTGGAAGCAGGAAGAACTCAAGTTTAAGACAGGCTTGCGGAGGCTGCAGCACCGA ENSG00000 140 V G E I H L L R E A L Q K G A E A G Q V ENSG00000 420 GTAGGGGAGATCCACCTTCTCCGAGAAGCCCTGCAGAAGGGGGCTGAGGCTGGCCAAGTG ENSG00000 160 S L H S L I E T P A N G T G P S E A L A ENSG00000 480 TCTCTGCACAGCTTGATAGAAACTCCTGCTAATGGGACTGGGCCAAGTGAGGCCCTGGCC ENSG00000 180 M L L Q E T T G E L E A A K A L V L K R ENSG00000 540 ATGCTACTGCAGGAGACCACTGGAGAGCTAGAGGCAGCCAAAGCCCTAGTGCTGAAGAGG ENSG00000 200 I Q I W K R Q Q Q L A G N G A P F E E S ENSG00000 600 ATCCAGATTTGGAAACGGCAGCAGCAGCTGGCAGGGAATGGCGCACCGTTTGAGGAGAGC ENSG00000 220 L A P L Q E R C E S L V D I Y S Q L Q Q ENSG00000 660 CTGGCCCCACTCCAGGAGAGGTGTGAAAGCCTGGTGGACATTTATTCCCAGCTACAGCAG ENSG00000 240 E V G A A G G E L E P K T R A S L T G R ENSG00000 720 GAGGTAGGGGCGGCTGGTGGGGAGCTTGAGCCCAAGACCCGGGCATCGCTGACTGGCCGG ENSG00000 260 L D E V L R T L V T S C F L V E K Q P P ENSG00000 780 CTGGATGAAGTCCTGAGAACCCTCGTCACCAGTTGCTTCCTGGTGGAGAAGCAGCCCCCC ENSG00000 280 Q V L K T Q T K F Q A G V R F L L G L R ENSG00000 840 CAGGTACTGAAGACTCAGACCAAGTTCCAGGCTGGAGTTCGATTCCTGTTGGGCTTGAGG ENSG00000 300 F L G A P A K P P L V R A D M V T E K Q ENSG00000 900 TTCCTGGGGGCCCCAGCCAAGCCTCCGCTGGTCAGGGCCGACATGGTGACAGAGAAGCAG ENSG00000 320 A R E L S V P Q G P G A G A E S T G E I ENSG00000 960 GCGCGGGAGCTGAGTGTGCCTCAGGGTCCTGGGGCTGGAGCAGAAAGCACTGGAGAAATC ENSG00000 340 I N N T V P L E N S I P G N C C S A L F ENSG00000 1020 ATCAACAACACTGTGCCCTTGGAGAACAGCATTCCTGGGAACTGCTGCTCTGCCCTGTTC ENSG00000 360 K N L L L K K I K R C E R K G T E S V T ENSG00000 1080 AAGAACCTGCTTCTCAAGAAGATCAAGCGGTGTGAGCGGAAGGGCACTGAGTCTGTCACA ENSG00000 380 E E K C A V L F S A S F T L G P G K L P ENSG00000 1140 GAGGAGAAGTGCGCTGTGCTCTTCTCTGCCAGCTTCACACTTGGCCCCGGCAAACTCCCC ENSG00000 400 I Q L Q A L S L P L V V I V H G N Q D N ENSG00000 1200 ATCCAGCTCCAGGCCCTGTCTCTGCCCCTGGTGGTCATCGTCCATGGCAACCAAGACAAC ENSG00000 420 N A K A T I L W D N A F S E M D R V P F ENSG00000 1260 AATGCCAAAGCCACTATCCTGTGGGACAATGCCTTCTCTGAGATGGACCGCGTGCCCTTT ENSG00000 440 V V A E R V P W E K M C E T L N L K F M ENSG00000 1320 GTGGTGGCTGAGCGGGTGCCCTGGGAGAAGATGTGTGAAACTCTGAACCTGAAGTTCATG ENSG00000 460 A E V G T N R G L L P E H F L F L A Q K ENSG00000 1380 GCTGAGGTGGGGACCAACCGGGGGCTGCTCCCAGAGCACTTCCTCTTCCTGGCCCAGAAG ENSG00000 480 I F N D N S L S M E A F Q H R S V S W S ENSG00000 1440 ATCTTCAATGACAACAGCCTCAGTATGGAGGCCTTCCAGCACCGTTCTGTGTCCTGGTCG ENSG00000 500 Q F N K E I L L G R G F T F W Q W F D G ENSG00000 1500 CAGTTCAACAAGGAGATCCTGCTGGGCCGTGGCTTCACCTTTTGGCAGTGGTTTGATGGT ENSG00000 520 V L D L T K R C L R S Y W S D R L I I G ENSG00000 1560 GTCCTGGACCTCACCAAACGCTGTCTCCGGAGCTACTGGTCTGACCGGCTGATCATTGGC ENSG00000 540 F I S K Q Y V T S L L L N E P D G T F L ENSG00000 1620 TTCATCAGCAAACAGTACGTTACTAGCCTTCTTCTCAATGAGCCCGACGGAACCTTTCTC ENSG00000 560 L R F S D S E I G G I T I A H V I R G Q ENSG00000 1680 CTCCGCTTCAGCGACTCAGAGATTGGGGGCATCACCATTGCCCATGTCATCCGGGGCCAG ENSG00000 580 D G S P Q I E N I Q P F S A K D L S I R ENSG00000 1740 GATGGCTCTCCACAGATAGAGAACATCCAGCCATTCTCTGCCAAAGACCTGTCCATTCGC ENSG00000 600 S L G D R I R D L A Q L K N L Y P K K P ENSG00000 1800 TCACTGGGGGACCGAATCCGGGATCTTGCTCAGCTCAAAAATCTCTATCCCAAGAAGCCC ENSG00000 620 K D E A F R S H Y K P E Q M G K D G R G ENSG00000 1860 AAGGATGAGGCTTTCCGGAGCCACTACAAGCCTGAACAGATGGGTAAGGATGGCAGGGGT ENSG00000 640 Y V P A T I K M T V E R D Q P L P T P E ENSG00000 1920 TATGTCCCAGCTACCATCAAGATGACCGTGGAAAGGGACCAACCACTTCCTACCCCAGAG ENSG00000 660 L Q M P T M V P S Y D L G M A P D S S M ENSG00000 1980 CTCCAGATGCCTACCATGGTGCCTTCTTATGACCTTGGAATGGCCCCTGATTCCTCCATG ENSG00000 680 S M Q L G P D M V P Q V Y P P H S H S I ENSG00000 2040 AGCATGCAGCTTGGCCCAGATATGGTGCCCCAGGTGTACCCACCACACTCTCACTCCATC ENSG00000 700 P P Y Q G L S P E E S V N V L S A F Q E ENSG00000 2100 CCCCCGTATCAAGGCCTCTCCCCAGAAGAATCAGTCAACGTGTTGTCAGCCTTCCAGGAG ENSG00000 720 P H L Q M P P S L G Q M S L P F D Q P H ENSG00000 2160 CCTCACCTGCAGATGCCCCCCAGCCTGGGCCAGATGAGCCTGCCCTTTGACCAGCCTCAC ENSG00000 740 P Q G L L P C Q P Q E H A V S S P D P L ENSG00000 2220 CCCCAGGGCCTGCTGCCGTGCCAGCCTCAGGAGCATGCTGTGTCCAGCCCTGACCCCCTG ENSG00000 760 L C S D V T M V E D S C L S Q P V T A F ENSG00000 2280 CTCTGCTCAGATGTGACCATGGTGGAAGACAGCTGCCTGAGCCAGCCAGTGACAGCGTTT ENSG00000 780 P Q G T W I G E D I F P P L L P P T E Q ENSG00000 2340 CCTCAGGGCACTTGGATTGGTGAAGACATATTCCCTCCTCTGCTGCCTCCCACTGAACAG ENSG00000 800 D L T K L L L E G Q G E S G G G S L G A ENSG00000 2400 GACCTCACTAAGCTTCTCCTGGAGGGGCAAGGGGAGTCGGGGGGAGGGTCCTTGGGGGCA ENSG00000 820 Q P L L Q P S H Y G Q S G I S M S H M D ENSG00000 2460 CAGCCCCTCCTGCAGCCCTCCCACTATGGGCAATCTGGGATCTCAATGTCCCACATGGAC ENSG00000 840 L R A N P S W 847 ENSG00000 2520 CTAAGGGCCAACCCCAGTTGG 2541 """, ) protein_record = protein_alignment.sequences[2] nucleotide_record = nucleotide_records[protein_record.id] self.assertEqual(nucleotide_record.id, protein_record.id) alignments = aligner.align(protein_record, nucleotide_record) self.assertEqual(len(alignments), 1) alignment = next(alignments) codon_alignments.append(alignment) self.assertTrue( np.array_equal(alignment.coordinates, np.array([[0, 847], [0, 2541]])) ) self.assertEqual( str(alignment), """\ ENSG00000 0 M S L W G L V S K M P P E K V Q R L Y V ENSG00000 0 ATGTCTCTGTGGGGTCTGGTCTCCAAGATGCCCCCAGAAAAAGTGCAGCGGCTCTATGTC ENSG00000 20 D F P Q H L R H L L G D W L E S Q P W E ENSG00000 60 GACTTTCCCCAACACCTGCGGCATCTTCTGGGTGACTGGCTGGAGAGCCAGCCCTGGGAG ENSG00000 40 F L V G S D A F C C N L A S A L L S D T ENSG00000 120 TTCCTGGTCGGCTCCGACGCCTTCTGCTGCAACTTGGCTAGTGCCCTACTTTCAGACACT ENSG00000 60 V Q H L Q A S V G E Q G E G S T I L Q H ENSG00000 180 GTCCAGCACCTTCAGGCCTCGGTGGGAGAGCAGGGGGAGGGGAGCACCATCTTGCAACAC ENSG00000 80 I S T L E S I Y Q R D P L K L V A T F R ENSG00000 240 ATCAGCACCCTTGAGAGCATATATCAGAGGGACCCCCTGAAGCTGGTGGCCACTTTCAGA ENSG00000 100 Q I L Q G E K K A V M E Q F R H L P M P ENSG00000 300 CAAATACTTCAAGGAGAGAAAAAAGCTGTTATGGAACAGTTCCGCCACTTGCCAATGCCT ENSG00000 120 F H W K Q E E L K F K T G L R R L Q H R ENSG00000 360 TTCCACTGGAAGCAGGAAGAACTCAAGTTTAAGACAGGCTTGCGGAGGCTGCAGCACCGA ENSG00000 140 V G E I H L L R E A L Q K G A E A G Q V ENSG00000 420 GTAGGGGAGATCCACCTTCTCCGAGAAGCCCTGCAGAAGGGGGCTGAGGCTGGCCAAGTG ENSG00000 160 S L H S L I E T P A N G T G P S E A L A ENSG00000 480 TCTCTGCACAGCTTGATAGAAACTCCTGCTAATGGGACTGGGCCAAGTGAGGCCCTGGCC ENSG00000 180 M L L Q E T T G E L E A A K A L V L K R ENSG00000 540 ATGCTACTGCAGGAGACCACTGGAGAGCTAGAGGCAGCCAAAGCCCTAGTGCTGAAGAGG ENSG00000 200 I Q I W K R Q Q Q L A G N G A P F E E S ENSG00000 600 ATCCAGATTTGGAAACGGCAGCAGCAGCTGGCAGGGAATGGCGCACCGTTTGAGGAGAGC ENSG00000 220 L A P L Q E R C E S L V D I Y S Q L Q Q ENSG00000 660 CTGGCCCCACTCCAGGAGAGGTGTGAAAGCCTGGTGGACATTTATTCCCAGCTACAGCAG ENSG00000 240 E V G A A G G E L E P K T R A S L T G R ENSG00000 720 GAGGTAGGGGCGGCTGGTGGGGAGCTTGAGCCCAAGACCCGGGCATCGCTGACTGGCCGG ENSG00000 260 L D E V L R T L V T S C F L V E K Q P P ENSG00000 780 CTGGATGAAGTCCTGAGAACCCTCGTCACCAGTTGCTTCCTGGTGGAGAAGCAGCCCCCC ENSG00000 280 Q V L K T Q T K F Q A G V R F L L G L R ENSG00000 840 CAGGTACTGAAGACTCAGACCAAGTTCCAGGCTGGAGTTCGATTCCTGTTGGGCTTGAGG ENSG00000 300 F L G A P A K P P L V R A D M V T E K Q ENSG00000 900 TTCCTGGGGGCCCCAGCCAAGCCTCCGCTGGTCAGGGCCGACATGGTGACAGAGAAGCAG ENSG00000 320 A R E L S V P Q G P G A G A E S T G E I ENSG00000 960 GCGCGGGAGCTGAGTGTGCCTCAGGGTCCTGGGGCTGGAGCAGAAAGCACTGGAGAAATC ENSG00000 340 I N N T V P L E N S I P G N C C S A L F ENSG00000 1020 ATCAACAACACTGTGCCCTTGGAGAACAGCATTCCTGGGAACTGCTGCTCTGCCCTGTTC ENSG00000 360 K N L L L K K I K R C E R K G T E S V T ENSG00000 1080 AAGAACCTGCTTCTCAAGAAGATCAAGCGGTGTGAGCGGAAGGGCACTGAGTCTGTCACA ENSG00000 380 E E K C A V L F S A S F T L G P G K L P ENSG00000 1140 GAGGAGAAGTGCGCTGTGCTCTTCTCTGCCAGCTTCACACTTGGCCCCGGCAAACTCCCC ENSG00000 400 I Q L Q A L S L P L V V I V H G N Q D N ENSG00000 1200 ATCCAGCTCCAGGCCCTGTCTCTGCCCCTGGTGGTCATCGTCCATGGCAACCAAGACAAC ENSG00000 420 N A K A T I L W D N A F S E M D R V P F ENSG00000 1260 AATGCCAAAGCCACTATCCTGTGGGACAATGCCTTCTCTGAGATGGACCGCGTGCCCTTT ENSG00000 440 V V A E R V P W E K M C E T L N L K F M ENSG00000 1320 GTGGTGGCTGAGCGGGTGCCCTGGGAGAAGATGTGTGAAACTCTGAACCTGAAGTTCATG ENSG00000 460 A E V G T N R G L L P E H F L F L A Q K ENSG00000 1380 GCTGAGGTGGGGACCAACCGGGGGCTGCTCCCAGAGCACTTCCTCTTCCTGGCCCAGAAG ENSG00000 480 I F N D N S L S M E A F Q H R S V S W S ENSG00000 1440 ATCTTCAATGACAACAGCCTCAGTATGGAGGCCTTCCAGCACCGTTCTGTGTCCTGGTCG ENSG00000 500 Q F N K E I L L G R G F T F W Q W F D G ENSG00000 1500 CAGTTCAACAAGGAGATCCTGCTGGGCCGTGGCTTCACCTTTTGGCAGTGGTTTGATGGT ENSG00000 520 V L D L T K R C L R S Y W S D R L I I G ENSG00000 1560 GTCCTGGACCTCACCAAACGCTGTCTCCGGAGCTACTGGTCTGACCGGCTGATCATTGGC ENSG00000 540 F I S K Q Y V T S L L L N E P D G T F L ENSG00000 1620 TTCATCAGCAAACAGTACGTTACTAGCCTTCTTCTCAATGAGCCCGACGGAACCTTTCTC ENSG00000 560 L R F S D S E I G G I T I A H V I R G Q ENSG00000 1680 CTCCGCTTCAGCGACTCAGAGATTGGGGGCATCACCATTGCCCATGTCATCCGGGGCCAG ENSG00000 580 D G S P Q I E N I Q P F S A K D L S I R ENSG00000 1740 GATGGCTCTCCACAGATAGAGAACATCCAGCCATTCTCTGCCAAAGACCTGTCCATTCGC ENSG00000 600 S L G D R I R D L A Q L K N L Y P K K P ENSG00000 1800 TCACTGGGGGACCGAATCCGGGATCTTGCTCAGCTCAAAAATCTCTATCCCAAGAAGCCC ENSG00000 620 K D E A F R S H Y K P E Q M G K D G R G ENSG00000 1860 AAGGATGAGGCTTTCCGGAGCCACTACAAGCCTGAACAGATGGGTAAGGATGGCAGGGGT ENSG00000 640 Y V P A T I K M T V E R D Q P L P T P E ENSG00000 1920 TATGTCCCAGCTACCATCAAGATGACCGTGGAAAGGGACCAACCACTTCCTACCCCAGAG ENSG00000 660 L Q M P T M V P S Y D L G M A P D S S M ENSG00000 1980 CTCCAGATGCCTACCATGGTGCCTTCTTATGACCTTGGAATGGCCCCTGATTCCTCCATG ENSG00000 680 S M Q L G P D M V P Q V Y P P H S H S I ENSG00000 2040 AGCATGCAGCTTGGCCCAGATATGGTGCCCCAGGTGTACCCACCACACTCTCACTCCATC ENSG00000 700 P P Y Q G L S P E E S V N V L S A F Q E ENSG00000 2100 CCCCCGTATCAAGGCCTCTCCCCAGAAGAATCAGTCAACGTGTTGTCAGCCTTCCAGGAG ENSG00000 720 P H L Q M P P S L G Q M S L P F D Q P H ENSG00000 2160 CCTCACCTGCAGATGCCCCCCAGCCTGGGCCAGATGAGCCTGCCCTTTGACCAGCCTCAC ENSG00000 740 P Q G L L P C Q P Q E H A V S S P D P L ENSG00000 2220 CCCCAGGGCCTGCTGCCGTGCCAGCCTCAGGAGCATGCTGTGTCCAGCCCTGACCCCCTG ENSG00000 760 L C S D V T M V E D S C L S Q P V T A F ENSG00000 2280 CTCTGCTCAGATGTGACCATGGTGGAAGACAGCTGCCTGAGCCAGCCAGTGACAGCGTTT ENSG00000 780 P Q G T W I G E D I F P P L L P P T E Q ENSG00000 2340 CCTCAGGGCACTTGGATTGGTGAAGACATATTCCCTCCTCTGCTGCCTCCCACTGAACAG ENSG00000 800 D L T K L L L E G Q G E S G G G S L G A ENSG00000 2400 GACCTCACTAAGCTTCTCCTGGAGGGGCAAGGGGAGTCGGGGGGAGGGTCCTTGGGGGCA ENSG00000 820 Q P L L Q P S H Y G Q S G I S M S H M D ENSG00000 2460 CAGCCCCTCCTGCAGCCCTCCCACTATGGGCAATCTGGGATCTCAATGTCCCACATGGAC ENSG00000 840 L R A N P S W 847 ENSG00000 2520 CTAAGGGCCAACCCCAGTTGG 2541 """, ) protein_record = protein_alignment.sequences[3] nucleotide_record = nucleotide_records[protein_record.id] self.assertEqual(nucleotide_record.id, protein_record.id) alignments = aligner.align(protein_record, nucleotide_record) self.assertEqual(len(alignments), 1) alignment = next(alignments) codon_alignments.append(alignment) self.assertTrue( np.array_equal(alignment.coordinates, np.array([[0, 847], [0, 2541]])) ) self.assertEqual( str(alignment), """\ ENSG00000 0 M S L W G L V S K M P P E K V Q R L Y V ENSG00000 0 ATGTCTCTGTGGGGTCTGGTCTCCAAGATGCCCCCAGAAAAAGTGCAGCGGCTCTATGTC ENSG00000 20 D F P Q H L R H L L G D W L E S Q P W E ENSG00000 60 GACTTTCCCCAACACCTGCGGCATCTTCTGGGTGACTGGCTGGAGAGCCAGCCCTGGGAG ENSG00000 40 F L V G S D A F C C N L A S A L L S D T ENSG00000 120 TTCCTGGTCGGCTCCGACGCCTTCTGCTGCAACTTGGCTAGTGCCCTACTTTCAGACACT ENSG00000 60 V Q H L Q A S V G E Q G E G S T I L Q H ENSG00000 180 GTCCAGCACCTTCAGGCCTCGGTGGGAGAGCAGGGGGAGGGGAGCACCATCTTGCAACAC ENSG00000 80 I S T L E S I Y Q R D P L K L V A T F R ENSG00000 240 ATCAGCACCCTTGAGAGCATATATCAGAGGGACCCCCTGAAGCTGGTGGCCACTTTCAGA ENSG00000 100 Q I L Q G E K K A V M E Q F R H L P M P ENSG00000 300 CAAATACTTCAAGGAGAGAAAAAAGCTGTTATGGAACAGTTCCGCCACTTGCCAATGCCT ENSG00000 120 F H W K Q E E L K F K T G L R R L Q H R ENSG00000 360 TTCCACTGGAAGCAGGAAGAACTCAAGTTTAAGACAGGCTTGCGGAGGCTGCAGCACCGA ENSG00000 140 V G E I H L L R E A L Q K G A E A G Q V ENSG00000 420 GTAGGGGAGATCCACCTTCTCCGAGAAGCCCTGCAGAAGGGGGCTGAGGCTGGCCAAGTG ENSG00000 160 S L H S L I E T P A N G T G P S E A L A ENSG00000 480 TCTCTGCACAGCTTGATAGAAACTCCTGCTAATGGGACTGGGCCAAGTGAGGCCCTGGCC ENSG00000 180 M L L Q E T T G E L E A A K A L V L K R ENSG00000 540 ATGCTACTGCAGGAGACCACTGGAGAGCTAGAGGCAGCCAAAGCCCTAGTGCTGAAGAGG ENSG00000 200 I Q I W K R Q Q Q L A G N G A P F E E S ENSG00000 600 ATCCAGATTTGGAAACGGCAGCAGCAGCTGGCAGGGAATGGCGCACCGTTTGAGGAGAGC ENSG00000 220 L A P L Q E R C E S L V D I Y S Q L Q Q ENSG00000 660 CTGGCCCCACTCCAGGAGAGGTGTGAAAGCCTGGTGGACATTTATTCCCAGCTACAGCAG ENSG00000 240 E V G A A G G E L E P K T R A S L T G R ENSG00000 720 GAGGTAGGGGCGGCTGGTGGGGAGCTTGAGCCCAAGACCCGGGCATCGCTGACTGGCCGG ENSG00000 260 L D E V L R T L V T S C F L V E K Q P P ENSG00000 780 CTGGATGAAGTCCTGAGAACCCTCGTCACCAGTTGCTTCCTGGTGGAGAAGCAGCCCCCC ENSG00000 280 Q V L K T Q T K F Q A G V R F L L G L R ENSG00000 840 CAGGTACTGAAGACTCAGACCAAGTTCCAGGCTGGAGTTCGATTCCTGTTGGGCTTGAGG ENSG00000 300 F L G A P A K P P L V R A D M V T E K Q ENSG00000 900 TTCCTGGGGGCCCCAGCCAAGCCTCCGCTGGTCAGGGCCGACATGGTGACAGAGAAGCAG ENSG00000 320 A R E L S V P Q G P G A G A E S T G E I ENSG00000 960 GCGCGGGAGCTGAGTGTGCCTCAGGGTCCTGGGGCTGGAGCAGAAAGCACTGGAGAAATC ENSG00000 340 I N N T V P L E N S I P G N C C S A L F ENSG00000 1020 ATCAACAACACTGTGCCCTTGGAGAACAGCATTCCTGGGAACTGCTGCTCTGCCCTGTTC ENSG00000 360 K N L L L K K I K R C E R K G T E S V T ENSG00000 1080 AAGAACCTGCTTCTCAAGAAGATCAAGCGGTGTGAGCGGAAGGGCACTGAGTCTGTCACA ENSG00000 380 E E K C A V L F S A S F T L G P G K L P ENSG00000 1140 GAGGAGAAGTGCGCTGTGCTCTTCTCTGCCAGCTTCACACTTGGCCCCGGCAAACTCCCC ENSG00000 400 I Q L Q A L S L P L V V I V H G N Q D N ENSG00000 1200 ATCCAGCTCCAGGCCCTGTCTCTGCCCCTGGTGGTCATCGTCCATGGCAACCAAGACAAC ENSG00000 420 N A K A T I L W D N A F S E M D R V P F ENSG00000 1260 AATGCCAAAGCCACTATCCTGTGGGACAATGCCTTCTCTGAGATGGACCGCGTGCCCTTT ENSG00000 440 V V A E R V P W E K M C E T L N L K F M ENSG00000 1320 GTGGTGGCTGAGCGGGTGCCCTGGGAGAAGATGTGTGAAACTCTGAACCTGAAGTTCATG ENSG00000 460 A E V G T N R G L L P E H F L F L A Q K ENSG00000 1380 GCTGAGGTGGGGACCAACCGGGGGCTGCTCCCAGAGCACTTCCTCTTCCTGGCCCAGAAG ENSG00000 480 I F N D N S L S M E A F Q H R S V S W S ENSG00000 1440 ATCTTCAATGACAACAGCCTCAGTATGGAGGCCTTCCAGCACCGTTCTGTGTCCTGGTCG ENSG00000 500 Q F N K E I L L G R G F T F W Q W F D G ENSG00000 1500 CAGTTCAACAAGGAGATCCTGCTGGGCCGTGGCTTCACCTTTTGGCAGTGGTTTGATGGT ENSG00000 520 V L D L T K R C L R S Y W S D R L I I G ENSG00000 1560 GTCCTGGACCTCACCAAACGCTGTCTCCGGAGCTACTGGTCTGACCGGCTGATCATTGGC ENSG00000 540 F I S K Q Y V T S L L L N E P D G T F L ENSG00000 1620 TTCATCAGCAAACAGTACGTTACTAGCCTTCTTCTCAATGAGCCCGACGGAACCTTTCTC ENSG00000 560 L R F S D S E I G G I T I A H V I R G Q ENSG00000 1680 CTCCGCTTCAGCGACTCAGAGATTGGGGGCATCACCATTGCCCATGTCATCCGGGGCCAG ENSG00000 580 D G S P Q I E N I Q P F S A K D L S I R ENSG00000 1740 GATGGCTCTCCACAGATAGAGAACATCCAGCCATTCTCTGCCAAAGACCTGTCCATTCGC ENSG00000 600 S L G D R I R D L A Q L K N L Y P K K P ENSG00000 1800 TCACTGGGGGACCGAATCCGGGATCTTGCTCAGCTCAAAAATCTCTATCCCAAGAAGCCC ENSG00000 620 K D E A F R S H Y K P E Q M G K D G R G ENSG00000 1860 AAGGATGAGGCTTTCCGGAGCCACTACAAGCCTGAACAGATGGGTAAGGATGGCAGGGGT ENSG00000 640 Y V P A T I K M T V E R D Q P L P T P E ENSG00000 1920 TATGTCCCAGCTACCATCAAGATGACCGTGGAAAGGGACCAACCACTTCCTACCCCAGAG ENSG00000 660 L Q M P T M V P S Y D L G M A P D S S M ENSG00000 1980 CTCCAGATGCCTACCATGGTGCCTTCTTATGACCTTGGAATGGCCCCTGATTCCTCCATG ENSG00000 680 S M Q L G P D M V P Q V Y P P H S H S I ENSG00000 2040 AGCATGCAGCTTGGCCCAGATATGGTGCCCCAGGTGTACCCACCACACTCTCACTCCATC ENSG00000 700 P P Y Q G L S P E E S V N V L S A F Q E ENSG00000 2100 CCCCCGTATCAAGGCCTCTCCCCAGAAGAATCAGTCAACGTGTTGTCAGCCTTCCAGGAG ENSG00000 720 P H L Q M P P S L G Q M S L P F D Q P H ENSG00000 2160 CCTCACCTGCAGATGCCCCCCAGCCTGGGCCAGATGAGCCTGCCCTTTGACCAGCCTCAC ENSG00000 740 P Q G L L P C Q P Q E H A V S S P D P L ENSG00000 2220 CCCCAGGGCCTGCTGCCGTGCCAGCCTCAGGAGCATGCTGTGTCCAGCCCTGACCCCCTG ENSG00000 760 L C S D V T M V E D S C L S Q P V T A F ENSG00000 2280 CTCTGCTCAGATGTGACCATGGTGGAAGACAGCTGCCTGAGCCAGCCAGTGACAGCGTTT ENSG00000 780 P Q G T W I G E D I F P P L L P P T E Q ENSG00000 2340 CCTCAGGGCACTTGGATTGGTGAAGACATATTCCCTCCTCTGCTGCCTCCCACTGAACAG ENSG00000 800 D L T K L L L E G Q G E S G G G S L G A ENSG00000 2400 GACCTCACTAAGCTTCTCCTGGAGGGGCAAGGGGAGTCGGGGGGAGGGTCCTTGGGGGCA ENSG00000 820 Q P L L Q P S H Y G Q S G I S M S H M D ENSG00000 2460 CAGCCCCTCCTGCAGCCCTCCCACTATGGGCAATCTGGGATCTCAATGTCCCACATGGAC ENSG00000 840 L R A N P S W 847 ENSG00000 2520 CTAAGGGCCAACCCCAGTTGG 2541 """, ) protein_record = protein_alignment.sequences[4] nucleotide_record = nucleotide_records[protein_record.id] self.assertEqual(nucleotide_record.id, protein_record.id) alignments = aligner.align(protein_record, nucleotide_record) self.assertEqual(len(alignments), 1) alignment = next(alignments) codon_alignments.append(alignment) self.assertTrue( np.array_equal(alignment.coordinates, np.array([[0, 737], [0, 2211]])) ) self.assertEqual( str(alignment), """\ ENSG00000 0 M E Q F R H L P M P F H W K Q E E L K F ENSG00000 0 ATGGAACAGTTCCGCCACTTGCCAATGCCTTTCCACTGGAAGCAGGAAGAACTCAAGTTT ENSG00000 20 K T G L R R L Q H R V G E I H L L R E A ENSG00000 60 AAGACAGGCTTGCGGAGGCTGCAGCACCGAGTAGGGGAGATCCACCTTCTCCGAGAAGCC ENSG00000 40 L Q K G A E A G Q V S L H S L I E T P A ENSG00000 120 CTGCAGAAGGGGGCTGAGGCTGGCCAAGTGTCTCTGCACAGCTTGATAGAAACTCCTGCT ENSG00000 60 N G T G P S E A L A M L L Q E T T G E L ENSG00000 180 AATGGGACTGGGCCAAGTGAGGCCCTGGCCATGCTACTGCAGGAGACCACTGGAGAGCTA ENSG00000 80 E A A K A L V L K R I Q I W K R Q Q Q L ENSG00000 240 GAGGCAGCCAAAGCCCTAGTGCTGAAGAGGATCCAGATTTGGAAACGGCAGCAGCAGCTG ENSG00000 100 A G N G A P F E E S L A P L Q E R C E S ENSG00000 300 GCAGGGAATGGCGCACCGTTTGAGGAGAGCCTGGCCCCACTCCAGGAGAGGTGTGAAAGC ENSG00000 120 L V D I Y S Q L Q Q E V G A A G G E L E ENSG00000 360 CTGGTGGACATTTATTCCCAGCTACAGCAGGAGGTAGGGGCGGCTGGTGGGGAGCTTGAG ENSG00000 140 P K T R A S L T G R L D E V L R T L V T ENSG00000 420 CCCAAGACCCGGGCATCGCTGACTGGCCGGCTGGATGAAGTCCTGAGAACCCTCGTCACC ENSG00000 160 S C F L V E K Q P P Q V L K T Q T K F Q ENSG00000 480 AGTTGCTTCCTGGTGGAGAAGCAGCCCCCCCAGGTACTGAAGACTCAGACCAAGTTCCAG ENSG00000 180 A G V R F L L G L R F L G A P A K P P L ENSG00000 540 GCTGGAGTTCGATTCCTGTTGGGCTTGAGGTTCCTGGGGGCCCCAGCCAAGCCTCCGCTG ENSG00000 200 V R A D M V T E K Q A R E L S V P Q G P ENSG00000 600 GTCAGGGCCGACATGGTGACAGAGAAGCAGGCGCGGGAGCTGAGTGTGCCTCAGGGTCCT ENSG00000 220 G A G A E S T G E I I N N T V P L E N S ENSG00000 660 GGGGCTGGAGCAGAAAGCACTGGAGAAATCATCAACAACACTGTGCCCTTGGAGAACAGC ENSG00000 240 I P G N C C S A L F K N L L L K K I K R ENSG00000 720 ATTCCTGGGAACTGCTGCTCTGCCCTGTTCAAGAACCTGCTTCTCAAGAAGATCAAGCGG ENSG00000 260 C E R K G T E S V T E E K C A V L F S A ENSG00000 780 TGTGAGCGGAAGGGCACTGAGTCTGTCACAGAGGAGAAGTGCGCTGTGCTCTTCTCTGCC ENSG00000 280 S F T L G P G K L P I Q L Q A L S L P L ENSG00000 840 AGCTTCACACTTGGCCCCGGCAAACTCCCCATCCAGCTCCAGGCCCTGTCTCTGCCCCTG ENSG00000 300 V V I V H G N Q D N N A K A T I L W D N ENSG00000 900 GTGGTCATCGTCCATGGCAACCAAGACAACAATGCCAAAGCCACTATCCTGTGGGACAAT ENSG00000 320 A F S E M D R V P F V V A E R V P W E K ENSG00000 960 GCCTTCTCTGAGATGGACCGCGTGCCCTTTGTGGTGGCTGAGCGGGTGCCCTGGGAGAAG ENSG00000 340 M C E T L N L K F M A E V G T N R G L L ENSG00000 1020 ATGTGTGAAACTCTGAACCTGAAGTTCATGGCTGAGGTGGGGACCAACCGGGGGCTGCTC ENSG00000 360 P E H F L F L A Q K I F N D N S L S M E ENSG00000 1080 CCAGAGCACTTCCTCTTCCTGGCCCAGAAGATCTTCAATGACAACAGCCTCAGTATGGAG ENSG00000 380 A F Q H R S V S W S Q F N K E I L L G R ENSG00000 1140 GCCTTCCAGCACCGTTCTGTGTCCTGGTCGCAGTTCAACAAGGAGATCCTGCTGGGCCGT ENSG00000 400 G F T F W Q W F D G V L D L T K R C L R ENSG00000 1200 GGCTTCACCTTTTGGCAGTGGTTTGATGGTGTCCTGGACCTCACCAAACGCTGTCTCCGG ENSG00000 420 S Y W S D R L I I G F I S K Q Y V T S L ENSG00000 1260 AGCTACTGGTCTGACCGGCTGATCATTGGCTTCATCAGCAAACAGTACGTTACTAGCCTT ENSG00000 440 L L N E P D G T F L L R F S D S E I G G ENSG00000 1320 CTTCTCAATGAGCCCGACGGAACCTTTCTCCTCCGCTTCAGCGACTCAGAGATTGGGGGC ENSG00000 460 I T I A H V I R G Q D G S P Q I E N I Q ENSG00000 1380 ATCACCATTGCCCATGTCATCCGGGGCCAGGATGGCTCTCCACAGATAGAGAACATCCAG ENSG00000 480 P F S A K D L S I R S L G D R I R D L A ENSG00000 1440 CCATTCTCTGCCAAAGACCTGTCCATTCGCTCACTGGGGGACCGAATCCGGGATCTTGCT ENSG00000 500 Q L K N L Y P K K P K D E A F R S H Y K ENSG00000 1500 CAGCTCAAAAATCTCTATCCCAAGAAGCCCAAGGATGAGGCTTTCCGGAGCCACTACAAG ENSG00000 520 P E Q M G K D G R G Y V P A T I K M T V ENSG00000 1560 CCTGAACAGATGGGTAAGGATGGCAGGGGTTATGTCCCAGCTACCATCAAGATGACCGTG ENSG00000 540 E R D Q P L P T P E L Q M P T M V P S Y ENSG00000 1620 GAAAGGGACCAACCACTTCCTACCCCAGAGCTCCAGATGCCTACCATGGTGCCTTCTTAT ENSG00000 560 D L G M A P D S S M S M Q L G P D M V P ENSG00000 1680 GACCTTGGAATGGCCCCTGATTCCTCCATGAGCATGCAGCTTGGCCCAGATATGGTGCCC ENSG00000 580 Q V Y P P H S H S I P P Y Q G L S P E E ENSG00000 1740 CAGGTGTACCCACCACACTCTCACTCCATCCCCCCGTATCAAGGCCTCTCCCCAGAAGAA ENSG00000 600 S V N V L S A F Q E P H L Q M P P S L G ENSG00000 1800 TCAGTCAACGTGTTGTCAGCCTTCCAGGAGCCTCACCTGCAGATGCCCCCCAGCCTGGGC ENSG00000 620 Q M S L P F D Q P H P Q G L L P C Q P Q ENSG00000 1860 CAGATGAGCCTGCCCTTTGACCAGCCTCACCCCCAGGGCCTGCTGCCGTGCCAGCCTCAG ENSG00000 640 E H A V S S P D P L L C S D V T M V E D ENSG00000 1920 GAGCATGCTGTGTCCAGCCCTGACCCCCTGCTCTGCTCAGATGTGACCATGGTGGAAGAC ENSG00000 660 S C L S Q P V T A F P Q G T W I G E D I ENSG00000 1980 AGCTGCCTGAGCCAGCCAGTGACAGCGTTTCCTCAGGGCACTTGGATTGGTGAAGACATA ENSG00000 680 F P P L L P P T E Q D L T K L L L E G Q ENSG00000 2040 TTCCCTCCTCTGCTGCCTCCCACTGAACAGGACCTCACTAAGCTTCTCCTGGAGGGGCAA ENSG00000 700 G E S G G G S L G A Q P L L Q P S H Y G ENSG00000 2100 GGGGAGTCGGGGGGAGGGTCCTTGGGGGCACAGCCCCTCCTGCAGCCCTCCCACTATGGG ENSG00000 720 Q S G I S M S H M D L R A N P S W 737 ENSG00000 2160 CAATCTGGGATCTCAATGTCCCACATGGACCTAAGGGCCAACCCCAGTTGG 2211 """, ) protein_record = protein_alignment.sequences[5] nucleotide_record = nucleotide_records[protein_record.id] self.assertEqual(nucleotide_record.id, protein_record.id) alignments = aligner.align(protein_record, nucleotide_record) self.assertEqual(len(alignments), 1) alignment = next(alignments) codon_alignments.append(alignment) self.assertTrue( np.array_equal(alignment.coordinates, np.array([[0, 737], [0, 2211]])) ) self.assertEqual( str(alignment), """\ ENSG00000 0 M E Q F R H L P M P F H W K Q E E L K F ENSG00000 0 ATGGAACAGTTCCGCCACTTGCCAATGCCTTTCCACTGGAAGCAGGAAGAACTCAAGTTT ENSG00000 20 K T G L R R L Q H R V G E I H L L R E A ENSG00000 60 AAGACAGGCTTGCGGAGGCTGCAGCACCGAGTAGGGGAGATCCACCTTCTCCGAGAAGCC ENSG00000 40 L Q K G A E A G Q V S L H S L I E T P A ENSG00000 120 CTGCAGAAGGGGGCTGAGGCTGGCCAAGTGTCTCTGCACAGCTTGATAGAAACTCCTGCT ENSG00000 60 N G T G P S E A L A M L L Q E T T G E L ENSG00000 180 AATGGGACTGGGCCAAGTGAGGCCCTGGCCATGCTACTGCAGGAGACCACTGGAGAGCTA ENSG00000 80 E A A K A L V L K R I Q I W K R Q Q Q L ENSG00000 240 GAGGCAGCCAAAGCCCTAGTGCTGAAGAGGATCCAGATTTGGAAACGGCAGCAGCAGCTG ENSG00000 100 A G N G A P F E E S L A P L Q E R C E S ENSG00000 300 GCAGGGAATGGCGCACCGTTTGAGGAGAGCCTGGCCCCACTCCAGGAGAGGTGTGAAAGC ENSG00000 120 L V D I Y S Q L Q Q E V G A A G G E L E ENSG00000 360 CTGGTGGACATTTATTCCCAGCTACAGCAGGAGGTAGGGGCGGCTGGTGGGGAGCTTGAG ENSG00000 140 P K T R A S L T G R L D E V L R T L V T ENSG00000 420 CCCAAGACCCGGGCATCGCTGACTGGCCGGCTGGATGAAGTCCTGAGAACCCTCGTCACC ENSG00000 160 S C F L V E K Q P P Q V L K T Q T K F Q ENSG00000 480 AGTTGCTTCCTGGTGGAGAAGCAGCCCCCCCAGGTACTGAAGACTCAGACCAAGTTCCAG ENSG00000 180 A G V R F L L G L R F L G A P A K P P L ENSG00000 540 GCTGGAGTTCGATTCCTGTTGGGCTTGAGGTTCCTGGGGGCCCCAGCCAAGCCTCCGCTG ENSG00000 200 V R A D M V T E K Q A R E L S V P Q G P ENSG00000 600 GTCAGGGCCGACATGGTGACAGAGAAGCAGGCGCGGGAGCTGAGTGTGCCTCAGGGTCCT ENSG00000 220 G A G A E S T G E I I N N T V P L E N S ENSG00000 660 GGGGCTGGAGCAGAAAGCACTGGAGAAATCATCAACAACACTGTGCCCTTGGAGAACAGC ENSG00000 240 I P G N C C S A L F K N L L L K K I K R ENSG00000 720 ATTCCTGGGAACTGCTGCTCTGCCCTGTTCAAGAACCTGCTTCTCAAGAAGATCAAGCGG ENSG00000 260 C E R K G T E S V T E E K C A V L F S A ENSG00000 780 TGTGAGCGGAAGGGCACTGAGTCTGTCACAGAGGAGAAGTGCGCTGTGCTCTTCTCTGCC ENSG00000 280 S F T L G P G K L P I Q L Q A L S L P L ENSG00000 840 AGCTTCACACTTGGCCCCGGCAAACTCCCCATCCAGCTCCAGGCCCTGTCTCTGCCCCTG ENSG00000 300 V V I V H G N Q D N N A K A T I L W D N ENSG00000 900 GTGGTCATCGTCCATGGCAACCAAGACAACAATGCCAAAGCCACTATCCTGTGGGACAAT ENSG00000 320 A F S E M D R V P F V V A E R V P W E K ENSG00000 960 GCCTTCTCTGAGATGGACCGCGTGCCCTTTGTGGTGGCTGAGCGGGTGCCCTGGGAGAAG ENSG00000 340 M C E T L N L K F M A E V G T N R G L L ENSG00000 1020 ATGTGTGAAACTCTGAACCTGAAGTTCATGGCTGAGGTGGGGACCAACCGGGGGCTGCTC ENSG00000 360 P E H F L F L A Q K I F N D N S L S M E ENSG00000 1080 CCAGAGCACTTCCTCTTCCTGGCCCAGAAGATCTTCAATGACAACAGCCTCAGTATGGAG ENSG00000 380 A F Q H R S V S W S Q F N K E I L L G R ENSG00000 1140 GCCTTCCAGCACCGTTCTGTGTCCTGGTCGCAGTTCAACAAGGAGATCCTGCTGGGCCGT ENSG00000 400 G F T F W Q W F D G V L D L T K R C L R ENSG00000 1200 GGCTTCACCTTTTGGCAGTGGTTTGATGGTGTCCTGGACCTCACCAAACGCTGTCTCCGG ENSG00000 420 S Y W S D R L I I G F I S K Q Y V T S L ENSG00000 1260 AGCTACTGGTCTGACCGGCTGATCATTGGCTTCATCAGCAAACAGTACGTTACTAGCCTT ENSG00000 440 L L N E P D G T F L L R F S D S E I G G ENSG00000 1320 CTTCTCAATGAGCCCGACGGAACCTTTCTCCTCCGCTTCAGCGACTCAGAGATTGGGGGC ENSG00000 460 I T I A H V I R G Q D G S P Q I E N I Q ENSG00000 1380 ATCACCATTGCCCATGTCATCCGGGGCCAGGATGGCTCTCCACAGATAGAGAACATCCAG ENSG00000 480 P F S A K D L S I R S L G D R I R D L A ENSG00000 1440 CCATTCTCTGCCAAAGACCTGTCCATTCGCTCACTGGGGGACCGAATCCGGGATCTTGCT ENSG00000 500 Q L K N L Y P K K P K D E A F R S H Y K ENSG00000 1500 CAGCTCAAAAATCTCTATCCCAAGAAGCCCAAGGATGAGGCTTTCCGGAGCCACTACAAG ENSG00000 520 P E Q M G K D G R G Y V P A T I K M T V ENSG00000 1560 CCTGAACAGATGGGTAAGGATGGCAGGGGTTATGTCCCAGCTACCATCAAGATGACCGTG ENSG00000 540 E R D Q P L P T P E L Q M P T M V P S Y ENSG00000 1620 GAAAGGGACCAACCACTTCCTACCCCAGAGCTCCAGATGCCTACCATGGTGCCTTCTTAT ENSG00000 560 D L G M A P D S S M S M Q L G P D M V P ENSG00000 1680 GACCTTGGAATGGCCCCTGATTCCTCCATGAGCATGCAGCTTGGCCCAGATATGGTGCCC ENSG00000 580 Q V Y P P H S H S I P P Y Q G L S P E E ENSG00000 1740 CAGGTGTACCCACCACACTCTCACTCCATCCCCCCGTATCAAGGCCTCTCCCCAGAAGAA ENSG00000 600 S V N V L S A F Q E P H L Q M P P S L G ENSG00000 1800 TCAGTCAACGTGTTGTCAGCCTTCCAGGAGCCTCACCTGCAGATGCCCCCCAGCCTGGGC ENSG00000 620 Q M S L P F D Q P H P Q G L L P C Q P Q ENSG00000 1860 CAGATGAGCCTGCCCTTTGACCAGCCTCACCCCCAGGGCCTGCTGCCGTGCCAGCCTCAG ENSG00000 640 E H A V S S P D P L L C S D V T M V E D ENSG00000 1920 GAGCATGCTGTGTCCAGCCCTGACCCCCTGCTCTGCTCAGATGTGACCATGGTGGAAGAC ENSG00000 660 S C L S Q P V T A F P Q G T W I G E D I ENSG00000 1980 AGCTGCCTGAGCCAGCCAGTGACAGCGTTTCCTCAGGGCACTTGGATTGGTGAAGACATA ENSG00000 680 F P P L L P P T E Q D L T K L L L E G Q ENSG00000 2040 TTCCCTCCTCTGCTGCCTCCCACTGAACAGGACCTCACTAAGCTTCTCCTGGAGGGGCAA ENSG00000 700 G E S G G G S L G A Q P L L Q P S H Y G ENSG00000 2100 GGGGAGTCGGGGGGAGGGTCCTTGGGGGCACAGCCCCTCCTGCAGCCCTCCCACTATGGG ENSG00000 720 Q S G I S M S H M D L R A N P S W 737 ENSG00000 2160 CAATCTGGGATCTCAATGTCCCACATGGACCTAAGGGCCAACCCCAGTTGG 2211 """, ) protein_record = protein_alignment.sequences[6] nucleotide_record = nucleotide_records[protein_record.id] self.assertEqual(nucleotide_record.id, protein_record.id) alignments = aligner.align(protein_record, nucleotide_record) self.assertEqual(len(alignments), 1) alignment = next(alignments) codon_alignments.append(alignment) self.assertTrue( np.array_equal(alignment.coordinates, np.array([[0, 737], [0, 2211]])) ) self.assertEqual( str(alignment), """\ ENSG00000 0 M E Q F R H L P M P F H W K Q E E L K F ENSG00000 0 ATGGAACAGTTCCGCCACTTGCCAATGCCTTTCCACTGGAAGCAGGAAGAACTCAAGTTT ENSG00000 20 K T G L R R L Q H R V G E I H L L R E A ENSG00000 60 AAGACAGGCTTGCGGAGGCTGCAGCACCGAGTAGGGGAGATCCACCTTCTCCGAGAAGCC ENSG00000 40 L Q K G A E A G Q V S L H S L I E T P A ENSG00000 120 CTGCAGAAGGGGGCTGAGGCTGGCCAAGTGTCTCTGCACAGCTTGATAGAAACTCCTGCT ENSG00000 60 N G T G P S E A L A M L L Q E T T G E L ENSG00000 180 AATGGGACTGGGCCAAGTGAGGCCCTGGCCATGCTACTGCAGGAGACCACTGGAGAGCTA ENSG00000 80 E A A K A L V L K R I Q I W K R Q Q Q L ENSG00000 240 GAGGCAGCCAAAGCCCTAGTGCTGAAGAGGATCCAGATTTGGAAACGGCAGCAGCAGCTG ENSG00000 100 A G N G A P F E E S L A P L Q E R C E S ENSG00000 300 GCAGGGAATGGCGCACCGTTTGAGGAGAGCCTGGCCCCACTCCAGGAGAGGTGTGAAAGC ENSG00000 120 L V D I Y S Q L Q Q E V G A A G G E L E ENSG00000 360 CTGGTGGACATTTATTCCCAGCTACAGCAGGAGGTAGGGGCGGCTGGTGGGGAGCTTGAG ENSG00000 140 P K T R A S L T G R L D E V L R T L V T ENSG00000 420 CCCAAGACCCGGGCATCGCTGACTGGCCGGCTGGATGAAGTCCTGAGAACCCTCGTCACC ENSG00000 160 S C F L V E K Q P P Q V L K T Q T K F Q ENSG00000 480 AGTTGCTTCCTGGTGGAGAAGCAGCCCCCCCAGGTACTGAAGACTCAGACCAAGTTCCAG ENSG00000 180 A G V R F L L G L R F L G A P A K P P L ENSG00000 540 GCTGGAGTTCGATTCCTGTTGGGCTTGAGGTTCCTGGGGGCCCCAGCCAAGCCTCCGCTG ENSG00000 200 V R A D M V T E K Q A R E L S V P Q G P ENSG00000 600 GTCAGGGCCGACATGGTGACAGAGAAGCAGGCGCGGGAGCTGAGTGTGCCTCAGGGTCCT ENSG00000 220 G A G A E S T G E I I N N T V P L E N S ENSG00000 660 GGGGCTGGAGCAGAAAGCACTGGAGAAATCATCAACAACACTGTGCCCTTGGAGAACAGC ENSG00000 240 I P G N C C S A L F K N L L L K K I K R ENSG00000 720 ATTCCTGGGAACTGCTGCTCTGCCCTGTTCAAGAACCTGCTTCTCAAGAAGATCAAGCGG ENSG00000 260 C E R K G T E S V T E E K C A V L F S A ENSG00000 780 TGTGAGCGGAAGGGCACTGAGTCTGTCACAGAGGAGAAGTGCGCTGTGCTCTTCTCTGCC ENSG00000 280 S F T L G P G K L P I Q L Q A L S L P L ENSG00000 840 AGCTTCACACTTGGCCCCGGCAAACTCCCCATCCAGCTCCAGGCCCTGTCTCTGCCCCTG ENSG00000 300 V V I V H G N Q D N N A K A T I L W D N ENSG00000 900 GTGGTCATCGTCCATGGCAACCAAGACAACAATGCCAAAGCCACTATCCTGTGGGACAAT ENSG00000 320 A F S E M D R V P F V V A E R V P W E K ENSG00000 960 GCCTTCTCTGAGATGGACCGCGTGCCCTTTGTGGTGGCTGAGCGGGTGCCCTGGGAGAAG ENSG00000 340 M C E T L N L K F M A E V G T N R G L L ENSG00000 1020 ATGTGTGAAACTCTGAACCTGAAGTTCATGGCTGAGGTGGGGACCAACCGGGGGCTGCTC ENSG00000 360 P E H F L F L A Q K I F N D N S L S M E ENSG00000 1080 CCAGAGCACTTCCTCTTCCTGGCCCAGAAGATCTTCAATGACAACAGCCTCAGTATGGAG ENSG00000 380 A F Q H R S V S W S Q F N K E I L L G R ENSG00000 1140 GCCTTCCAGCACCGTTCTGTGTCCTGGTCGCAGTTCAACAAGGAGATCCTGCTGGGCCGT ENSG00000 400 G F T F W Q W F D G V L D L T K R C L R ENSG00000 1200 GGCTTCACCTTTTGGCAGTGGTTTGATGGTGTCCTGGACCTCACCAAACGCTGTCTCCGG ENSG00000 420 S Y W S D R L I I G F I S K Q Y V T S L ENSG00000 1260 AGCTACTGGTCTGACCGGCTGATCATTGGCTTCATCAGCAAACAGTACGTTACTAGCCTT ENSG00000 440 L L N E P D G T F L L R F S D S E I G G ENSG00000 1320 CTTCTCAATGAGCCCGACGGAACCTTTCTCCTCCGCTTCAGCGACTCAGAGATTGGGGGC ENSG00000 460 I T I A H V I R G Q D G S P Q I E N I Q ENSG00000 1380 ATCACCATTGCCCATGTCATCCGGGGCCAGGATGGCTCTCCACAGATAGAGAACATCCAG ENSG00000 480 P F S A K D L S I R S L G D R I R D L A ENSG00000 1440 CCATTCTCTGCCAAAGACCTGTCCATTCGCTCACTGGGGGACCGAATCCGGGATCTTGCT ENSG00000 500 Q L K N L Y P K K P K D E A F R S H Y K ENSG00000 1500 CAGCTCAAAAATCTCTATCCCAAGAAGCCCAAGGATGAGGCTTTCCGGAGCCACTACAAG ENSG00000 520 P E Q M G K D G R G Y V P A T I K M T V ENSG00000 1560 CCTGAACAGATGGGTAAGGATGGCAGGGGTTATGTCCCAGCTACCATCAAGATGACCGTG ENSG00000 540 E R D Q P L P T P E L Q M P T M V P S Y ENSG00000 1620 GAAAGGGACCAACCACTTCCTACCCCAGAGCTCCAGATGCCTACCATGGTGCCTTCTTAT ENSG00000 560 D L G M A P D S S M S M Q L G P D M V P ENSG00000 1680 GACCTTGGAATGGCCCCTGATTCCTCCATGAGCATGCAGCTTGGCCCAGATATGGTGCCC ENSG00000 580 Q V Y P P H S H S I P P Y Q G L S P E E ENSG00000 1740 CAGGTGTACCCACCACACTCTCACTCCATCCCCCCGTATCAAGGCCTCTCCCCAGAAGAA ENSG00000 600 S V N V L S A F Q E P H L Q M P P S L G ENSG00000 1800 TCAGTCAACGTGTTGTCAGCCTTCCAGGAGCCTCACCTGCAGATGCCCCCCAGCCTGGGC ENSG00000 620 Q M S L P F D Q P H P Q G L L P C Q P Q ENSG00000 1860 CAGATGAGCCTGCCCTTTGACCAGCCTCACCCCCAGGGCCTGCTGCCGTGCCAGCCTCAG ENSG00000 640 E H A V S S P D P L L C S D V T M V E D ENSG00000 1920 GAGCATGCTGTGTCCAGCCCTGACCCCCTGCTCTGCTCAGATGTGACCATGGTGGAAGAC ENSG00000 660 S C L S Q P V T A F P Q G T W I G E D I ENSG00000 1980 AGCTGCCTGAGCCAGCCAGTGACAGCGTTTCCTCAGGGCACTTGGATTGGTGAAGACATA ENSG00000 680 F P P L L P P T E Q D L T K L L L E G Q ENSG00000 2040 TTCCCTCCTCTGCTGCCTCCCACTGAACAGGACCTCACTAAGCTTCTCCTGGAGGGGCAA ENSG00000 700 G E S G G G S L G A Q P L L Q P S H Y G ENSG00000 2100 GGGGAGTCGGGGGGAGGGTCCTTGGGGGCACAGCCCCTCCTGCAGCCCTCCCACTATGGG ENSG00000 720 Q S G I S M S H M D L R A N P S W 737 ENSG00000 2160 CAATCTGGGATCTCAATGTCCCACATGGACCTAAGGGCCAACCCCAGTTGG 2211 """, ) protein_record = protein_alignment.sequences[7] nucleotide_record = nucleotide_records[protein_record.id] self.assertEqual(nucleotide_record.id, protein_record.id) nucleotide_record = nucleotide_record.upper() alignments = aligner.align(protein_record, nucleotide_record) self.assertEqual(len(alignments), 1) alignment = next(alignments) codon_alignments.append(alignment) self.assertTrue( np.array_equal(alignment.coordinates, np.array([[0, 1021], [0, 3063]])) ) self.assertEqual( str(alignment), """\ isotig466 0 E V T Q S R R K P V R E G R P W E P S Q isotig466 0 GAGGTTACTCAGAGTAGGAGGAAGCCGGTCAGAGAGGGCAGACCCTGGGAACCTTCGCAG isotig466 20 E L A Q T P E G G C P R Q E S R P E G G isotig466 60 GAGTTGGCCCAAACCCCTGAGGGAGGCTGTCCTCGGCAGGAGAGCAGACCTGAGGGAGGT isotig466 40 W C A G P G C P A L P S H P R A G S P E isotig466 120 TGGTGTGCCGGTCCTGGTTGTCCAGCCCTCCCGTCCCATCCCAGGGCTGGCTCACCAGAA isotig466 60 K S T G I P G P L G R E Q R V S S C P G isotig466 180 AAAAGTACAGGCATCCCAGGCCCTCTGGGGCGGGAGCAGAGGGTCTCCTCTTGTCCGGGG isotig466 80 E D K N K N K K R V C S P H W K S S G A isotig466 240 GAAGACAAAAACAAAAACAAAAAACGAGTGTGTAGCCCTCACTGGAAGTCTTCTGGTGCT isotig466 100 L G P F A L G S L A S G H G G R A P P G isotig466 300 CTGGGGCCGTTTGCACTTGGGAGCCTGGCTTCTGGGCATGGTGGCCGGGCTCCGCCGGGG isotig466 120 A S A L G K A F L E Q S G W E P T E V P isotig466 360 GCTTCAGCCCTCGGCAAAGCGTTTCTAGAACAGAGTGGGTGGGAGCCGACTGAAGTCCCA isotig466 140 E P R T L T H R K A S S G W R N A N P P isotig466 420 GAACCGCGAACACTGACGCACAGGAAAGCCTCGAGTGGGTGGAGAAATGCAAATCCCCCA isotig466 160 V A W P Q P L R T L T A D S D F G L E R isotig466 480 GTGGCATGGCCTCAGCCGCTGCGGACCCTGACGGCCGATTCTGACTTCGGACTTGAGCGG isotig466 180 D Q H P D P G R A S M S Q W N Q V Q Q L isotig466 540 GACCAGCACCCGGACCCAGGGCGAGCCAGCATGTCTCAGTGGAATCAAGTCCAACAGTTA isotig466 200 E I K F L E Q V D Q F Y D D N F P M E I isotig466 600 GAAATCAAGTTTTTGGAGCAAGTTGATCAGTTCTATGATGACAACTTTCCCATGGAAATC isotig466 220 R H L L A Q W I E H Q D W E V A S N N E isotig466 660 CGACATCTGCTGGCCCAGTGGATTGAGCATCAAGACTGGGAGGTGGCCTCTAACAATGAA isotig466 240 T M A T I L L Q N L L I Q L D E Q L G R isotig466 720 ACTATGGCAACAATTCTTCTTCAAAACTTATTAATACAATTGGATGAACAGTTAGGTCGT isotig466 260 V S K E K N L L L I H N L K R I R K V L isotig466 780 GTTTCCAAAGAGAAAAACCTGCTATTGATCCACAATCTAAAGAGAATTAGAAAAGTACTT isotig466 280 Q G K F H G N P M H V A V V I S N C L R isotig466 840 CAGGGGAAGTTTCATGGAAATCCAATGCATGTAGCCGTGGTAATCTCAAATTGTTTAAGG isotig466 300 E E R R I L A A A N M P I Q G P L E K S isotig466 900 GAAGAGAGGAGAATACTGGCTGCAGCGAACATGCCTATCCAGGGACCTCTGGAGAAATCC isotig466 320 L Q S S S V S E R Q R N V E H K V A A I isotig466 960 TTACAAAGTTCGTCGGTTTCAGAAAGACAGAGAAATGTGGAACACAAAGTGGCTGCCATT isotig466 340 K N S V Q M T E Q D T K Y L E D L Q D E isotig466 1020 AAAAACAGTGTGCAGATGACAGAACAAGACACCAAATACTTGGAAGATCTGCAAGATGAA isotig466 360 F D Y R Y K T I Q T M D Q G D K N S I L isotig466 1080 TTTGACTACAGGTATAAAACAATTCAGACAATGGACCAGGGTGACAAGAATAGCATCCTA isotig466 380 M N Q E V L T L Q E M L N S L D F K R K isotig466 1140 ATGAACCAGGAGGTTTTGACACTCCAAGAAATGCTTAATAGCCTGGACTTCAAGAGAAAG isotig466 400 E A L T K M T Q I V N E S D L L M S S M isotig466 1200 GAAGCACTCACTAAGATGACACAGATAGTGAACGAGTCGGACCTGCTGATGAGCAGCATG isotig466 420 L I E E L Q D W K R R Q Q I A C I G G P isotig466 1260 CTCATAGAAGAGCTGCAGGACTGGAAGAGGAGGCAGCAGATCGCCTGCATCGGTGGCCCA isotig466 440 L H N G L D Q L Q N C F T L L A E S L F isotig466 1320 CTCCACAACGGGCTGGACCAGCTTCAGAACTGCTTTACCCTGTTGGCAGAAAGTCTTTTC isotig466 460 Q L R R Q L E K L E E Q S S K M T Y E G isotig466 1380 CAACTCAGACGACAGCTGGAGAAATTAGAGGAGCAGTCTTCCAAGATGACTTACGAAGGA isotig466 480 D P I P T Q R A H L L E R A T F L I Y N isotig466 1440 GACCCCATCCCCACGCAGAGAGCACACCTGCTGGAGAGAGCCACCTTCCTGATCTACAAC isotig466 500 L F K N S F V V E R Q P C M P T H P Q R isotig466 1500 CTTTTCAAGAACTCATTTGTGGTTGAGCGACAGCCCTGCATGCCAACACACCCTCAGAGG isotig466 520 P L V L K T L I Q F T A K L R L L I K L isotig466 1560 CCGCTGGTACTCAAAACCCTCATTCAGTTCACCGCGAAACTGAGACTACTAATAAAATTG isotig466 540 P E L N Y Q V K V K A S I D K N V S T L isotig466 1620 CCGGAACTCAACTATCAGGTGAAAGTAAAGGCATCGATCGACAAGAATGTTTCAACGCTA isotig466 560 S N R R F V L C G T Q V K A M S I E E S isotig466 1680 AGCAATAGAAGATTTGTGCTTTGTGGAACTCAAGTCAAAGCCATGTCCATCGAGGAATCC isotig466 580 S N G S L S V E F R H L Q P K E M K S S isotig466 1740 TCCAATGGGAGCCTCTCAGTAGAATTTAGACATTTGCAACCGAAGGAAATGAAATCCAGT isotig466 600 A G S K G N E G C H M V T E E L H S I A isotig466 1800 GCCGGAAGTAAAGGAAATGAGGGCTGCCACATGGTGACGGAAGAGCTGCATTCCATAGCC isotig466 620 F E T Q I C L Y G L T I D L E T S S L P isotig466 1860 TTTGAGACCCAGATCTGCCTCTATGGCCTCACCATCGACTTGGAGACAAGCTCATTACCT isotig466 640 V V M I S N V S Q L P N A W A S I I W Y isotig466 1920 GTGGTGATGATTTCTAATGTCAGCCAACTGCCTAATGCTTGGGCATCCATCATTTGGTAC isotig466 660 N V S T N D C Q N L V F F N N P P P V T isotig466 1980 AATGTGTCAACCAACGATTGCCAGAACTTGGTTTTCTTTAATAATCCTCCGCCTGTCACT isotig466 680 L S Q L L E V M S W Q F S S Y V G R G L isotig466 2040 TTGAGTCAACTCCTGGAAGTGATGAGCTGGCAGTTTTCATCCTATGTTGGTCGTGGCCTT isotig466 700 N S D Q L N M L A E K L T V Q S N Y S D isotig466 2100 AATTCAGACCAGCTCAACATGCTGGCAGAGAAGCTCACAGTTCAGTCTAACTACAGCGAT isotig466 720 G H L T W A K F C K E H L P G K P F T F isotig466 2160 GGTCACCTCACCTGGGCCAAGTTCTGCAAGGAACACTTGCCTGGCAAACCATTTACCTTC isotig466 740 W T W L E A I L D L I K K H I L P L W I isotig466 2220 TGGACCTGGCTTGAAGCAATATTGGACCTAATTAAAAAACACATTCTTCCCCTCTGGATT isotig466 760 D G Y I M G F V S K E K E R F L L K D K isotig466 2280 GATGGGTACATCATGGGCTTCGTGAGCAAAGAGAAGGAGAGGTTTCTGCTCAAGGATAAA isotig466 780 M P G T F L L R F S E S H L G G I T F T isotig466 2340 ATGCCCGGGACATTTTTGTTACGATTCAGTGAGAGCCATCTCGGAGGGATCACCTTCACC isotig466 800 W V D H S E N G E V R F H S V E P Y N K isotig466 2400 TGGGTGGACCACTCTGAAAACGGAGAAGTGAGATTCCACTCCGTAGAACCCTACAACAAA isotig466 820 G R L S A L P F A D I L R D Y K V I M A isotig466 2460 GGGCGTCTGTCGGCCCTGCCATTTGCTGACATCCTGCGGGACTACAAGGTCATCATGGCT isotig466 840 E N I P E N P L K Y L Y P D I P K D K A isotig466 2520 GAGAACATTCCCGAGAACCCTCTCAAGTACCTCTACCCCGACATCCCCAAAGACAAAGCC isotig466 860 F G K H Y S S Q P C E V S R P T E R G D isotig466 2580 TTCGGTAAACACTACAGCTCCCAGCCTTGCGAAGTTTCAAGGCCAACAGAACGGGGAGAC isotig466 880 K G Y V P S V F I P I S T I R S D A M E isotig466 2640 AAAGGTTATGTTCCTTCAGTTTTTATCCCTATTTCAACAATCCGCAGCGACGCCATGGAG isotig466 900 P Q S P S D L L P M S P S V Y A V L R E isotig466 2700 CCGCAGTCTCCTTCAGACCTTCTCCCCATGTCTCCGAGTGTATACGCTGTGCTGAGAGAA isotig466 920 N L S P T T I E T A M K S P Y S E R Y K isotig466 2760 AACCTGAGCCCTACCACAATTGAAACAGCAATGAAGTCTCCATATTCTGAGCGGTACAAA isotig466 940 A T L Q G R E Q M K T E T A L C Q S P Q isotig466 2820 GCGACTCTTCAAGGAAGAGAGCAGATGAAAACGGAGACTGCTCTTTGCCAAAGTCCACAA isotig466 960 F I S S A L I L V S R K W H K S E A F L isotig466 2880 TTCATTTCTTCAGCTTTGATACTGGTTTCTAGAAAATGGCACAAATCCGAAGCTTTCCTC isotig466 980 S L G D I P Q L G V L L K C K P K L Q I isotig466 2940 TCACTAGGTGACATTCCCCAACTGGGAGTGCTGCTGAAATGCAAACCAAAGCTTCAGATA isotig466 1000 N T Q E K T A S R N L C S Q Y N R R L L isotig466 3000 AACACGCAGGAAAAGACAGCTTCGAGAAACCTATGTTCGCAATATAACAGAAGGCTGCTT isotig466 1020 C 1021 isotig466 3060 TGC 3063 """, ) protein_record = protein_alignment.sequences[8] nucleotide_record = nucleotide_records[protein_record.id] self.assertEqual(nucleotide_record.id, protein_record.id) nucleotide_record = nucleotide_record.upper() alignments = aligner.align(protein_record, nucleotide_record) self.assertEqual(len(alignments), 1) alignment = next(alignments) codon_alignments.append(alignment) self.assertTrue( np.array_equal(alignment.coordinates, np.array([[0, 806], [0, 2418]])) ) self.assertEqual( str(alignment), """\ isotig125 0 A R R G Q A A L G S P A A R T W S Q R S isotig125 0 GCTAGGAGAGGCCAGGCGGCCCTCGGGAGCCCAGCTGCTCGCACCTGGAGCCAGCGCAGC isotig125 20 P A S R A S A R E T V T P P D C G R M A isotig125 60 CCGGCCAGTCGGGCCTCAGCCCGGGAGACAGTTACGCCCCCTGATTGCGGCAGGATGGCC isotig125 40 Q W N Q L Q Q L D T R Y L E Q L H Q L Y isotig125 120 CAGTGGAACCAGCTGCAGCAGCTGGACACTCGGTACCTGGAGCAGCTGCACCAGCTGTAC isotig125 60 S D S F P M E L R Q F L A P W I E S Q D isotig125 180 AGCGACAGCTTCCCCATGGAGCTGCGGCAGTTCCTGGCACCTTGGATTGAGAGTCAAGAT isotig125 80 W A Y A A S K E S H A T L V F H N L L G isotig125 240 TGGGCATATGCAGCCAGCAAAGAGTCACATGCCACACTGGTGTTTCATAATCTCTTGGGT isotig125 100 E I D Q Q Y S R F L Q E S N V L Y Q H N isotig125 300 GAGATTGACCAGCAGTACAGCCGATTCCTGCAAGAGTCCAACGTCCTCTATCAGCACAAC isotig125 120 L R R I K Q F L Q S R Y L E K P M E I A isotig125 360 CTTCGGAGGATCAAGCAGTTCCTACAGAGCAGGTATCTTGAGAAGCCGATGGAAATCGCC isotig125 140 R I V A R C L W E E S R L L Q T A A T A isotig125 420 CGCATCGTGGCCCGATGCCTGTGGGAAGAGTCTCGCCTCCTCCAGACGGCAGCCACTGCA isotig125 160 A Q Q G G Q A N H P T A A V V T E K Q Q isotig125 480 GCCCAGCAAGGAGGCCAGGCCAACCACCCAACAGCTGCTGTGGTGACGGAGAAACAGCAG isotig125 180 M L E Q H L Q D V R K R V Q D L E Q K M isotig125 540 ATGCTGGAGCAGCATCTTCAGGATGTCCGGAAACGTGTGCAGGATCTAGAACAGAAAATG isotig125 200 K V V E N L Q D D F D F N Y K T L K S Q isotig125 600 AAAGTGGTAGAGAATCTCCAGGATGACTTTGATTTCAACTATAAAACCCTCAAGAGTCAA isotig125 220 G D M Q D L N G N N Q S V T R Q K M Q Q isotig125 660 GGAGACATGCAGGATCTGAATGGAAACAACCAGTCTGTGACCAGGCAGAAGATGCAGCAG isotig125 240 L E Q M L T A L D Q M R R S I V S E L A isotig125 720 CTGGAACAGATGCTCACGGCGCTGGACCAGATGCGGAGAAGCATTGTGAGTGAGCTGGCG isotig125 260 G L L S A M E Y V Q K T L T D E E L A D isotig125 780 GGGCTTTTGTCGGCAATGGAGTACGTGCAGAAAACACTCACAGACGAGGAGCTGGCTGAC isotig125 280 W K R R Q Q I A C I G G P P N I C L D R isotig125 840 TGGAAGAGGCGGCAGCAGATCGCGTGCATTGGAGGCCCTCCCAACATCTGCCTGGATCGC isotig125 300 L E N W I T S L A E S Q L Q T R Q Q I K isotig125 900 CTGGAAAACTGGATAACTTCGTTAGCAGAATCTCAACTTCAGACCCGCCAACAAATTAAG isotig125 320 K L E E L Q Q K V S Y K G D P I V Q H R isotig125 960 AAACTGGAGGAGCTACAGCAGAAGGTGTCCTACAAGGGGGACCCCATTGTGCAGCACCGG isotig125 340 P M L E E R I V E L F R N L M K S A F V isotig125 1020 CCGATGCTGGAGGAGCGGATCGTGGAGCTGTTCAGAAACTTGATGAAGAGTGCCTTCGTG isotig125 360 V E R Q P C M P M H P D R P L V I K T G isotig125 1080 GTGGAGCGACAGCCCTGCATGCCGATGCACCCCGACCGGCCCTTGGTCATCAAGACTGGT isotig125 380 V Q F T T K V R L L V K F P E L N Y Q L isotig125 1140 GTCCAGTTCACTACTAAAGTCAGGTTGTTGGTCAAGTTTCCCGAGTTGAATTATCAGCTT isotig125 400 K I K V C I D K D S G D V A A L R G S R isotig125 1200 AAAATTAAAGTGTGCATTGACAAAGATTCTGGGGACGTTGCTGCTCTCAGAGGATCTCGG isotig125 420 K F N I L G T N T K V M N M E E S N N G isotig125 1260 AAATTTAACATTCTGGGCACAAACACGAAGGTGATGAACATGGAAGAATCCAACAACGGC isotig125 440 S L S A E F K H L T L R E Q R C G N G G isotig125 1320 AGCCTGTCTGCGGAGTTCAAGCACTTGACCCTGAGGGAGCAGAGATGTGGGAATGGAGGC isotig125 460 R A N C D A S L I V T E E L H L I T F E isotig125 1380 CGTGCCAATTGTGATGCCTCCTTGATTGTGACCGAGGAGCTGCATCTGATCACCTTCGAG isotig125 480 T E V Y H Q G L K I D L E T H S L P V V isotig125 1440 ACTGAGGTGTACCACCAAGGCCTCAAGATTGACCTGGAGACCCATTCTTTGCCAGTTGTG isotig125 500 V I S N I C Q M P N A W A S I L W Y N M isotig125 1500 GTGATCTCCAACATCTGTCAGATGCCAAATGCCTGGGCATCCATCCTGTGGTATAACATG isotig125 520 L T N N P K N V N F F T K P P I G T W D isotig125 1560 CTGACCAACAACCCCAAGAACGTGAACTTCTTCACCAAGCCACCAATCGGAACCTGGGAC isotig125 540 Q V A E V L S W Q F S S T T K R G L S I isotig125 1620 CAGGTGGCCGAGGTGCTCAGCTGGCAGTTCTCATCCACCACAAAGCGAGGGCTGAGCATC isotig125 560 E Q L T T L A E K L L G P G V N Y S G C isotig125 1680 GAGCAGCTGACTACGCTGGCCGAGAAGCTCCTAGGACCTGGTGTCAACTACTCCGGGTGT isotig125 580 Q I T W A K F C K E N M A G K G F S F W isotig125 1740 CAGATCACATGGGCTAAATTTTGCAAAGAAAACATGGCTGGCAAGGGCTTCTCCTTCTGG isotig125 600 V W L D N I I D L V K K Y I L A L W N E isotig125 1800 GTGTGGCTAGACAATATCATTGACCTTGTGAAAAAGTATATCTTGGCCCTCTGGAATGAA isotig125 620 G Y I M G F I S K E R E R A I L S T K P isotig125 1860 GGGTACATCATGGGCTTCATTAGCAAGGAGCGGGAGCGGGCGATCCTGAGCACGAAACCC isotig125 640 P G T F L L R F S E S S K E G G V T F T isotig125 1920 CCGGGCACCTTCCTGCTGAGATTCAGCGAGAGCAGCAAAGAAGGAGGGGTCACTTTCACT isotig125 660 W V E K D I S G K T Q I Q S V E P Y T K isotig125 1980 TGGGTGGAAAAGGACATCAGTGGCAAGACCCAGATCCAGTCTGTAGAGCCGTACACCAAG isotig125 680 Q Q L N N M S F A E I I M G Y K I M D A isotig125 2040 CAGCAGCTGAACAACATGTCCTTTGCTGAAATCATCATGGGCTACAAGATCATGGATGCC isotig125 700 T N I L V S P L V Y L Y P D I P K E E A isotig125 2100 ACCAACATCCTGGTGTCCCCATTGGTCTACCTCTACCCTGACATTCCCAAGGAGGAGGCG isotig125 720 F G K Y C R P E S Q E H P E A D P G S A isotig125 2160 TTCGGGAAGTACTGTCGACCAGAGAGCCAGGAGCATCCTGAAGCTGACCCCGGTAGTGCC isotig125 740 A P Y L K T K F I C V T P T T C S N T I isotig125 2220 GCCCCTTACCTGAAGACCAAGTTCATCTGTGTGACACCAACGACCTGCAGCAATACCATT isotig125 760 D L P M S P P H F R F I D A V W K R R C isotig125 2280 GACCTGCCGATGTCCCCCCCGCACTTTAGATTCATTGATGCAGTTTGGAAACGGAGGTGC isotig125 780 A L G R R A V V T H V H G S D F G V R Y isotig125 2340 GCCCTCGGCAGGAGGGCAGTTGTCACTCACGTTCATGGATCTGACTTCGGAGTGCGCTAC isotig125 800 L P H V R S 806 isotig125 2400 CTCCCCCATGTGAGGAGC 2418 """, ) protein_record = protein_alignment.sequences[9] nucleotide_record = nucleotide_records[protein_record.id] self.assertEqual(nucleotide_record.id, protein_record.id) nucleotide_record = nucleotide_record.upper() alignments = aligner.align(protein_record, nucleotide_record) self.assertEqual(len(alignments), 1) alignment = next(alignments) codon_alignments.append(alignment) self.assertTrue( np.array_equal(alignment.coordinates, np.array([[0, 796], [0, 2388]])) ) self.assertEqual( str(alignment), """\ isotig125 0 A R R G Q A A L G S P A A R T W S Q R S isotig125 0 GCTAGGAGAGGCCAGGCGGCCCTCGGGAGCCCAGCTGCTCGCACCTGGAGCCAGCGCAGC isotig125 20 P A S R A S A R E T V T P P D C G R M A isotig125 60 CCGGCCAGTCGGGCCTCAGCCCGGGAGACAGTTACGCCCCCTGATTGCGGCAGGATGGCC isotig125 40 Q W N Q L Q Q L D T R Y L E Q L H Q L Y isotig125 120 CAGTGGAACCAGCTGCAGCAGCTGGACACTCGGTACCTGGAGCAGCTGCACCAGCTGTAC isotig125 60 S D S F P M E L R Q F L A P W I E S Q D isotig125 180 AGCGACAGCTTCCCCATGGAGCTGCGGCAGTTCCTGGCACCTTGGATTGAGAGTCAAGAT isotig125 80 W A Y A A S K E S H A T L V F H N L L G isotig125 240 TGGGCATATGCAGCCAGCAAAGAGTCACATGCCACACTGGTGTTTCATAATCTCTTGGGT isotig125 100 E I D Q Q Y S R F L Q E S N V L Y Q H N isotig125 300 GAGATTGACCAGCAGTACAGCCGATTCCTGCAAGAGTCCAACGTCCTCTATCAGCACAAC isotig125 120 L R R I K Q F L Q S R Y L E K P M E I A isotig125 360 CTTCGGAGGATCAAGCAGTTCCTACAGAGCAGGTATCTTGAGAAGCCGATGGAAATCGCC isotig125 140 R I V A R C L W E E S R L L Q T A A T A isotig125 420 CGCATCGTGGCCCGATGCCTGTGGGAAGAGTCTCGCCTCCTCCAGACGGCAGCCACTGCA isotig125 160 A Q Q G G Q A N H P T A A V V T E K Q Q isotig125 480 GCCCAGCAAGGAGGCCAGGCCAACCACCCAACAGCTGCTGTGGTGACGGAGAAACAGCAG isotig125 180 M L E Q H L Q D V R K R V Q D L E Q K M isotig125 540 ATGCTGGAGCAGCATCTTCAGGATGTCCGGAAACGTGTGCAGGATCTAGAACAGAAAATG isotig125 200 K V V E N L Q D D F D F N Y K T L K S Q isotig125 600 AAAGTGGTAGAGAATCTCCAGGATGACTTTGATTTCAACTATAAAACCCTCAAGAGTCAA isotig125 220 G D M Q D L N G N N Q S V T R Q K M Q Q isotig125 660 GGAGACATGCAGGATCTGAATGGAAACAACCAGTCTGTGACCAGGCAGAAGATGCAGCAG isotig125 240 L E Q M L T A L D Q M R R S I V S E L A isotig125 720 CTGGAACAGATGCTCACGGCGCTGGACCAGATGCGGAGAAGCATTGTGAGTGAGCTGGCG isotig125 260 G L L S A M E Y V Q K T L T D E E L A D isotig125 780 GGGCTTTTGTCGGCAATGGAGTACGTGCAGAAAACACTCACAGACGAGGAGCTGGCTGAC isotig125 280 W K R R Q Q I A C I G G P P N I C L D R isotig125 840 TGGAAGAGGCGGCAGCAGATCGCGTGCATTGGAGGCCCTCCCAACATCTGCCTGGATCGC isotig125 300 L E N W I T S L A E S Q L Q T R Q Q I K isotig125 900 CTGGAAAACTGGATAACTTCGTTAGCAGAATCTCAACTTCAGACCCGCCAACAAATTAAG isotig125 320 K L E E L Q Q K V S Y K G D P I V Q H R isotig125 960 AAACTGGAGGAGCTACAGCAGAAGGTGTCCTACAAGGGGGACCCCATTGTGCAGCACCGG isotig125 340 P M L E E R I V E L F R N L M K S A F V isotig125 1020 CCGATGCTGGAGGAGCGGATCGTGGAGCTGTTCAGAAACTTGATGAAGAGTGCCTTCGTG isotig125 360 V E R Q P C M P M H P D R P L V I K T G isotig125 1080 GTGGAGCGACAGCCCTGCATGCCGATGCACCCCGACCGGCCCTTGGTCATCAAGACTGGT isotig125 380 V Q F T T K V R L L V K F P E L N Y Q L isotig125 1140 GTCCAGTTCACTACTAAAGTCAGGTTGTTGGTCAAGTTTCCCGAGTTGAATTATCAGCTT isotig125 400 K I K V C I D K D S G D V A A L R G S R isotig125 1200 AAAATTAAAGTGTGCATTGACAAAGATTCTGGGGACGTTGCTGCTCTCAGAGGATCTCGG isotig125 420 K F N I L G T N T K V M N M E E S N N G isotig125 1260 AAATTTAACATTCTGGGCACAAACACGAAGGTGATGAACATGGAAGAATCCAACAACGGC isotig125 440 S L S A E F K H L T L R E Q R C G N G G isotig125 1320 AGCCTGTCTGCGGAGTTCAAGCACTTGACCCTGAGGGAGCAGAGATGTGGGAATGGAGGC isotig125 460 R A N C D A S L I V T E E L H L I T F E isotig125 1380 CGTGCCAATTGTGATGCCTCCTTGATTGTGACCGAGGAGCTGCATCTGATCACCTTCGAG isotig125 480 T E V Y H Q G L K I D L E T H S L P V V isotig125 1440 ACTGAGGTGTACCACCAAGGCCTCAAGATTGACCTGGAGACCCATTCTTTGCCAGTTGTG isotig125 500 V I S N I C Q M P N A W A S I L W Y N M isotig125 1500 GTGATCTCCAACATCTGTCAGATGCCAAATGCCTGGGCATCCATCCTGTGGTATAACATG isotig125 520 L T N N P K N V N F F T K P P I G T W D isotig125 1560 CTGACCAACAACCCCAAGAACGTGAACTTCTTCACCAAGCCACCAATCGGAACCTGGGAC isotig125 540 Q V A E V L S W Q F S S T T K R G L S I isotig125 1620 CAGGTGGCCGAGGTGCTCAGCTGGCAGTTCTCATCCACCACAAAGCGAGGGCTGAGCATC isotig125 560 E Q L T T L A E K L L G P G V N Y S G C isotig125 1680 GAGCAGCTGACTACGCTGGCCGAGAAGCTCCTAGGACCTGGTGTCAACTACTCCGGGTGT isotig125 580 Q I T W A K F C K E N M A G K G F S F W isotig125 1740 CAGATCACATGGGCTAAATTTTGCAAAGAAAACATGGCTGGCAAGGGCTTCTCCTTCTGG isotig125 600 V W L D N I I D L V K K Y I L A L W N E isotig125 1800 GTGTGGCTAGACAATATCATTGACCTTGTGAAAAAGTATATCTTGGCCCTCTGGAATGAA isotig125 620 G Y I M G F I S K E R E R A I L S T K P isotig125 1860 GGGTACATCATGGGCTTCATTAGCAAGGAGCGGGAGCGGGCGATCCTGAGCACGAAACCC isotig125 640 P G T F L L R F S E S S K E G G V T F T isotig125 1920 CCGGGCACCTTCCTGCTGAGATTCAGCGAGAGCAGCAAAGAAGGAGGGGTCACTTTCACT isotig125 660 W V E K D I S G K T Q I Q S V E P Y T K isotig125 1980 TGGGTGGAAAAGGACATCAGTGGCAAGACCCAGATCCAGTCTGTAGAGCCGTACACCAAG isotig125 680 Q Q L N N M S F A E I I M G Y K I M D A isotig125 2040 CAGCAGCTGAACAACATGTCCTTTGCTGAAATCATCATGGGCTACAAGATCATGGATGCC isotig125 700 T N I L V S P L V Y L Y P D I P K E E A isotig125 2100 ACCAACATCCTGGTGTCCCCATTGGTCTACCTCTACCCTGACATTCCCAAGGAGGAGGCG isotig125 720 F G K Y C R P E S Q E H P E A D P G S C isotig125 2160 TTCGGGAAGTACTGTCGACCAGAGAGCCAGGAGCATCCTGAAGCTGACCCCGGTAGTTGT isotig125 740 F S M V L V S L L G K G G Q C R S L E E isotig125 2220 TTTTCCATGGTTCTGGTTTCGCTGTTAGGGAAAGGGGGACAGTGCAGGTCCTTGGAGGAG isotig125 760 R Q G H D R V S G G E S C Y G R A V Y W isotig125 2280 AGACAAGGACATGACCGGGTGTCTGGTGGTGAGTCCTGCTATGGAAGAGCTGTTTATTGG isotig125 780 V L Q G D R D S R E D Q N Q A S 796 isotig125 2340 GTACTTCAGGGTGACCGGGATTCAAGAGAAGACCAGAATCAGGCCTCA 2388 """, ) alignment = protein_alignment.mapall(codon_alignments) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 36, 36, 63, 63, 213, 222, 240, 240, 330, 330, 330, 405, 405, 438, 450, 579, 579, 729, 729, 837, 837, 897, 912, 975, 987, 1020, 1026, 1074, 1077, 1107, 1107, 1116, 1119, 1182, 1188, 1302, 1302, 1392, 1398, 1455, 1458, 1470, 1695, 1695, 1824, 1824, 1887, 1887, 1896, 1902, 1956, 1980, 2022, 2025, 2043, 2046, 2061, 2106, 2187, 2220, 2232, 2253, 2271, 2331, 2334, 2352, 2364, 2373, 2382, 2424, 2463, 2484, 2517, 2541], [ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 36, 36, 63, 63, 213, 222, 240, 240, 330, 330, 330, 405, 405, 438, 450, 579, 579, 729, 729, 837, 837, 897, 912, 975, 987, 1020, 1026, 1074, 1077, 1107, 1107, 1116, 1119, 1182, 1188, 1302, 1302, 1392, 1398, 1455, 1458, 1470, 1695, 1695, 1824, 1824, 1887, 1887, 1896, 1902, 1956, 1980, 2022, 2025, 2043, 2046, 2061, 2106, 2187, 2220, 2232, 2253, 2271, 2331, 2334, 2352, 2364, 2373, 2382, 2424, 2463, 2484, 2517, 2541], [ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 36, 36, 63, 63, 213, 222, 240, 240, 330, 330, 330, 405, 405, 438, 450, 579, 579, 729, 729, 837, 837, 897, 912, 975, 987, 1020, 1026, 1074, 1077, 1107, 1107, 1116, 1119, 1182, 1188, 1302, 1302, 1392, 1398, 1455, 1458, 1470, 1695, 1695, 1824, 1824, 1887, 1887, 1896, 1902, 1956, 1980, 2022, 2025, 2043, 2046, 2061, 2106, 2187, 2220, 2232, 2253, 2271, 2331, 2334, 2352, 2364, 2373, 2382, 2424, 2463, 2484, 2517, 2541], [ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 36, 36, 63, 63, 213, 222, 240, 240, 330, 330, 330, 405, 405, 438, 450, 579, 579, 729, 729, 837, 837, 897, 912, 975, 987, 1020, 1026, 1074, 1077, 1107, 1107, 1116, 1119, 1182, 1188, 1302, 1302, 1392, 1398, 1455, 1458, 1470, 1695, 1695, 1824, 1824, 1887, 1887, 1896, 1902, 1956, 1980, 2022, 2025, 2043, 2046, 2061, 2106, 2187, 2220, 2232, 2253, 2271, 2331, 2334, 2352, 2364, 2373, 2382, 2424, 2463, 2484, 2517, 2541], [ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 75, 75, 108, 120, 249, 249, 399, 399, 507, 507, 567, 582, 645, 657, 690, 696, 744, 747, 777, 777, 786, 789, 852, 858, 972, 972, 1062, 1068, 1125, 1128, 1140, 1365, 1365, 1494, 1494, 1557, 1557, 1566, 1572, 1626, 1650, 1692, 1695, 1713, 1716, 1731, 1776, 1857, 1890, 1902, 1923, 1941, 2001, 2004, 2022, 2034, 2043, 2052, 2094, 2133, 2154, 2187, 2211], [ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 75, 75, 108, 120, 249, 249, 399, 399, 507, 507, 567, 582, 645, 657, 690, 696, 744, 747, 777, 777, 786, 789, 852, 858, 972, 972, 1062, 1068, 1125, 1128, 1140, 1365, 1365, 1494, 1494, 1557, 1557, 1566, 1572, 1626, 1650, 1692, 1695, 1713, 1716, 1731, 1776, 1857, 1890, 1902, 1923, 1941, 2001, 2004, 2022, 2034, 2043, 2052, 2094, 2133, 2154, 2187, 2211], [ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 75, 75, 108, 120, 249, 249, 399, 399, 507, 507, 567, 582, 645, 657, 690, 696, 744, 747, 777, 777, 786, 789, 852, 858, 972, 972, 1062, 1068, 1125, 1128, 1140, 1365, 1365, 1494, 1494, 1557, 1557, 1566, 1572, 1626, 1650, 1692, 1695, 1713, 1716, 1731, 1776, 1857, 1890, 1902, 1923, 1941, 2001, 2004, 2022, 2034, 2043, 2052, 2094, 2133, 2154, 2187, 2211], [ 0, 12, 21, 357, 378, 417, 444, 474, 516, 549, 564, 570, 606, 615, 642, 645, 795, 795, 813, 828, 918, 918, 999, 1074, 1077, 1110, 1110, 1239, 1251, 1401, 1428, 1536, 1560, 1620, 1620, 1683, 1683, 1716, 1716, 1764, 1764, 1794, 1809, 1818, 1818, 1881, 1881, 1995, 2001, 2091, 2091, 2148, 2148, 2148, 2373, 2373, 2502, 2532, 2595, 2619, 2628, 2628, 2682, 2706, 2706, 2709, 2727, 2727, 2727, 2772, 2772, 2805, 2817, 2817, 2835, 2895, 2898, 2916, 2928, 2937, 2946, 2946, 2985, 3006, 3039, 3063], [ 0, 0, 9, 9, 30, 30, 57, 57, 99, 99, 114, 114, 150, 159, 186, 189, 339, 339, 357, 372, 462, 465, 546, 621, 624, 657, 669, 798, 810, 960, 987, 1095, 1119, 1179, 1179, 1242, 1254, 1287, 1287, 1335, 1335, 1365, 1380, 1389, 1392, 1455, 1455, 1569, 1575, 1665, 1665, 1722, 1725, 1725, 1950, 1953, 2082, 2112, 2175, 2175, 2184, 2184, 2184, 2208, 2208, 2208, 2226, 2226, 2226, 2271, 2271, 2304, 2304, 2304, 2304, 2304, 2307, 2325, 2337, 2346, 2346, 2346, 2385, 2385, 2418, 2418], [ 0, 0, 9, 9, 30, 30, 57, 57, 99, 99, 114, 114, 150, 159, 186, 189, 339, 339, 357, 372, 462, 465, 546, 621, 624, 657, 669, 798, 810, 960, 987, 1095, 1119, 1179, 1179, 1242, 1254, 1287, 1287, 1335, 1335, 1365, 1380, 1389, 1392, 1455, 1455, 1569, 1575, 1665, 1665, 1722, 1725, 1725, 1950, 1953, 2082, 2112, 2175, 2175, 2184, 2184, 2184, 2208, 2208, 2208, 2226, 2229, 2229, 2229, 2229, 2262, 2274, 2274, 2274, 2334, 2337, 2337, 2349, 2349, 2349, 2349, 2388, 2388, 2388, 2388]]) # fmt: on ) ) self.assertEqual( format(alignment, "clustal"), """\ ENSG00000166888:ENST0000030013 -------------------------------------------------- ENSG00000166888:ENST0000054387 -------------------------------------------------- ENSG00000166888:ENST0000055615 -------------------------------------------------- ENSG00000166888:ENST0000045407 -------------------------------------------------- ENSG00000166888:ENST0000053891 -------------------------------------------------- ENSG00000166888:ENST0000053721 -------------------------------------------------- ENSG00000166888:ENST0000053520 -------------------------------------------------- isotig46679 GAGGTTACTCAGAGTAGGAGGAAGCCGGTCAGAGAGGGCAGACCCTGGGA isotig12565 ------------GCTAGGAGA----------------------------- isotig12566 ------------GCTAGGAGA----------------------------- ENSG00000166888:ENST0000030013 -------------------------------------------------- ENSG00000166888:ENST0000054387 -------------------------------------------------- ENSG00000166888:ENST0000055615 -------------------------------------------------- ENSG00000166888:ENST0000045407 -------------------------------------------------- ENSG00000166888:ENST0000053891 -------------------------------------------------- ENSG00000166888:ENST0000053721 -------------------------------------------------- ENSG00000166888:ENST0000053520 -------------------------------------------------- isotig46679 ACCTTCGCAGGAGTTGGCCCAAACCCCTGAGGGAGGCTGTCCTCGGCAGG isotig12565 -------------------------------------------------- isotig12566 -------------------------------------------------- ENSG00000166888:ENST0000030013 -------------------------------------------------- ENSG00000166888:ENST0000054387 -------------------------------------------------- ENSG00000166888:ENST0000055615 -------------------------------------------------- ENSG00000166888:ENST0000045407 -------------------------------------------------- ENSG00000166888:ENST0000053891 -------------------------------------------------- ENSG00000166888:ENST0000053721 -------------------------------------------------- ENSG00000166888:ENST0000053520 -------------------------------------------------- isotig46679 AGAGCAGACCTGAGGGAGGTTGGTGTGCCGGTCCTGGTTGTCCAGCCCTC isotig12565 -------------------------------------------------- isotig12566 -------------------------------------------------- ENSG00000166888:ENST0000030013 -------------------------------------------------- ENSG00000166888:ENST0000054387 -------------------------------------------------- ENSG00000166888:ENST0000055615 -------------------------------------------------- ENSG00000166888:ENST0000045407 -------------------------------------------------- ENSG00000166888:ENST0000053891 -------------------------------------------------- ENSG00000166888:ENST0000053721 -------------------------------------------------- ENSG00000166888:ENST0000053520 -------------------------------------------------- isotig46679 CCGTCCCATCCCAGGGCTGGCTCACCAGAAAAAAGTACAGGCATCCCAGG isotig12565 -------------------------------------------------- isotig12566 -------------------------------------------------- ENSG00000166888:ENST0000030013 -------------------------------------------------- ENSG00000166888:ENST0000054387 -------------------------------------------------- ENSG00000166888:ENST0000055615 -------------------------------------------------- ENSG00000166888:ENST0000045407 -------------------------------------------------- ENSG00000166888:ENST0000053891 -------------------------------------------------- ENSG00000166888:ENST0000053721 -------------------------------------------------- ENSG00000166888:ENST0000053520 -------------------------------------------------- isotig46679 CCCTCTGGGGCGGGAGCAGAGGGTCTCCTCTTGTCCGGGGGAAGACAAAA isotig12565 -------------------------------------------------- isotig12566 -------------------------------------------------- ENSG00000166888:ENST0000030013 -------------------------------------------------- ENSG00000166888:ENST0000054387 -------------------------------------------------- ENSG00000166888:ENST0000055615 -------------------------------------------------- ENSG00000166888:ENST0000045407 -------------------------------------------------- ENSG00000166888:ENST0000053891 -------------------------------------------------- ENSG00000166888:ENST0000053721 -------------------------------------------------- ENSG00000166888:ENST0000053520 -------------------------------------------------- isotig46679 ACAAAAACAAAAAACGAGTGTGTAGCCCTCACTGGAAGTCTTCTGGTGCT isotig12565 -------------------------------------------------- isotig12566 -------------------------------------------------- ENSG00000166888:ENST0000030013 -------------------------------------------------- ENSG00000166888:ENST0000054387 -------------------------------------------------- ENSG00000166888:ENST0000055615 -------------------------------------------------- ENSG00000166888:ENST0000045407 -------------------------------------------------- ENSG00000166888:ENST0000053891 -------------------------------------------------- ENSG00000166888:ENST0000053721 -------------------------------------------------- ENSG00000166888:ENST0000053520 -------------------------------------------------- isotig46679 CTGGGGCCGTTTGCACTTGGGAGCCTGGCTTCTGGGCATGGTGGCCGGGC isotig12565 -------------------------------------------------- isotig12566 -------------------------------------------------- ENSG00000166888:ENST0000030013 -------------------------------------------------- ENSG00000166888:ENST0000054387 -------------------------------------------------- ENSG00000166888:ENST0000055615 -------------------------------------------------- ENSG00000166888:ENST0000045407 -------------------------------------------------- ENSG00000166888:ENST0000053891 -------------------------------------------------- ENSG00000166888:ENST0000053721 -------------------------------------------------- ENSG00000166888:ENST0000053520 -------------------------------------------------- isotig46679 TCCGCCGGGGGCTTCAGCCCTCGGCAAAGCGTTTCTAGAACAGAGTGGGT isotig12565 -------GGCCAGGCGGCCCTCGGGAGC---------------------- isotig12566 -------GGCCAGGCGGCCCTCGGGAGC---------------------- ENSG00000166888:ENST0000030013 -------------------------------------------------- ENSG00000166888:ENST0000054387 -------------------------------------------------- ENSG00000166888:ENST0000055615 -------------------------------------------------- ENSG00000166888:ENST0000045407 -------------------------------------------------- ENSG00000166888:ENST0000053891 -------------------------------------------------- ENSG00000166888:ENST0000053721 -------------------------------------------------- ENSG00000166888:ENST0000053520 -------------------------------------------------- isotig46679 GGGAGCCGACTGAAGTCCCAGAACCGCGAACACTGACGCACAGGAAAGCC isotig12565 -----------------CCAGCTGCTCGCACCTGGAGCCAGCGC------ isotig12566 -----------------CCAGCTGCTCGCACCTGGAGCCAGCGC------ ENSG00000166888:ENST0000030013 -------------------------------------------------- ENSG00000166888:ENST0000054387 -------------------------------------------------- ENSG00000166888:ENST0000055615 -------------------------------------------------- ENSG00000166888:ENST0000045407 -------------------------------------------------- ENSG00000166888:ENST0000053891 -------------------------------------------------- ENSG00000166888:ENST0000053721 -------------------------------------------------- ENSG00000166888:ENST0000053520 -------------------------------------------------- isotig46679 TCGAGTGGGTGGAGAAATGCAAATCCCCCAGTGGCATGGCCTCAGCCGCT isotig12565 ------------------------AGCCCGGCCAGTCGGGCCTCAGCCCG isotig12566 ------------------------AGCCCGGCCAGTCGGGCCTCAGCCCG ENSG00000166888:ENST0000030013 -------------------------------------------------- ENSG00000166888:ENST0000054387 -------------------------------------------------- ENSG00000166888:ENST0000055615 -------------------------------------------------- ENSG00000166888:ENST0000045407 -------------------------------------------------- ENSG00000166888:ENST0000053891 -------------------------------------------------- ENSG00000166888:ENST0000053721 -------------------------------------------------- ENSG00000166888:ENST0000053520 -------------------------------------------------- isotig46679 GCGGACCCTGACGGCCGATTCTGACTTCGGACTTGAGCGGGACCAGCACC isotig12565 GGAGACAGTTACGCCC---------------------------------C isotig12566 GGAGACAGTTACGCCC---------------------------------C ENSG00000166888:ENST0000030013 --------------------ATGTCTCTGTGGGGTCTGGTCTCCAAGATG ENSG00000166888:ENST0000054387 --------------------ATGTCTCTGTGGGGTCTGGTCTCCAAGATG ENSG00000166888:ENST0000055615 --------------------ATGTCTCTGTGGGGTCTGGTCTCCAAGATG ENSG00000166888:ENST0000045407 --------------------ATGTCTCTGTGGGGTCTGGTCTCCAAGATG ENSG00000166888:ENST0000053891 -------------------------------------------------- ENSG00000166888:ENST0000053721 -------------------------------------------------- ENSG00000166888:ENST0000053520 -------------------------------------------------- isotig46679 CGGACCCAGGGCGAGCCAGCATGTCTCAGTGGAATCAAGTCCAACAGTTA isotig12565 CTGATTGCGGCAGG------ATGGCCCAGTGGAACCAGCTGCAGCAGCTG isotig12566 CTGATTGCGGCAGG------ATGGCCCAGTGGAACCAGCTGCAGCAGCTG ENSG00000166888:ENST0000030013 CCCCCA---------GAAAAAGTGCAGCGGCTCTATGTCGAC---TTTCC ENSG00000166888:ENST0000054387 CCCCCA---------GAAAAAGTGCAGCGGCTCTATGTCGAC---TTTCC ENSG00000166888:ENST0000055615 CCCCCA---------GAAAAAGTGCAGCGGCTCTATGTCGAC---TTTCC ENSG00000166888:ENST0000045407 CCCCCA---------GAAAAAGTGCAGCGGCTCTATGTCGAC---TTTCC ENSG00000166888:ENST0000053891 -------------------------------------------------- ENSG00000166888:ENST0000053721 -------------------------------------------------- ENSG00000166888:ENST0000053520 -------------------------------------------------- isotig46679 GAAATCAAGTTTTTGGAGCAAGTTGATCAGTTCTATGATGACAACTTTCC isotig12565 GACACTCGGTACCTGGAGCAGCTGCACCAGCTGTACAGCGACAGCTTCCC isotig12566 GACACTCGGTACCTGGAGCAGCTGCACCAGCTGTACAGCGACAGCTTCCC ENSG00000166888:ENST0000030013 CCAACACCTGCGGCATCTTCTGGGTGACTGGCTGGAGAGCCAGCCCTGGG ENSG00000166888:ENST0000054387 CCAACACCTGCGGCATCTTCTGGGTGACTGGCTGGAGAGCCAGCCCTGGG ENSG00000166888:ENST0000055615 CCAACACCTGCGGCATCTTCTGGGTGACTGGCTGGAGAGCCAGCCCTGGG ENSG00000166888:ENST0000045407 CCAACACCTGCGGCATCTTCTGGGTGACTGGCTGGAGAGCCAGCCCTGGG ENSG00000166888:ENST0000053891 -------------------------------------------------- ENSG00000166888:ENST0000053721 -------------------------------------------------- ENSG00000166888:ENST0000053520 -------------------------------------------------- isotig46679 CATGGAAATCCGACATCTGCTGGCCCAGTGGATTGAGCATCAAGACTGGG isotig12565 CATGGAGCTGCGGCAGTTCCTGGCACCTTGGATTGAGAGTCAAGATTGGG isotig12566 CATGGAGCTGCGGCAGTTCCTGGCACCTTGGATTGAGAGTCAAGATTGGG ENSG00000166888:ENST0000030013 AGTTCCTGGTCGGCTCCGACGCCTTCTGCTGCAACTTGGCTAGTGCCCTA ENSG00000166888:ENST0000054387 AGTTCCTGGTCGGCTCCGACGCCTTCTGCTGCAACTTGGCTAGTGCCCTA ENSG00000166888:ENST0000055615 AGTTCCTGGTCGGCTCCGACGCCTTCTGCTGCAACTTGGCTAGTGCCCTA ENSG00000166888:ENST0000045407 AGTTCCTGGTCGGCTCCGACGCCTTCTGCTGCAACTTGGCTAGTGCCCTA ENSG00000166888:ENST0000053891 -------------------------------------------------- ENSG00000166888:ENST0000053721 -------------------------------------------------- ENSG00000166888:ENST0000053520 -------------------------------------------------- isotig46679 AGGTGGCCTCTAACAATGAAACTATGGCAACAATTCTTCTTCAAAACTTA isotig12565 CATATGCAGCCAGCAAAGAGTCACATGCCACACTGGTGTTTCATAATCTC isotig12566 CATATGCAGCCAGCAAAGAGTCACATGCCACACTGGTGTTTCATAATCTC ENSG00000166888:ENST0000030013 CTTTCAGACACTGTCCAGCACCTTCAGGCCTCGGTGGGAGAGCAGGGGGA ENSG00000166888:ENST0000054387 CTTTCAGACACTGTCCAGCACCTTCAGGCCTCGGTGGGAGAGCAGGGGGA ENSG00000166888:ENST0000055615 CTTTCAGACACTGTCCAGCACCTTCAGGCCTCGGTGGGAGAGCAGGGGGA ENSG00000166888:ENST0000045407 CTTTCAGACACTGTCCAGCACCTTCAGGCCTCGGTGGGAGAGCAGGGGGA ENSG00000166888:ENST0000053891 -------------------------------------------------- ENSG00000166888:ENST0000053721 -------------------------------------------------- ENSG00000166888:ENST0000053520 -------------------------------------------------- isotig46679 TTAATACAATTGGATGAACAGTTAGGTCGTGTTTCCAAAGAGAAA----- isotig12565 TTGGGTGAGATTGACCAGCAGTACAGCCGATTCCTGCAAGAGTCC----- isotig12566 TTGGGTGAGATTGACCAGCAGTACAGCCGATTCCTGCAAGAGTCC----- ENSG00000166888:ENST0000030013 GGGGAGCACCATCTTGCAACAC---------------ATCAGCACCCTTG ENSG00000166888:ENST0000054387 GGGGAGCACCATCTTGCAACAC---------------ATCAGCACCCTTG ENSG00000166888:ENST0000055615 GGGGAGCACCATCTTGCAACAC---------------ATCAGCACCCTTG ENSG00000166888:ENST0000045407 GGGGAGCACCATCTTGCAACAC---------------ATCAGCACCCTTG ENSG00000166888:ENST0000053891 -------------------------------------------------- ENSG00000166888:ENST0000053721 -------------------------------------------------- ENSG00000166888:ENST0000053520 -------------------------------------------------- isotig46679 ----AACCTGCTATTGATCCACAATCTAAAGAGAATTAGAAAAGTACTTC isotig12565 ----AACGTCCTCTATCAGCACAACCTTCGGAGGATCAAGCAGTTCCTAC isotig12566 ----AACGTCCTCTATCAGCACAACCTTCGGAGGATCAAGCAGTTCCTAC ENSG00000166888:ENST0000030013 AGAGCATATATCAGAGGGACCCCCTGAAGCTGGTGGCCACTTTCAGACAA ENSG00000166888:ENST0000054387 AGAGCATATATCAGAGGGACCCCCTGAAGCTGGTGGCCACTTTCAGACAA ENSG00000166888:ENST0000055615 AGAGCATATATCAGAGGGACCCCCTGAAGCTGGTGGCCACTTTCAGACAA ENSG00000166888:ENST0000045407 AGAGCATATATCAGAGGGACCCCCTGAAGCTGGTGGCCACTTTCAGACAA ENSG00000166888:ENST0000053891 -------------------------------------------------- ENSG00000166888:ENST0000053721 -------------------------------------------------- ENSG00000166888:ENST0000053520 -------------------------------------------------- isotig46679 AGGGGAAGTTTCATGGAAATCCAATGCATGTAGCCGTGGTAATCTCAAAT isotig12565 AGAGCAGGTATCTTGAGAAGCCGATGGAAATCGCCCGCATCGTGGCCCGA isotig12566 AGAGCAGGTATCTTGAGAAGCCGATGGAAATCGCCCGCATCGTGGCCCGA ENSG00000166888:ENST0000030013 ATACTTCAAGGAGAGAAAAAAGCTGTT----------------------- ENSG00000166888:ENST0000054387 ATACTTCAAGGAGAGAAAAAAGCTGTT----------------------- ENSG00000166888:ENST0000055615 ATACTTCAAGGAGAGAAAAAAGCTGTT----------------------- ENSG00000166888:ENST0000045407 ATACTTCAAGGAGAGAAAAAAGCTGTT----------------------- ENSG00000166888:ENST0000053891 -------------------------------------------------- ENSG00000166888:ENST0000053721 -------------------------------------------------- ENSG00000166888:ENST0000053520 -------------------------------------------------- isotig46679 TGTTTAAGGGAAGAGAGGAGAATACTG---GCTGCAGCGAACATGCCTAT isotig12565 TGCCTGTGGGAAGAGTCTCGCCTCCTCCAGACGGCAGCCACTGCAGCCCA isotig12566 TGCCTGTGGGAAGAGTCTCGCCTCCTCCAGACGGCAGCCACTGCAGCCCA ENSG00000166888:ENST0000030013 -------------------------------------------------- ENSG00000166888:ENST0000054387 -------------------------------------------------- ENSG00000166888:ENST0000055615 -------------------------------------------------- ENSG00000166888:ENST0000045407 -------------------------------------------------- ENSG00000166888:ENST0000053891 -------------------------------------------------- ENSG00000166888:ENST0000053721 -------------------------------------------------- ENSG00000166888:ENST0000053520 -------------------------------------------------- isotig46679 CCAGGGACCTCTGGAGAAATCCTTACAAAGTTCGTCGGTTTCAGAAAGAC isotig12565 GCAAGGAGGCCAGGCCAACCACCCAACAGCTGCTGTGGTGACGGAGAAAC isotig12566 GCAAGGAGGCCAGGCCAACCACCCAACAGCTGCTGTGGTGACGGAGAAAC ENSG00000166888:ENST0000030013 -----------ATGGAACAGTTCCGCCACTTGCCAATGCCTTTCCACTGG ENSG00000166888:ENST0000054387 -----------ATGGAACAGTTCCGCCACTTGCCAATGCCTTTCCACTGG ENSG00000166888:ENST0000055615 -----------ATGGAACAGTTCCGCCACTTGCCAATGCCTTTCCACTGG ENSG00000166888:ENST0000045407 -----------ATGGAACAGTTCCGCCACTTGCCAATGCCTTTCCACTGG ENSG00000166888:ENST0000053891 -----------ATGGAACAGTTCCGCCACTTGCCAATGCCTTTCCACTGG ENSG00000166888:ENST0000053721 -----------ATGGAACAGTTCCGCCACTTGCCAATGCCTTTCCACTGG ENSG00000166888:ENST0000053520 -----------ATGGAACAGTTCCGCCACTTGCCAATGCCTTTCCACTGG isotig46679 AGAGAAATGTGGAACACAAAGTGGCTGCCATTAAAAACAGTGTGCAGATG isotig12565 AGCAGATGCTGGAGCAGCATCTTCAGGATGTCCGGAAACGTGTGCAGGAT isotig12566 AGCAGATGCTGGAGCAGCATCTTCAGGATGTCCGGAAACGTGTGCAGGAT ENSG00000166888:ENST0000030013 AAGCAGGAAGAACTCAAGTTTAAGACAGGCTTGCGG---AGGCTGCAGCA ENSG00000166888:ENST0000054387 AAGCAGGAAGAACTCAAGTTTAAGACAGGCTTGCGG---AGGCTGCAGCA ENSG00000166888:ENST0000055615 AAGCAGGAAGAACTCAAGTTTAAGACAGGCTTGCGG---AGGCTGCAGCA ENSG00000166888:ENST0000045407 AAGCAGGAAGAACTCAAGTTTAAGACAGGCTTGCGG---AGGCTGCAGCA ENSG00000166888:ENST0000053891 AAGCAGGAAGAACTCAAGTTTAAGACAGGCTTGCGG---AGGCTGCAGCA ENSG00000166888:ENST0000053721 AAGCAGGAAGAACTCAAGTTTAAGACAGGCTTGCGG---AGGCTGCAGCA ENSG00000166888:ENST0000053520 AAGCAGGAAGAACTCAAGTTTAAGACAGGCTTGCGG---AGGCTGCAGCA isotig46679 ACAGAACAAGACACCAAATACTTGGAAGATCTGCAAGATGAATTTGACTA isotig12565 CTAGAACAGAAAATGAAAGTGGTAGAGAATCTCCAGGATGACTTTGATTT isotig12566 CTAGAACAGAAAATGAAAGTGGTAGAGAATCTCCAGGATGACTTTGATTT ENSG00000166888:ENST0000030013 CCGAGTAGGGGAGATCCACCTTCTCCGAGAAGCCCTGCAGAAGGGGGCTG ENSG00000166888:ENST0000054387 CCGAGTAGGGGAGATCCACCTTCTCCGAGAAGCCCTGCAGAAGGGGGCTG ENSG00000166888:ENST0000055615 CCGAGTAGGGGAGATCCACCTTCTCCGAGAAGCCCTGCAGAAGGGGGCTG ENSG00000166888:ENST0000045407 CCGAGTAGGGGAGATCCACCTTCTCCGAGAAGCCCTGCAGAAGGGGGCTG ENSG00000166888:ENST0000053891 CCGAGTAGGGGAGATCCACCTTCTCCGAGAAGCCCTGCAGAAGGGGGCTG ENSG00000166888:ENST0000053721 CCGAGTAGGGGAGATCCACCTTCTCCGAGAAGCCCTGCAGAAGGGGGCTG ENSG00000166888:ENST0000053520 CCGAGTAGGGGAGATCCACCTTCTCCGAGAAGCCCTGCAGAAGGGGGCTG isotig46679 CAGGTATAAAACAATTCAGACA------------ATGGACCAGGGTGACA isotig12565 CAACTATAAAACCCTCAAGAGTCAAGGAGACATGCAGGATCTGAATGGAA isotig12566 CAACTATAAAACCCTCAAGAGTCAAGGAGACATGCAGGATCTGAATGGAA ENSG00000166888:ENST0000030013 AGGCTGGCCAAGTGTCTCTGCACAGCTTGATAGAAACTCCTGCTAATGGG ENSG00000166888:ENST0000054387 AGGCTGGCCAAGTGTCTCTGCACAGCTTGATAGAAACTCCTGCTAATGGG ENSG00000166888:ENST0000055615 AGGCTGGCCAAGTGTCTCTGCACAGCTTGATAGAAACTCCTGCTAATGGG ENSG00000166888:ENST0000045407 AGGCTGGCCAAGTGTCTCTGCACAGCTTGATAGAAACTCCTGCTAATGGG ENSG00000166888:ENST0000053891 AGGCTGGCCAAGTGTCTCTGCACAGCTTGATAGAAACTCCTGCTAATGGG ENSG00000166888:ENST0000053721 AGGCTGGCCAAGTGTCTCTGCACAGCTTGATAGAAACTCCTGCTAATGGG ENSG00000166888:ENST0000053520 AGGCTGGCCAAGTGTCTCTGCACAGCTTGATAGAAACTCCTGCTAATGGG isotig46679 AGAATAGCATCCTAATGAACCAGGAGGTTTTGACACTCCAAGAAATGCTT isotig12565 ACAACCAGTCTGTGACCAGGCAGAAGATGCAGCAGCTGGAACAGATGCTC isotig12566 ACAACCAGTCTGTGACCAGGCAGAAGATGCAGCAGCTGGAACAGATGCTC ENSG00000166888:ENST0000030013 ACTGGGCCAAGTGAGGCCCTGGCCATGCTACTGCAGGAGACCACTGGAGA ENSG00000166888:ENST0000054387 ACTGGGCCAAGTGAGGCCCTGGCCATGCTACTGCAGGAGACCACTGGAGA ENSG00000166888:ENST0000055615 ACTGGGCCAAGTGAGGCCCTGGCCATGCTACTGCAGGAGACCACTGGAGA ENSG00000166888:ENST0000045407 ACTGGGCCAAGTGAGGCCCTGGCCATGCTACTGCAGGAGACCACTGGAGA ENSG00000166888:ENST0000053891 ACTGGGCCAAGTGAGGCCCTGGCCATGCTACTGCAGGAGACCACTGGAGA ENSG00000166888:ENST0000053721 ACTGGGCCAAGTGAGGCCCTGGCCATGCTACTGCAGGAGACCACTGGAGA ENSG00000166888:ENST0000053520 ACTGGGCCAAGTGAGGCCCTGGCCATGCTACTGCAGGAGACCACTGGAGA isotig46679 AATAGCCTGGACTTCAAGAGAAAGGAAGCACTCACTAAGATGACACAGAT isotig12565 ACGGCGCTGGACCAGATGCGGAGAAGCATTGTGAGTGAGCTGGCGGGGCT isotig12566 ACGGCGCTGGACCAGATGCGGAGAAGCATTGTGAGTGAGCTGGCGGGGCT ENSG00000166888:ENST0000030013 GCTAGAGGCAGCC------------AAAGCCCTAGTGCTGAAGAGGATCC ENSG00000166888:ENST0000054387 GCTAGAGGCAGCC------------AAAGCCCTAGTGCTGAAGAGGATCC ENSG00000166888:ENST0000055615 GCTAGAGGCAGCC------------AAAGCCCTAGTGCTGAAGAGGATCC ENSG00000166888:ENST0000045407 GCTAGAGGCAGCC------------AAAGCCCTAGTGCTGAAGAGGATCC ENSG00000166888:ENST0000053891 GCTAGAGGCAGCC------------AAAGCCCTAGTGCTGAAGAGGATCC ENSG00000166888:ENST0000053721 GCTAGAGGCAGCC------------AAAGCCCTAGTGCTGAAGAGGATCC ENSG00000166888:ENST0000053520 GCTAGAGGCAGCC------------AAAGCCCTAGTGCTGAAGAGGATCC isotig46679 AGTGAACGAGTCGGACCTGCTGATGAGCAGCATGCTCATAGAAGAGCTGC isotig12565 TTTGTCGGCAATGGAGTACGTGCAGAAAACACTCACAGACGAGGAGCTGG isotig12566 TTTGTCGGCAATGGAGTACGTGCAGAAAACACTCACAGACGAGGAGCTGG ENSG00000166888:ENST0000030013 AGATTTGGAAACGGCAGCAGCAGCTGGCAGGGAATGGCGCACCGTTTGAG ENSG00000166888:ENST0000054387 AGATTTGGAAACGGCAGCAGCAGCTGGCAGGGAATGGCGCACCGTTTGAG ENSG00000166888:ENST0000055615 AGATTTGGAAACGGCAGCAGCAGCTGGCAGGGAATGGCGCACCGTTTGAG ENSG00000166888:ENST0000045407 AGATTTGGAAACGGCAGCAGCAGCTGGCAGGGAATGGCGCACCGTTTGAG ENSG00000166888:ENST0000053891 AGATTTGGAAACGGCAGCAGCAGCTGGCAGGGAATGGCGCACCGTTTGAG ENSG00000166888:ENST0000053721 AGATTTGGAAACGGCAGCAGCAGCTGGCAGGGAATGGCGCACCGTTTGAG ENSG00000166888:ENST0000053520 AGATTTGGAAACGGCAGCAGCAGCTGGCAGGGAATGGCGCACCGTTTGAG isotig46679 AGGACTGGAAGAGGAGGCAGCAGATCGCCTGCATCGGTGGCCCACTCCAC isotig12565 CTGACTGGAAGAGGCGGCAGCAGATCGCGTGCATTGGAGGCCCTCCCAAC isotig12566 CTGACTGGAAGAGGCGGCAGCAGATCGCGTGCATTGGAGGCCCTCCCAAC ENSG00000166888:ENST0000030013 GAGAGCCTGGCCCCACTCCAGGAGAGGTGTGAAAGCCTGGTGGACATTTA ENSG00000166888:ENST0000054387 GAGAGCCTGGCCCCACTCCAGGAGAGGTGTGAAAGCCTGGTGGACATTTA ENSG00000166888:ENST0000055615 GAGAGCCTGGCCCCACTCCAGGAGAGGTGTGAAAGCCTGGTGGACATTTA ENSG00000166888:ENST0000045407 GAGAGCCTGGCCCCACTCCAGGAGAGGTGTGAAAGCCTGGTGGACATTTA ENSG00000166888:ENST0000053891 GAGAGCCTGGCCCCACTCCAGGAGAGGTGTGAAAGCCTGGTGGACATTTA ENSG00000166888:ENST0000053721 GAGAGCCTGGCCCCACTCCAGGAGAGGTGTGAAAGCCTGGTGGACATTTA ENSG00000166888:ENST0000053520 GAGAGCCTGGCCCCACTCCAGGAGAGGTGTGAAAGCCTGGTGGACATTTA isotig46679 AACGGGCTGGACCAGCTTCAGAACTGCTTTACCCTGTTGGCAGAAAGTCT isotig12565 ATCTGCCTGGATCGCCTGGAAAACTGGATAACTTCGTTAGCAGAATCTCA isotig12566 ATCTGCCTGGATCGCCTGGAAAACTGGATAACTTCGTTAGCAGAATCTCA ENSG00000166888:ENST0000030013 TTCCCAGCTACAGCAGGAGGTAGGG------------------------- ENSG00000166888:ENST0000054387 TTCCCAGCTACAGCAGGAGGTAGGG------------------------- ENSG00000166888:ENST0000055615 TTCCCAGCTACAGCAGGAGGTAGGG------------------------- ENSG00000166888:ENST0000045407 TTCCCAGCTACAGCAGGAGGTAGGG------------------------- ENSG00000166888:ENST0000053891 TTCCCAGCTACAGCAGGAGGTAGGG------------------------- ENSG00000166888:ENST0000053721 TTCCCAGCTACAGCAGGAGGTAGGG------------------------- ENSG00000166888:ENST0000053520 TTCCCAGCTACAGCAGGAGGTAGGG------------------------- isotig46679 TTTCCAACTCAGACGACAGCTGGAGAAATTAGAGGAGCAGTCTTCCAAGA isotig12565 ACTTCAGACCCGCCAACAAATTAAGAAACTGGAGGAGCTACAGCAGAAGG isotig12566 ACTTCAGACCCGCCAACAAATTAAGAAACTGGAGGAGCTACAGCAGAAGG ENSG00000166888:ENST0000030013 --GCGGCTGGTGGGGAGCTTGAGCCCAAGACCCGGGCATCGCTGACTGGC ENSG00000166888:ENST0000054387 --GCGGCTGGTGGGGAGCTTGAGCCCAAGACCCGGGCATCGCTGACTGGC ENSG00000166888:ENST0000055615 --GCGGCTGGTGGGGAGCTTGAGCCCAAGACCCGGGCATCGCTGACTGGC ENSG00000166888:ENST0000045407 --GCGGCTGGTGGGGAGCTTGAGCCCAAGACCCGGGCATCGCTGACTGGC ENSG00000166888:ENST0000053891 --GCGGCTGGTGGGGAGCTTGAGCCCAAGACCCGGGCATCGCTGACTGGC ENSG00000166888:ENST0000053721 --GCGGCTGGTGGGGAGCTTGAGCCCAAGACCCGGGCATCGCTGACTGGC ENSG00000166888:ENST0000053520 --GCGGCTGGTGGGGAGCTTGAGCCCAAGACCCGGGCATCGCTGACTGGC isotig46679 TGACTTACGAAGGAGACCCCATCCCCACGCAGAGAGCACACCTGCTGGAG isotig12565 TGTCCTACAAGGGGGACCCCATTGTGCAGCACCGGCCGATGCTGGAGGAG isotig12566 TGTCCTACAAGGGGGACCCCATTGTGCAGCACCGGCCGATGCTGGAGGAG ENSG00000166888:ENST0000030013 CGGCTGGATGAAGTCCTGAGAACCCTCGTCACCAGTTGCTTCCTGGTGGA ENSG00000166888:ENST0000054387 CGGCTGGATGAAGTCCTGAGAACCCTCGTCACCAGTTGCTTCCTGGTGGA ENSG00000166888:ENST0000055615 CGGCTGGATGAAGTCCTGAGAACCCTCGTCACCAGTTGCTTCCTGGTGGA ENSG00000166888:ENST0000045407 CGGCTGGATGAAGTCCTGAGAACCCTCGTCACCAGTTGCTTCCTGGTGGA ENSG00000166888:ENST0000053891 CGGCTGGATGAAGTCCTGAGAACCCTCGTCACCAGTTGCTTCCTGGTGGA ENSG00000166888:ENST0000053721 CGGCTGGATGAAGTCCTGAGAACCCTCGTCACCAGTTGCTTCCTGGTGGA ENSG00000166888:ENST0000053520 CGGCTGGATGAAGTCCTGAGAACCCTCGTCACCAGTTGCTTCCTGGTGGA isotig46679 AGAGCCACCTTCCTGATCTACAACCTTTTCAAGAACTCATTTGTGGTTGA isotig12565 CGGATCGTGGAGCTGTTCAGAAACTTGATGAAGAGTGCCTTCGTGGTGGA isotig12566 CGGATCGTGGAGCTGTTCAGAAACTTGATGAAGAGTGCCTTCGTGGTGGA ENSG00000166888:ENST0000030013 GAAGCAGCCC------------------------CCCCAGGTACTGAAGA ENSG00000166888:ENST0000054387 GAAGCAGCCC------------------------CCCCAGGTACTGAAGA ENSG00000166888:ENST0000055615 GAAGCAGCCC------------------------CCCCAGGTACTGAAGA ENSG00000166888:ENST0000045407 GAAGCAGCCC------------------------CCCCAGGTACTGAAGA ENSG00000166888:ENST0000053891 GAAGCAGCCC------------------------CCCCAGGTACTGAAGA ENSG00000166888:ENST0000053721 GAAGCAGCCC------------------------CCCCAGGTACTGAAGA ENSG00000166888:ENST0000053520 GAAGCAGCCC------------------------CCCCAGGTACTGAAGA isotig46679 GCGACAGCCCTGCATGCCAACACACCCTCAGAGGCCGCTGGTACTCAAAA isotig12565 GCGACAGCCCTGCATGCCGATGCACCCCGACCGGCCCTTGGTCATCAAGA isotig12566 GCGACAGCCCTGCATGCCGATGCACCCCGACCGGCCCTTGGTCATCAAGA ENSG00000166888:ENST0000030013 CTCAGACCAAGTTCCAGGCTGGAGTTCGATTCCTGTTGGGCTTGAGGTTC ENSG00000166888:ENST0000054387 CTCAGACCAAGTTCCAGGCTGGAGTTCGATTCCTGTTGGGCTTGAGGTTC ENSG00000166888:ENST0000055615 CTCAGACCAAGTTCCAGGCTGGAGTTCGATTCCTGTTGGGCTTGAGGTTC ENSG00000166888:ENST0000045407 CTCAGACCAAGTTCCAGGCTGGAGTTCGATTCCTGTTGGGCTTGAGGTTC ENSG00000166888:ENST0000053891 CTCAGACCAAGTTCCAGGCTGGAGTTCGATTCCTGTTGGGCTTGAGGTTC ENSG00000166888:ENST0000053721 CTCAGACCAAGTTCCAGGCTGGAGTTCGATTCCTGTTGGGCTTGAGGTTC ENSG00000166888:ENST0000053520 CTCAGACCAAGTTCCAGGCTGGAGTTCGATTCCTGTTGGGCTTGAGGTTC isotig46679 CCCTCATTCAGTTCACCGCGAAACTGAGACTACTAATAAAATTG------ isotig12565 CTGGTGTCCAGTTCACTACTAAAGTCAGGTTGTTGGTCAAGTTT------ isotig12566 CTGGTGTCCAGTTCACTACTAAAGTCAGGTTGTTGGTCAAGTTT------ ENSG00000166888:ENST0000030013 CTGGGGGCCCCAGCCAAGCCTCCGCTGGTCAGGGCCGACATGGTGACAGA ENSG00000166888:ENST0000054387 CTGGGGGCCCCAGCCAAGCCTCCGCTGGTCAGGGCCGACATGGTGACAGA ENSG00000166888:ENST0000055615 CTGGGGGCCCCAGCCAAGCCTCCGCTGGTCAGGGCCGACATGGTGACAGA ENSG00000166888:ENST0000045407 CTGGGGGCCCCAGCCAAGCCTCCGCTGGTCAGGGCCGACATGGTGACAGA ENSG00000166888:ENST0000053891 CTGGGGGCCCCAGCCAAGCCTCCGCTGGTCAGGGCCGACATGGTGACAGA ENSG00000166888:ENST0000053721 CTGGGGGCCCCAGCCAAGCCTCCGCTGGTCAGGGCCGACATGGTGACAGA ENSG00000166888:ENST0000053520 CTGGGGGCCCCAGCCAAGCCTCCGCTGGTCAGGGCCGACATGGTGACAGA isotig46679 ---------CCGGAACTCAACTATCAGGTGAAAGTAAAGGCATCGATCGA isotig12565 ---------CCCGAGTTGAATTATCAGCTTAAAATTAAAGTGTGCATTGA isotig12566 ---------CCCGAGTTGAATTATCAGCTTAAAATTAAAGTGTGCATTGA ENSG00000166888:ENST0000030013 GAAGCAGGCGCGGGAGCTGAGTGTGCCTCAGGGTCCTGGGGCTGGAGCAG ENSG00000166888:ENST0000054387 GAAGCAGGCGCGGGAGCTGAGTGTGCCTCAGGGTCCTGGGGCTGGAGCAG ENSG00000166888:ENST0000055615 GAAGCAGGCGCGGGAGCTGAGTGTGCCTCAGGGTCCTGGGGCTGGAGCAG ENSG00000166888:ENST0000045407 GAAGCAGGCGCGGGAGCTGAGTGTGCCTCAGGGTCCTGGGGCTGGAGCAG ENSG00000166888:ENST0000053891 GAAGCAGGCGCGGGAGCTGAGTGTGCCTCAGGGTCCTGGGGCTGGAGCAG ENSG00000166888:ENST0000053721 GAAGCAGGCGCGGGAGCTGAGTGTGCCTCAGGGTCCTGGGGCTGGAGCAG ENSG00000166888:ENST0000053520 GAAGCAGGCGCGGGAGCTGAGTGTGCCTCAGGGTCCTGGGGCTGGAGCAG isotig46679 CAAGAATGTTTCAACGCTAAGC------------AATAGAAGATTTGTGC isotig12565 CAAAGATTCTGGGGACGTTGCTGCTCTCAGAGGATCTCGGAAATTTAACA isotig12566 CAAAGATTCTGGGGACGTTGCTGCTCTCAGAGGATCTCGGAAATTTAACA ENSG00000166888:ENST0000030013 AAAGCACTGGAGAAATCATCAACAACACTGTGCCCTTGGAGAACAGCATT ENSG00000166888:ENST0000054387 AAAGCACTGGAGAAATCATCAACAACACTGTGCCCTTGGAGAACAGCATT ENSG00000166888:ENST0000055615 AAAGCACTGGAGAAATCATCAACAACACTGTGCCCTTGGAGAACAGCATT ENSG00000166888:ENST0000045407 AAAGCACTGGAGAAATCATCAACAACACTGTGCCCTTGGAGAACAGCATT ENSG00000166888:ENST0000053891 AAAGCACTGGAGAAATCATCAACAACACTGTGCCCTTGGAGAACAGCATT ENSG00000166888:ENST0000053721 AAAGCACTGGAGAAATCATCAACAACACTGTGCCCTTGGAGAACAGCATT ENSG00000166888:ENST0000053520 AAAGCACTGGAGAAATCATCAACAACACTGTGCCCTTGGAGAACAGCATT isotig46679 TTTGTGGAACTCAAGTC------AAAGCCATGTCCATCGAGGAATCCTCC isotig12565 TTCTGGGCACAAACACG------AAGGTGATGAACATGGAAGAATCCAAC isotig12566 TTCTGGGCACAAACACG------AAGGTGATGAACATGGAAGAATCCAAC ENSG00000166888:ENST0000030013 CCTGGGAACTGCTGCTCTGCCCTGTTCAAGAACCTGCTTCTCAAGAAGAT ENSG00000166888:ENST0000054387 CCTGGGAACTGCTGCTCTGCCCTGTTCAAGAACCTGCTTCTCAAGAAGAT ENSG00000166888:ENST0000055615 CCTGGGAACTGCTGCTCTGCCCTGTTCAAGAACCTGCTTCTCAAGAAGAT ENSG00000166888:ENST0000045407 CCTGGGAACTGCTGCTCTGCCCTGTTCAAGAACCTGCTTCTCAAGAAGAT ENSG00000166888:ENST0000053891 CCTGGGAACTGCTGCTCTGCCCTGTTCAAGAACCTGCTTCTCAAGAAGAT ENSG00000166888:ENST0000053721 CCTGGGAACTGCTGCTCTGCCCTGTTCAAGAACCTGCTTCTCAAGAAGAT ENSG00000166888:ENST0000053520 CCTGGGAACTGCTGCTCTGCCCTGTTCAAGAACCTGCTTCTCAAGAAGAT isotig46679 AATGGGAGCCTCTCAGTAGAA---TTTAGACATTTGCAACCGAAGGAAAT isotig12565 AACGGCAGCCTGTCTGCGGAG---TTCAAGCACTTGACCCTGAGGGAGCA isotig12566 AACGGCAGCCTGTCTGCGGAG---TTCAAGCACTTGACCCTGAGGGAGCA ENSG00000166888:ENST0000030013 CAAG---------------CGGTGTGAGCGGAAGGGCACTGAGTCTGTCA ENSG00000166888:ENST0000054387 CAAG---------------CGGTGTGAGCGGAAGGGCACTGAGTCTGTCA ENSG00000166888:ENST0000055615 CAAG---------------CGGTGTGAGCGGAAGGGCACTGAGTCTGTCA ENSG00000166888:ENST0000045407 CAAG---------------CGGTGTGAGCGGAAGGGCACTGAGTCTGTCA ENSG00000166888:ENST0000053891 CAAG---------------CGGTGTGAGCGGAAGGGCACTGAGTCTGTCA ENSG00000166888:ENST0000053721 CAAG---------------CGGTGTGAGCGGAAGGGCACTGAGTCTGTCA ENSG00000166888:ENST0000053520 CAAG---------------CGGTGTGAGCGGAAGGGCACTGAGTCTGTCA isotig46679 GAAATCCAGTGCCGGAAGTAAAGGAAAT---GAGGGCTGCCACATGGTGA isotig12565 GAGATGTGGGAATGGAGGCCGTGCCAATTGTGATGCCTCCTTGATTGTGA isotig12566 GAGATGTGGGAATGGAGGCCGTGCCAATTGTGATGCCTCCTTGATTGTGA ENSG00000166888:ENST0000030013 CAGAGGAGAAGTGCGCTGTGCTCTTCTCTGCCAGCTTCACACTTGGCCCC ENSG00000166888:ENST0000054387 CAGAGGAGAAGTGCGCTGTGCTCTTCTCTGCCAGCTTCACACTTGGCCCC ENSG00000166888:ENST0000055615 CAGAGGAGAAGTGCGCTGTGCTCTTCTCTGCCAGCTTCACACTTGGCCCC ENSG00000166888:ENST0000045407 CAGAGGAGAAGTGCGCTGTGCTCTTCTCTGCCAGCTTCACACTTGGCCCC ENSG00000166888:ENST0000053891 CAGAGGAGAAGTGCGCTGTGCTCTTCTCTGCCAGCTTCACACTTGGCCCC ENSG00000166888:ENST0000053721 CAGAGGAGAAGTGCGCTGTGCTCTTCTCTGCCAGCTTCACACTTGGCCCC ENSG00000166888:ENST0000053520 CAGAGGAGAAGTGCGCTGTGCTCTTCTCTGCCAGCTTCACACTTGGCCCC isotig46679 CGGAAGAGCTGCATTCCATAGCCTTTGAGACCCAGATCTGCCTC------ isotig12565 CCGAGGAGCTGCATCTGATCACCTTCGAGACTGAGGTGTACCAC------ isotig12566 CCGAGGAGCTGCATCTGATCACCTTCGAGACTGAGGTGTACCAC------ ENSG00000166888:ENST0000030013 GGCAAACTCCCCATCCAGCTCCAGGCCCTGTCTCTGCCCCTGGTGGTCAT ENSG00000166888:ENST0000054387 GGCAAACTCCCCATCCAGCTCCAGGCCCTGTCTCTGCCCCTGGTGGTCAT ENSG00000166888:ENST0000055615 GGCAAACTCCCCATCCAGCTCCAGGCCCTGTCTCTGCCCCTGGTGGTCAT ENSG00000166888:ENST0000045407 GGCAAACTCCCCATCCAGCTCCAGGCCCTGTCTCTGCCCCTGGTGGTCAT ENSG00000166888:ENST0000053891 GGCAAACTCCCCATCCAGCTCCAGGCCCTGTCTCTGCCCCTGGTGGTCAT ENSG00000166888:ENST0000053721 GGCAAACTCCCCATCCAGCTCCAGGCCCTGTCTCTGCCCCTGGTGGTCAT ENSG00000166888:ENST0000053520 GGCAAACTCCCCATCCAGCTCCAGGCCCTGTCTCTGCCCCTGGTGGTCAT isotig46679 TATGGCCTCACCATCGACTTGGAGACAAGCTCATTACCTGTGGTGATGAT isotig12565 CAAGGCCTCAAGATTGACCTGGAGACCCATTCTTTGCCAGTTGTGGTGAT isotig12566 CAAGGCCTCAAGATTGACCTGGAGACCCATTCTTTGCCAGTTGTGGTGAT ENSG00000166888:ENST0000030013 CGTCCATGGCAACCAAGACAACAATGCCAAAGCCACTATCCTGTGGGACA ENSG00000166888:ENST0000054387 CGTCCATGGCAACCAAGACAACAATGCCAAAGCCACTATCCTGTGGGACA ENSG00000166888:ENST0000055615 CGTCCATGGCAACCAAGACAACAATGCCAAAGCCACTATCCTGTGGGACA ENSG00000166888:ENST0000045407 CGTCCATGGCAACCAAGACAACAATGCCAAAGCCACTATCCTGTGGGACA ENSG00000166888:ENST0000053891 CGTCCATGGCAACCAAGACAACAATGCCAAAGCCACTATCCTGTGGGACA ENSG00000166888:ENST0000053721 CGTCCATGGCAACCAAGACAACAATGCCAAAGCCACTATCCTGTGGGACA ENSG00000166888:ENST0000053520 CGTCCATGGCAACCAAGACAACAATGCCAAAGCCACTATCCTGTGGGACA isotig46679 TTCTAATGTCAGCCAACTGCCTAATGCTTGGGCATCCATCATTTGGTACA isotig12565 CTCCAACATCTGTCAGATGCCAAATGCCTGGGCATCCATCCTGTGGTATA isotig12566 CTCCAACATCTGTCAGATGCCAAATGCCTGGGCATCCATCCTGTGGTATA ENSG00000166888:ENST0000030013 ATGCCTTCTCTGAG------ATGGACCGCGTGCCCTTTGTGGTGGCTGAG ENSG00000166888:ENST0000054387 ATGCCTTCTCTGAG------ATGGACCGCGTGCCCTTTGTGGTGGCTGAG ENSG00000166888:ENST0000055615 ATGCCTTCTCTGAG------ATGGACCGCGTGCCCTTTGTGGTGGCTGAG ENSG00000166888:ENST0000045407 ATGCCTTCTCTGAG------ATGGACCGCGTGCCCTTTGTGGTGGCTGAG ENSG00000166888:ENST0000053891 ATGCCTTCTCTGAG------ATGGACCGCGTGCCCTTTGTGGTGGCTGAG ENSG00000166888:ENST0000053721 ATGCCTTCTCTGAG------ATGGACCGCGTGCCCTTTGTGGTGGCTGAG ENSG00000166888:ENST0000053520 ATGCCTTCTCTGAG------ATGGACCGCGTGCCCTTTGTGGTGGCTGAG isotig46679 ATGTGTCAACCAACGATTGCCAGAACTTGGTTTTCTTTAATAATCCTCCG isotig12565 ACATGCTGACCAACAACCCCAAGAACGTGAACTTCTTCACCAAGCCACCA isotig12566 ACATGCTGACCAACAACCCCAAGAACGTGAACTTCTTCACCAAGCCACCA ENSG00000166888:ENST0000030013 CGGGTGCCCTGGGAGAAGATGTGTGAAACTCTGAACCTGAAGTTCATGGC ENSG00000166888:ENST0000054387 CGGGTGCCCTGGGAGAAGATGTGTGAAACTCTGAACCTGAAGTTCATGGC ENSG00000166888:ENST0000055615 CGGGTGCCCTGGGAGAAGATGTGTGAAACTCTGAACCTGAAGTTCATGGC ENSG00000166888:ENST0000045407 CGGGTGCCCTGGGAGAAGATGTGTGAAACTCTGAACCTGAAGTTCATGGC ENSG00000166888:ENST0000053891 CGGGTGCCCTGGGAGAAGATGTGTGAAACTCTGAACCTGAAGTTCATGGC ENSG00000166888:ENST0000053721 CGGGTGCCCTGGGAGAAGATGTGTGAAACTCTGAACCTGAAGTTCATGGC ENSG00000166888:ENST0000053520 CGGGTGCCCTGGGAGAAGATGTGTGAAACTCTGAACCTGAAGTTCATGGC isotig46679 CCTGTCACTTTGAGTCAACTCCTGGAAGTGATGAGCTGGCAGTTTTCATC isotig12565 ATCGGAACCTGGGACCAGGTGGCCGAGGTGCTCAGCTGGCAGTTCTCATC isotig12566 ATCGGAACCTGGGACCAGGTGGCCGAGGTGCTCAGCTGGCAGTTCTCATC ENSG00000166888:ENST0000030013 TGAGGTGGGGACCAACCGGGGGCTGCTCCCAGAGCACTTCCTCTTCCTGG ENSG00000166888:ENST0000054387 TGAGGTGGGGACCAACCGGGGGCTGCTCCCAGAGCACTTCCTCTTCCTGG ENSG00000166888:ENST0000055615 TGAGGTGGGGACCAACCGGGGGCTGCTCCCAGAGCACTTCCTCTTCCTGG ENSG00000166888:ENST0000045407 TGAGGTGGGGACCAACCGGGGGCTGCTCCCAGAGCACTTCCTCTTCCTGG ENSG00000166888:ENST0000053891 TGAGGTGGGGACCAACCGGGGGCTGCTCCCAGAGCACTTCCTCTTCCTGG ENSG00000166888:ENST0000053721 TGAGGTGGGGACCAACCGGGGGCTGCTCCCAGAGCACTTCCTCTTCCTGG ENSG00000166888:ENST0000053520 TGAGGTGGGGACCAACCGGGGGCTGCTCCCAGAGCACTTCCTCTTCCTGG isotig46679 CTATGTTGGT------CGTGGCCTTAATTCAGACCAGCTCAACATGCTGG isotig12565 CACCACAAAG------CGAGGGCTGAGCATCGAGCAGCTGACTACGCTGG isotig12566 CACCACAAAG------CGAGGGCTGAGCATCGAGCAGCTGACTACGCTGG ENSG00000166888:ENST0000030013 CCCAGAAGATCTTCAATGACAACAGCCTCAGTATGGAGGCCTTCCAGCAC ENSG00000166888:ENST0000054387 CCCAGAAGATCTTCAATGACAACAGCCTCAGTATGGAGGCCTTCCAGCAC ENSG00000166888:ENST0000055615 CCCAGAAGATCTTCAATGACAACAGCCTCAGTATGGAGGCCTTCCAGCAC ENSG00000166888:ENST0000045407 CCCAGAAGATCTTCAATGACAACAGCCTCAGTATGGAGGCCTTCCAGCAC ENSG00000166888:ENST0000053891 CCCAGAAGATCTTCAATGACAACAGCCTCAGTATGGAGGCCTTCCAGCAC ENSG00000166888:ENST0000053721 CCCAGAAGATCTTCAATGACAACAGCCTCAGTATGGAGGCCTTCCAGCAC ENSG00000166888:ENST0000053520 CCCAGAAGATCTTCAATGACAACAGCCTCAGTATGGAGGCCTTCCAGCAC isotig46679 CAGAGAAGCTCACAGTTCAGTCT---------------AACTACAGCGAT isotig12565 CCGAGAAGCTCCTAGGACCTGGTGTC------------AACTACTCCGGG isotig12566 CCGAGAAGCTCCTAGGACCTGGTGTC------------AACTACTCCGGG ENSG00000166888:ENST0000030013 CGTTCTGTGTCCTGGTCGCAGTTCAACAAGGAGATCCTGCTGGGCCGTGG ENSG00000166888:ENST0000054387 CGTTCTGTGTCCTGGTCGCAGTTCAACAAGGAGATCCTGCTGGGCCGTGG ENSG00000166888:ENST0000055615 CGTTCTGTGTCCTGGTCGCAGTTCAACAAGGAGATCCTGCTGGGCCGTGG ENSG00000166888:ENST0000045407 CGTTCTGTGTCCTGGTCGCAGTTCAACAAGGAGATCCTGCTGGGCCGTGG ENSG00000166888:ENST0000053891 CGTTCTGTGTCCTGGTCGCAGTTCAACAAGGAGATCCTGCTGGGCCGTGG ENSG00000166888:ENST0000053721 CGTTCTGTGTCCTGGTCGCAGTTCAACAAGGAGATCCTGCTGGGCCGTGG ENSG00000166888:ENST0000053520 CGTTCTGTGTCCTGGTCGCAGTTCAACAAGGAGATCCTGCTGGGCCGTGG isotig46679 GGTCACCTCACCTGGGCCAAGTTCTGCAAGGAACACTTGCCTGGCAAACC isotig12565 TGTCAGATCACATGGGCTAAATTTTGCAAAGAAAACATGGCTGGCAAGGG isotig12566 TGTCAGATCACATGGGCTAAATTTTGCAAAGAAAACATGGCTGGCAAGGG ENSG00000166888:ENST0000030013 CTTCACCTTTTGGCAGTGGTTTGATGGTGTCCTGGACCTCACCAAACGCT ENSG00000166888:ENST0000054387 CTTCACCTTTTGGCAGTGGTTTGATGGTGTCCTGGACCTCACCAAACGCT ENSG00000166888:ENST0000055615 CTTCACCTTTTGGCAGTGGTTTGATGGTGTCCTGGACCTCACCAAACGCT ENSG00000166888:ENST0000045407 CTTCACCTTTTGGCAGTGGTTTGATGGTGTCCTGGACCTCACCAAACGCT ENSG00000166888:ENST0000053891 CTTCACCTTTTGGCAGTGGTTTGATGGTGTCCTGGACCTCACCAAACGCT ENSG00000166888:ENST0000053721 CTTCACCTTTTGGCAGTGGTTTGATGGTGTCCTGGACCTCACCAAACGCT ENSG00000166888:ENST0000053520 CTTCACCTTTTGGCAGTGGTTTGATGGTGTCCTGGACCTCACCAAACGCT isotig46679 ATTTACCTTCTGGACCTGGCTTGAAGCAATATTGGACCTAATTAAAAAAC isotig12565 CTTCTCCTTCTGGGTGTGGCTAGACAATATCATTGACCTTGTGAAAAAGT isotig12566 CTTCTCCTTCTGGGTGTGGCTAGACAATATCATTGACCTTGTGAAAAAGT ENSG00000166888:ENST0000030013 GTCTCCGGAGCTACTGGTCTGACCGGCTGATCATTGGCTTCATCAGCAAA ENSG00000166888:ENST0000054387 GTCTCCGGAGCTACTGGTCTGACCGGCTGATCATTGGCTTCATCAGCAAA ENSG00000166888:ENST0000055615 GTCTCCGGAGCTACTGGTCTGACCGGCTGATCATTGGCTTCATCAGCAAA ENSG00000166888:ENST0000045407 GTCTCCGGAGCTACTGGTCTGACCGGCTGATCATTGGCTTCATCAGCAAA ENSG00000166888:ENST0000053891 GTCTCCGGAGCTACTGGTCTGACCGGCTGATCATTGGCTTCATCAGCAAA ENSG00000166888:ENST0000053721 GTCTCCGGAGCTACTGGTCTGACCGGCTGATCATTGGCTTCATCAGCAAA ENSG00000166888:ENST0000053520 GTCTCCGGAGCTACTGGTCTGACCGGCTGATCATTGGCTTCATCAGCAAA isotig46679 ACATTCTTCCCCTCTGGATTGATGGGTACATCATGGGCTTCGTGAGCAAA isotig12565 ATATCTTGGCCCTCTGGAATGAAGGGTACATCATGGGCTTCATTAGCAAG isotig12566 ATATCTTGGCCCTCTGGAATGAAGGGTACATCATGGGCTTCATTAGCAAG ENSG00000166888:ENST0000030013 CAGTACGTTACTAGCCTTCTTCTCAATGAGCCCGACGGAACCTTTCTCCT ENSG00000166888:ENST0000054387 CAGTACGTTACTAGCCTTCTTCTCAATGAGCCCGACGGAACCTTTCTCCT ENSG00000166888:ENST0000055615 CAGTACGTTACTAGCCTTCTTCTCAATGAGCCCGACGGAACCTTTCTCCT ENSG00000166888:ENST0000045407 CAGTACGTTACTAGCCTTCTTCTCAATGAGCCCGACGGAACCTTTCTCCT ENSG00000166888:ENST0000053891 CAGTACGTTACTAGCCTTCTTCTCAATGAGCCCGACGGAACCTTTCTCCT ENSG00000166888:ENST0000053721 CAGTACGTTACTAGCCTTCTTCTCAATGAGCCCGACGGAACCTTTCTCCT ENSG00000166888:ENST0000053520 CAGTACGTTACTAGCCTTCTTCTCAATGAGCCCGACGGAACCTTTCTCCT isotig46679 GAGAAGGAGAGGTTTCTGCTCAAGGATAAAATGCCCGGGACATTTTTGTT isotig12565 GAGCGGGAGCGGGCGATCCTGAGCACGAAACCCCCGGGCACCTTCCTGCT isotig12566 GAGCGGGAGCGGGCGATCCTGAGCACGAAACCCCCGGGCACCTTCCTGCT ENSG00000166888:ENST0000030013 CCGCTTCAGCGAC---TCAGAGATTGGGGGCATCACCATTGCCCATGTCA ENSG00000166888:ENST0000054387 CCGCTTCAGCGAC---TCAGAGATTGGGGGCATCACCATTGCCCATGTCA ENSG00000166888:ENST0000055615 CCGCTTCAGCGAC---TCAGAGATTGGGGGCATCACCATTGCCCATGTCA ENSG00000166888:ENST0000045407 CCGCTTCAGCGAC---TCAGAGATTGGGGGCATCACCATTGCCCATGTCA ENSG00000166888:ENST0000053891 CCGCTTCAGCGAC---TCAGAGATTGGGGGCATCACCATTGCCCATGTCA ENSG00000166888:ENST0000053721 CCGCTTCAGCGAC---TCAGAGATTGGGGGCATCACCATTGCCCATGTCA ENSG00000166888:ENST0000053520 CCGCTTCAGCGAC---TCAGAGATTGGGGGCATCACCATTGCCCATGTCA isotig46679 ACGATTCAGTGAG---AGCCATCTCGGAGGGATCACCTTCACCTGGGTGG isotig12565 GAGATTCAGCGAGAGCAGCAAAGAAGGAGGGGTCACTTTCACTTGGGTGG isotig12566 GAGATTCAGCGAGAGCAGCAAAGAAGGAGGGGTCACTTTCACTTGGGTGG ENSG00000166888:ENST0000030013 TCCGGGGCCAGGATGGCTCTCCACAGATAGAGAACATCCAGCCATTCTCT ENSG00000166888:ENST0000054387 TCCGGGGCCAGGATGGCTCTCCACAGATAGAGAACATCCAGCCATTCTCT ENSG00000166888:ENST0000055615 TCCGGGGCCAGGATGGCTCTCCACAGATAGAGAACATCCAGCCATTCTCT ENSG00000166888:ENST0000045407 TCCGGGGCCAGGATGGCTCTCCACAGATAGAGAACATCCAGCCATTCTCT ENSG00000166888:ENST0000053891 TCCGGGGCCAGGATGGCTCTCCACAGATAGAGAACATCCAGCCATTCTCT ENSG00000166888:ENST0000053721 TCCGGGGCCAGGATGGCTCTCCACAGATAGAGAACATCCAGCCATTCTCT ENSG00000166888:ENST0000053520 TCCGGGGCCAGGATGGCTCTCCACAGATAGAGAACATCCAGCCATTCTCT isotig46679 ACCACTCTGAAAACGGAGAAGTGAGATTCCACTCCGTAGAACCCTACAAC isotig12565 AAAAGGACATCAGTGGCAAGACCCAGATCCAGTCTGTAGAGCCGTACACC isotig12566 AAAAGGACATCAGTGGCAAGACCCAGATCCAGTCTGTAGAGCCGTACACC ENSG00000166888:ENST0000030013 GCCAAAGACCTGTCCATTCGCTCACTGGGGGACCGAATCCGGGAT----- ENSG00000166888:ENST0000054387 GCCAAAGACCTGTCCATTCGCTCACTGGGGGACCGAATCCGGGAT----- ENSG00000166888:ENST0000055615 GCCAAAGACCTGTCCATTCGCTCACTGGGGGACCGAATCCGGGAT----- ENSG00000166888:ENST0000045407 GCCAAAGACCTGTCCATTCGCTCACTGGGGGACCGAATCCGGGAT----- ENSG00000166888:ENST0000053891 GCCAAAGACCTGTCCATTCGCTCACTGGGGGACCGAATCCGGGAT----- ENSG00000166888:ENST0000053721 GCCAAAGACCTGTCCATTCGCTCACTGGGGGACCGAATCCGGGAT----- ENSG00000166888:ENST0000053520 GCCAAAGACCTGTCCATTCGCTCACTGGGGGACCGAATCCGGGAT----- isotig46679 AAAGGGCGTCTGTCGGCCCTGCCATTTGCTGACATCCTGCGGGACTACAA isotig12565 AAGCAGCAGCTGAACAACATGTCCTTTGCTGAAATCATCATGGGCTACAA isotig12566 AAGCAGCAGCTGAACAACATGTCCTTTGCTGAAATCATCATGGGCTACAA ENSG00000166888:ENST0000030013 -------------------------CTTGCTCAGCTCAAAAATCTCTATC ENSG00000166888:ENST0000054387 -------------------------CTTGCTCAGCTCAAAAATCTCTATC ENSG00000166888:ENST0000055615 -------------------------CTTGCTCAGCTCAAAAATCTCTATC ENSG00000166888:ENST0000045407 -------------------------CTTGCTCAGCTCAAAAATCTCTATC ENSG00000166888:ENST0000053891 -------------------------CTTGCTCAGCTCAAAAATCTCTATC ENSG00000166888:ENST0000053721 -------------------------CTTGCTCAGCTCAAAAATCTCTATC ENSG00000166888:ENST0000053520 -------------------------CTTGCTCAGCTCAAAAATCTCTATC isotig46679 GGTCATCATGGCTGAGAACATTCCCGAGAACCCTCTCAAGTACCTCTACC isotig12565 GATCATGGATGCCACCAACATCCTGGTGTCCCCATTGGTCTACCTCTACC isotig12566 GATCATGGATGCCACCAACATCCTGGTGTCCCCATTGGTCTACCTCTACC ENSG00000166888:ENST0000030013 CCAAGAAGCCCAAGGATGAGGCTTTCCGGAGCCACTAC------------ ENSG00000166888:ENST0000054387 CCAAGAAGCCCAAGGATGAGGCTTTCCGGAGCCACTAC------------ ENSG00000166888:ENST0000055615 CCAAGAAGCCCAAGGATGAGGCTTTCCGGAGCCACTAC------------ ENSG00000166888:ENST0000045407 CCAAGAAGCCCAAGGATGAGGCTTTCCGGAGCCACTAC------------ ENSG00000166888:ENST0000053891 CCAAGAAGCCCAAGGATGAGGCTTTCCGGAGCCACTAC------------ ENSG00000166888:ENST0000053721 CCAAGAAGCCCAAGGATGAGGCTTTCCGGAGCCACTAC------------ ENSG00000166888:ENST0000053520 CCAAGAAGCCCAAGGATGAGGCTTTCCGGAGCCACTAC------------ isotig46679 CCGACATCCCCAAAGACAAAGCCTTCGGTAAACACTACAGCTCCCAGCCT isotig12565 CTGACATTCCCAAGGAGGAGGCGTTCGGGAAGTACTGT------------ isotig12566 CTGACATTCCCAAGGAGGAGGCGTTCGGGAAGTACTGT------------ ENSG00000166888:ENST0000030013 ------------AAGCCTGAACAGATGGGTAAGGATGGCAGGGGTTATGT ENSG00000166888:ENST0000054387 ------------AAGCCTGAACAGATGGGTAAGGATGGCAGGGGTTATGT ENSG00000166888:ENST0000055615 ------------AAGCCTGAACAGATGGGTAAGGATGGCAGGGGTTATGT ENSG00000166888:ENST0000045407 ------------AAGCCTGAACAGATGGGTAAGGATGGCAGGGGTTATGT ENSG00000166888:ENST0000053891 ------------AAGCCTGAACAGATGGGTAAGGATGGCAGGGGTTATGT ENSG00000166888:ENST0000053721 ------------AAGCCTGAACAGATGGGTAAGGATGGCAGGGGTTATGT ENSG00000166888:ENST0000053520 ------------AAGCCTGAACAGATGGGTAAGGATGGCAGGGGTTATGT isotig46679 TGCGAAGTTTCAAGGCCAACA------GAACGGGGAGACAAAGGTTATGT isotig12565 ------------CGACCAGAG----------------------------- isotig12566 ------------CGACCAGAG----------------------------- ENSG00000166888:ENST0000030013 CCCAGCTACCATCAAGATGACCGTGGAAAGGGACCAACCACTTCCTACCC ENSG00000166888:ENST0000054387 CCCAGCTACCATCAAGATGACCGTGGAAAGGGACCAACCACTTCCTACCC ENSG00000166888:ENST0000055615 CCCAGCTACCATCAAGATGACCGTGGAAAGGGACCAACCACTTCCTACCC ENSG00000166888:ENST0000045407 CCCAGCTACCATCAAGATGACCGTGGAAAGGGACCAACCACTTCCTACCC ENSG00000166888:ENST0000053891 CCCAGCTACCATCAAGATGACCGTGGAAAGGGACCAACCACTTCCTACCC ENSG00000166888:ENST0000053721 CCCAGCTACCATCAAGATGACCGTGGAAAGGGACCAACCACTTCCTACCC ENSG00000166888:ENST0000053520 CCCAGCTACCATCAAGATGACCGTGGAAAGGGACCAACCACTTCCTACCC isotig46679 TCCTTCAGTTTTTATCCCTATTTCAACAATCCGCAGCGACGCCATGGAGC isotig12565 -------------------------------AGCCAGGAGCATCCTGAAG isotig12566 -------------------------------AGCCAGGAGCATCCTGAAG ENSG00000166888:ENST0000030013 CAGAGCTCCAGATGCCTACCATGGTGCCTTCTTATGACCTTGGAATGGCC ENSG00000166888:ENST0000054387 CAGAGCTCCAGATGCCTACCATGGTGCCTTCTTATGACCTTGGAATGGCC ENSG00000166888:ENST0000055615 CAGAGCTCCAGATGCCTACCATGGTGCCTTCTTATGACCTTGGAATGGCC ENSG00000166888:ENST0000045407 CAGAGCTCCAGATGCCTACCATGGTGCCTTCTTATGACCTTGGAATGGCC ENSG00000166888:ENST0000053891 CAGAGCTCCAGATGCCTACCATGGTGCCTTCTTATGACCTTGGAATGGCC ENSG00000166888:ENST0000053721 CAGAGCTCCAGATGCCTACCATGGTGCCTTCTTATGACCTTGGAATGGCC ENSG00000166888:ENST0000053520 CAGAGCTCCAGATGCCTACCATGGTGCCTTCTTATGACCTTGGAATGGCC isotig46679 CGCAG------------------------------------------TCT isotig12565 CTGAC--------------------------------------------- isotig12566 CTGAC--------------------------------------------- ENSG00000166888:ENST0000030013 CCTGATTCCTCCATGAGCATGCAGCTTGGCCCAGATATGGTGCCCCAGGT ENSG00000166888:ENST0000054387 CCTGATTCCTCCATGAGCATGCAGCTTGGCCCAGATATGGTGCCCCAGGT ENSG00000166888:ENST0000055615 CCTGATTCCTCCATGAGCATGCAGCTTGGCCCAGATATGGTGCCCCAGGT ENSG00000166888:ENST0000045407 CCTGATTCCTCCATGAGCATGCAGCTTGGCCCAGATATGGTGCCCCAGGT ENSG00000166888:ENST0000053891 CCTGATTCCTCCATGAGCATGCAGCTTGGCCCAGATATGGTGCCCCAGGT ENSG00000166888:ENST0000053721 CCTGATTCCTCCATGAGCATGCAGCTTGGCCCAGATATGGTGCCCCAGGT ENSG00000166888:ENST0000053520 CCTGATTCCTCCATGAGCATGCAGCTTGGCCCAGATATGGTGCCCCAGGT isotig46679 CCTTCAGACCTTCTCCCC------------------ATGTCTCCGAGTGT isotig12565 CCCGGTAGTGCCGCCCCT------------------TACCTGAAGACCAA isotig12566 CCCGGTAGTTGTTTTTCCATG----------------------------- ENSG00000166888:ENST0000030013 GTACCCACCACACTCTCACTCCATCCCCCCGTATCAAGGCCTCTCCCCAG ENSG00000166888:ENST0000054387 GTACCCACCACACTCTCACTCCATCCCCCCGTATCAAGGCCTCTCCCCAG ENSG00000166888:ENST0000055615 GTACCCACCACACTCTCACTCCATCCCCCCGTATCAAGGCCTCTCCCCAG ENSG00000166888:ENST0000045407 GTACCCACCACACTCTCACTCCATCCCCCCGTATCAAGGCCTCTCCCCAG ENSG00000166888:ENST0000053891 GTACCCACCACACTCTCACTCCATCCCCCCGTATCAAGGCCTCTCCCCAG ENSG00000166888:ENST0000053721 GTACCCACCACACTCTCACTCCATCCCCCCGTATCAAGGCCTCTCCCCAG ENSG00000166888:ENST0000053520 GTACCCACCACACTCTCACTCCATCCCCCCGTATCAAGGCCTCTCCCCAG isotig46679 ATACGCTGTGCTGAGAGAAAACCTGAGCCCT------------------- isotig12565 GTTCATCTGTGTGACACCAACGACCTGCAGC------------------- isotig12566 -------------------------------------------------- ENSG00000166888:ENST0000030013 AAGAATCAGTCAACGTGTTGTCAGCCTTCCAGGAGCCTCACCTGCAGATG ENSG00000166888:ENST0000054387 AAGAATCAGTCAACGTGTTGTCAGCCTTCCAGGAGCCTCACCTGCAGATG ENSG00000166888:ENST0000055615 AAGAATCAGTCAACGTGTTGTCAGCCTTCCAGGAGCCTCACCTGCAGATG ENSG00000166888:ENST0000045407 AAGAATCAGTCAACGTGTTGTCAGCCTTCCAGGAGCCTCACCTGCAGATG ENSG00000166888:ENST0000053891 AAGAATCAGTCAACGTGTTGTCAGCCTTCCAGGAGCCTCACCTGCAGATG ENSG00000166888:ENST0000053721 AAGAATCAGTCAACGTGTTGTCAGCCTTCCAGGAGCCTCACCTGCAGATG ENSG00000166888:ENST0000053520 AAGAATCAGTCAACGTGTTGTCAGCCTTCCAGGAGCCTCACCTGCAGATG isotig46679 -------------------------------------------------- isotig12565 -------------------------------------------------- isotig12566 -------------------------------------------------- ENSG00000166888:ENST0000030013 CCCCCCAGCCTGGGCCAGATGAGCCTGCCCTTTGACCAGCCTCACCCCCA ENSG00000166888:ENST0000054387 CCCCCCAGCCTGGGCCAGATGAGCCTGCCCTTTGACCAGCCTCACCCCCA ENSG00000166888:ENST0000055615 CCCCCCAGCCTGGGCCAGATGAGCCTGCCCTTTGACCAGCCTCACCCCCA ENSG00000166888:ENST0000045407 CCCCCCAGCCTGGGCCAGATGAGCCTGCCCTTTGACCAGCCTCACCCCCA ENSG00000166888:ENST0000053891 CCCCCCAGCCTGGGCCAGATGAGCCTGCCCTTTGACCAGCCTCACCCCCA ENSG00000166888:ENST0000053721 CCCCCCAGCCTGGGCCAGATGAGCCTGCCCTTTGACCAGCCTCACCCCCA ENSG00000166888:ENST0000053520 CCCCCCAGCCTGGGCCAGATGAGCCTGCCCTTTGACCAGCCTCACCCCCA isotig46679 ------------ACCACAATTGAAACAGCAATGAAGTCTCCATATTCTGA isotig12565 ------------AATACCATTGACCTGCCGATGTCCCCCCCGCAC----- isotig12566 ------------GTTCTGGTTTCGCTGTTAGGGAAAGGGGGACAGTGCAG ENSG00000166888:ENST0000030013 GGGCCTGCTGCCGTGCCAGCCTCAGGAGCATGCTGTGTCCAGCCCTGACC ENSG00000166888:ENST0000054387 GGGCCTGCTGCCGTGCCAGCCTCAGGAGCATGCTGTGTCCAGCCCTGACC ENSG00000166888:ENST0000055615 GGGCCTGCTGCCGTGCCAGCCTCAGGAGCATGCTGTGTCCAGCCCTGACC ENSG00000166888:ENST0000045407 GGGCCTGCTGCCGTGCCAGCCTCAGGAGCATGCTGTGTCCAGCCCTGACC ENSG00000166888:ENST0000053891 GGGCCTGCTGCCGTGCCAGCCTCAGGAGCATGCTGTGTCCAGCCCTGACC ENSG00000166888:ENST0000053721 GGGCCTGCTGCCGTGCCAGCCTCAGGAGCATGCTGTGTCCAGCCCTGACC ENSG00000166888:ENST0000053520 GGGCCTGCTGCCGTGCCAGCCTCAGGAGCATGCTGTGTCCAGCCCTGACC isotig46679 GCGGTAC---------------------AAAGCGACTCTTCAAGGAAGAG isotig12565 -------------------------------------------------- isotig12566 GTCCTTG---------------------------------------GAGG ENSG00000166888:ENST0000030013 CCCTGCTCTGCTCAGATGTGACCATGGTGGAAGACAGCTGCCTGAGCCAG ENSG00000166888:ENST0000054387 CCCTGCTCTGCTCAGATGTGACCATGGTGGAAGACAGCTGCCTGAGCCAG ENSG00000166888:ENST0000055615 CCCTGCTCTGCTCAGATGTGACCATGGTGGAAGACAGCTGCCTGAGCCAG ENSG00000166888:ENST0000045407 CCCTGCTCTGCTCAGATGTGACCATGGTGGAAGACAGCTGCCTGAGCCAG ENSG00000166888:ENST0000053891 CCCTGCTCTGCTCAGATGTGACCATGGTGGAAGACAGCTGCCTGAGCCAG ENSG00000166888:ENST0000053721 CCCTGCTCTGCTCAGATGTGACCATGGTGGAAGACAGCTGCCTGAGCCAG ENSG00000166888:ENST0000053520 CCCTGCTCTGCTCAGATGTGACCATGGTGGAAGACAGCTGCCTGAGCCAG isotig46679 AGCAGATGAAAACGGAGACTGCTCTTTGCCAAAGTCCACAATTCATTTCT isotig12565 -------------------------------------------------- isotig12566 AGAGACAAGGACATGACCGGGTGTCTGGTGGTGAGTCCTGCTATGGAAGA ENSG00000166888:ENST0000030013 CCAGTGACAGCGTTTCCTCAGGGCACTTGGATTGGTGAAGACATATTCCC ENSG00000166888:ENST0000054387 CCAGTGACAGCGTTTCCTCAGGGCACTTGGATTGGTGAAGACATATTCCC ENSG00000166888:ENST0000055615 CCAGTGACAGCGTTTCCTCAGGGCACTTGGATTGGTGAAGACATATTCCC ENSG00000166888:ENST0000045407 CCAGTGACAGCGTTTCCTCAGGGCACTTGGATTGGTGAAGACATATTCCC ENSG00000166888:ENST0000053891 CCAGTGACAGCGTTTCCTCAGGGCACTTGGATTGGTGAAGACATATTCCC ENSG00000166888:ENST0000053721 CCAGTGACAGCGTTTCCTCAGGGCACTTGGATTGGTGAAGACATATTCCC ENSG00000166888:ENST0000053520 CCAGTGACAGCGTTTCCTCAGGGCACTTGGATTGGTGAAGACATATTCCC isotig46679 TCAGCTTTGATACTGGTTTCTAGAAAATGGCACAAATCCGAAGCTTTCCT isotig12565 ------TTTAGATTCATTGATGCAGTTTGGAAACGGAGGTGCGCCCTC-- isotig12566 GCTGTTTAT------------------TGGGTACTTCAG----------- ENSG00000166888:ENST0000030013 TCCTCTGCTGCCTCCCACTGAACAGGACCTCACTAAGCTTCTCCTGGAGG ENSG00000166888:ENST0000054387 TCCTCTGCTGCCTCCCACTGAACAGGACCTCACTAAGCTTCTCCTGGAGG ENSG00000166888:ENST0000055615 TCCTCTGCTGCCTCCCACTGAACAGGACCTCACTAAGCTTCTCCTGGAGG ENSG00000166888:ENST0000045407 TCCTCTGCTGCCTCCCACTGAACAGGACCTCACTAAGCTTCTCCTGGAGG ENSG00000166888:ENST0000053891 TCCTCTGCTGCCTCCCACTGAACAGGACCTCACTAAGCTTCTCCTGGAGG ENSG00000166888:ENST0000053721 TCCTCTGCTGCCTCCCACTGAACAGGACCTCACTAAGCTTCTCCTGGAGG ENSG00000166888:ENST0000053520 TCCTCTGCTGCCTCCCACTGAACAGGACCTCACTAAGCTTCTCCTGGAGG isotig46679 CTCACTA------------------------------------------G isotig12565 -------------------------------------------------G isotig12566 -------------------------------------------------G ENSG00000166888:ENST0000030013 GGCAAGGGGAGTCGGGGGGAGGGTCCTTGGGGGCACAGCCCCTCCTGCAG ENSG00000166888:ENST0000054387 GGCAAGGGGAGTCGGGGGGAGGGTCCTTGGGGGCACAGCCCCTCCTGCAG ENSG00000166888:ENST0000055615 GGCAAGGGGAGTCGGGGGGAGGGTCCTTGGGGGCACAGCCCCTCCTGCAG ENSG00000166888:ENST0000045407 GGCAAGGGGAGTCGGGGGGAGGGTCCTTGGGGGCACAGCCCCTCCTGCAG ENSG00000166888:ENST0000053891 GGCAAGGGGAGTCGGGGGGAGGGTCCTTGGGGGCACAGCCCCTCCTGCAG ENSG00000166888:ENST0000053721 GGCAAGGGGAGTCGGGGGGAGGGTCCTTGGGGGCACAGCCCCTCCTGCAG ENSG00000166888:ENST0000053520 GGCAAGGGGAGTCGGGGGGAGGGTCCTTGGGGGCACAGCCCCTCCTGCAG isotig46679 GTGACATTCCCCAACTGGGAGTGCTGCTGAAATGCAAACCAAAGCTTCAG isotig12565 GCAGGAGGGCAGTTGTCACTCACGTTCATGGATCTGAC------------ isotig12566 GTGACCGGGATTCAAGAGAAGACCAGAATCAGGCCTCA------------ ENSG00000166888:ENST0000030013 CCCTCCCACTATGGGCAATCTGGGATCTCAATGTCCCACATGGACCTAAG ENSG00000166888:ENST0000054387 CCCTCCCACTATGGGCAATCTGGGATCTCAATGTCCCACATGGACCTAAG ENSG00000166888:ENST0000055615 CCCTCCCACTATGGGCAATCTGGGATCTCAATGTCCCACATGGACCTAAG ENSG00000166888:ENST0000045407 CCCTCCCACTATGGGCAATCTGGGATCTCAATGTCCCACATGGACCTAAG ENSG00000166888:ENST0000053891 CCCTCCCACTATGGGCAATCTGGGATCTCAATGTCCCACATGGACCTAAG ENSG00000166888:ENST0000053721 CCCTCCCACTATGGGCAATCTGGGATCTCAATGTCCCACATGGACCTAAG ENSG00000166888:ENST0000053520 CCCTCCCACTATGGGCAATCTGGGATCTCAATGTCCCACATGGACCTAAG isotig46679 ATAAACACGCAGGAAAAGACAGCTTCGAGAAACCTATGTTCGCAATATAA isotig12565 ---------TTCGGAGTGCGCTACCTCCCCCATGTGAGGAGC-------- isotig12566 -------------------------------------------------- ENSG00000166888:ENST0000030013 GGCCAACCCCAGTTGG ENSG00000166888:ENST0000054387 GGCCAACCCCAGTTGG ENSG00000166888:ENST0000055615 GGCCAACCCCAGTTGG ENSG00000166888:ENST0000045407 GGCCAACCCCAGTTGG ENSG00000166888:ENST0000053891 GGCCAACCCCAGTTGG ENSG00000166888:ENST0000053721 GGCCAACCCCAGTTGG ENSG00000166888:ENST0000053520 GGCCAACCCCAGTTGG isotig46679 CAGAAGGCTGCTTTGC isotig12565 ---------------- isotig12566 ---------------- """, ) def test4(self): aligner = CodonAligner() nucleotide_records = SeqIO.index("codonalign/nucl4.fa", "fasta") protein_alignment = Align.read("codonalign/pro4.aln", "clustal") self.assertEqual(len(protein_alignment.sequences), 10) codon_alignments = [] protein_record = protein_alignment.sequences[0] nucleotide_record = nucleotide_records[protein_record.id] self.assertEqual(nucleotide_record.id, protein_record.id) alignments = aligner.align(protein_record, nucleotide_record) self.assertEqual(len(alignments), 1) alignment = next(alignments) codon_alignments.append(alignment) self.assertTrue( np.array_equal(alignment.coordinates, np.array([[0, 847], [0, 2541]])) ) self.assertEqual( str(alignment), """\ ENSG00000 0 M S L W G L V S K M P P E K V Q R L Y V ENSG00000 0 ATGTCTCTGTGGGGTCTGGTCTCCAAGATGCCCCCAGAAAAAGTGCAGCGGCTCTATGTC ENSG00000 20 D F P Q H L R H L L G D W L E S Q P W E ENSG00000 60 GACTTTCCCCAACACCTGCGGCATCTTCTGGGTGACTGGCTGGAGAGCCAGCCCTGGGAG ENSG00000 40 F L V G S D A F C C N L A S A L L S D T ENSG00000 120 TTCCTGGTCGGCTCCGACGCCTTCTGCTGCAACTTGGCTAGTGCCCTACTTTCAGACACT ENSG00000 60 V Q H L Q A S V G E Q G E G S T I L Q H ENSG00000 180 GTCCAGCACCTTCAGGCCTCGGTGGGAGAGCAGGGGGAGGGGAGCACCATCTTGCAACAC ENSG00000 80 I S T L E S I Y Q R D P L K L V A T F R ENSG00000 240 ATCAGCACCCTTGAGAGCATATATCAGAGGGACCCCCTGAAGCTGGTGGCCACTTTCAGA ENSG00000 100 Q I L Q G E K K A V M E Q F R H L P M P ENSG00000 300 CAAATACTTCAAGGAGAGAAAAAAGCTGTTATGGAACAGTTCCGCCACTTGCCAATGCCT ENSG00000 120 F H W K Q E E L K F K T G L R R L Q H R ENSG00000 360 TTCCACTGGAAGCAGGAAGAACTCAAGTTTAAGACAGGCTTGCGGAGGCTGCAGCACCGA ENSG00000 140 V G E I H L L R E A L Q K G A E A G Q V ENSG00000 420 GTAGGGGAGATCCACCTTCTCCGAGAAGCCCTGCAGAAGGGGGCTGAGGCTGGCCAAGTG ENSG00000 160 S L H S L I E T P A N G T G P S E A L A ENSG00000 480 TCTCTGCACAGCTTGATAGAAACTCCTGCTAATGGGACTGGGCCAAGTGAGGCCCTGGCC ENSG00000 180 M L L Q E T T G E L E A A K A L V L K R ENSG00000 540 ATGCTACTGCAGGAGACCACTGGAGAGCTAGAGGCAGCCAAAGCCCTAGTGCTGAAGAGG ENSG00000 200 I Q I W K R Q Q Q L A G N G A P F E E S ENSG00000 600 ATCCAGATTTGGAAACGGCAGCAGCAGCTGGCAGGGAATGGCGCACCGTTTGAGGAGAGC ENSG00000 220 L A P L Q E R C E S L V D I Y S Q L Q Q ENSG00000 660 CTGGCCCCACTCCAGGAGAGGTGTGAAAGCCTGGTGGACATTTATTCCCAGCTACAGCAG ENSG00000 240 E V G A A G G E L E P K T R A S L T G R ENSG00000 720 GAGGTAGGGGCGGCTGGTGGGGAGCTTGAGCCCAAGACCCGGGCATCGCTGACTGGCCGG ENSG00000 260 L D E V L R T L V T S C F L V E K Q P P ENSG00000 780 CTGGATGAAGTCCTGAGAACCCTCGTCACCAGTTGCTTCCTGGTGGAGAAGCAGCCCCCC ENSG00000 280 Q V L K T Q T K F Q A G V R F L L G L R ENSG00000 840 CAGGTACTGAAGACTCAGACCAAGTTCCAGGCTGGAGTTCGATTCCTGTTGGGCTTGAGG ENSG00000 300 F L G A P A K P P L V R A D M V T E K Q ENSG00000 900 TTCCTGGGGGCCCCAGCCAAGCCTCCGCTGGTCAGGGCCGACATGGTGACAGAGAAGCAG ENSG00000 320 A R E L S V P Q G P G A G A E S T G E I ENSG00000 960 GCGCGGGAGCTGAGTGTGCCTCAGGGTCCTGGGGCTGGAGCAGAAAGCACTGGAGAAATC ENSG00000 340 I N N T V P L E N S I P G N C C S A L F ENSG00000 1020 ATCAACAACACTGTGCCCTTGGAGAACAGCATTCCTGGGAACTGCTGCTCTGCCCTGTTC ENSG00000 360 K N L L L K K I K R C E R K G T E S V T ENSG00000 1080 AAGAACCTGCTTCTCAAGAAGATCAAGCGGTGTGAGCGGAAGGGCACTGAGTCTGTCACA ENSG00000 380 E E K C A V L F S A S F T L G P G K L P ENSG00000 1140 GAGGAGAAGTGCGCTGTGCTCTTCTCTGCCAGCTTCACACTTGGCCCCGGCAAACTCCCC ENSG00000 400 I Q L Q A L S L P L V V I V H G N Q D N ENSG00000 1200 ATCCAGCTCCAGGCCCTGTCTCTGCCCCTGGTGGTCATCGTCCATGGCAACCAAGACAAC ENSG00000 420 N A K A T I L W D N A F S E M D R V P F ENSG00000 1260 AATGCCAAAGCCACTATCCTGTGGGACAATGCCTTCTCTGAGATGGACCGCGTGCCCTTT ENSG00000 440 V V A E R V P W E K M C E T L N L K F M ENSG00000 1320 GTGGTGGCTGAGCGGGTGCCCTGGGAGAAGATGTGTGAAACTCTGAACCTGAAGTTCATG ENSG00000 460 A E V G T N R G L L P E H F L F L A Q K ENSG00000 1380 GCTGAGGTGGGGACCAACCGGGGGCTGCTCCCAGAGCACTTCCTCTTCCTGGCCCAGAAG ENSG00000 480 I F N D N S L S M E A F Q H R S V S W S ENSG00000 1440 ATCTTCAATGACAACAGCCTCAGTATGGAGGCCTTCCAGCACCGTTCTGTGTCCTGGTCG ENSG00000 500 Q F N K E I L L G R G F T F W Q W F D G ENSG00000 1500 CAGTTCAACAAGGAGATCCTGCTGGGCCGTGGCTTCACCTTTTGGCAGTGGTTTGATGGT ENSG00000 520 V L D L T K R C L R S Y W S D R L I I G ENSG00000 1560 GTCCTGGACCTCACCAAACGCTGTCTCCGGAGCTACTGGTCTGACCGGCTGATCATTGGC ENSG00000 540 F I S K Q Y V T S L L L N E P D G T F L ENSG00000 1620 TTCATCAGCAAACAGTACGTTACTAGCCTTCTTCTCAATGAGCCCGACGGAACCTTTCTC ENSG00000 560 L R F S D S E I G G I T I A H V I R G Q ENSG00000 1680 CTCCGCTTCAGCGACTCAGAGATTGGGGGCATCACCATTGCCCATGTCATCCGGGGCCAG ENSG00000 580 D G S P Q I E N I Q P F S A K D L S I R ENSG00000 1740 GATGGCTCTCCACAGATAGAGAACATCCAGCCATTCTCTGCCAAAGACCTGTCCATTCGC ENSG00000 600 S L G D R I R D L A Q L K N L Y P K K P ENSG00000 1800 TCACTGGGGGACCGAATCCGGGATCTTGCTCAGCTCAAAAATCTCTATCCCAAGAAGCCC ENSG00000 620 K D E A F R S H Y K P E Q M G K E G R G ENSG00000 1860 AAGGATGAGGCTTTCCGGAGCCACTACAAGCCTGAACAGATGGGTAAGGATGGCAGGGGT ENSG00000 640 Y V P A T I K M T V E R D Q P L P T P E ENSG00000 1920 TATGTCCCAGCTACCATCAAGATGACCGTGGAAAGGGACCAACCACTTCCTACCCCAGAG ENSG00000 660 L Q M P T M V P S Y D L G M A P D S S M ENSG00000 1980 CTCCAGATGCCTACCATGGTGCCTTCTTATGACCTTGGAATGGCCCCTGATTCCTCCATG ENSG00000 680 S M Q L G P D M V P Q V Y P P H S H S I ENSG00000 2040 AGCATGCAGCTTGGCCCAGATATGGTGCCCCAGGTGTACCCACCACACTCTCACTCCATC ENSG00000 700 P P Y Q G L S P E E S V N V L S A F Q E ENSG00000 2100 CCCCCGTATCAAGGCCTCTCCCCAGAAGAATCAGTCAACGTGTTGTCAGCCTTCCAGGAG ENSG00000 720 P H L Q M P P S L G Q M S L P F D Q P H ENSG00000 2160 CCTCACCTGCAGATGCCCCCCAGCCTGGGCCAGATGAGCCTGCCCTTTGACCAGCCTCAC ENSG00000 740 P Q G L L P C Q P Q E H A V S S P D P L ENSG00000 2220 CCCCAGGGCCTGCTGCCGTGCCAGCCTCAGGAGCATGCTGTGTCCAGCCCTGACCCCCTG ENSG00000 760 L C S D V T M V E D S C L S Q P V T A F ENSG00000 2280 CTCTGCTCAGATGTGACCATGGTGGAAGACAGCTGCCTGAGCCAGCCAGTGACAGCGTTT ENSG00000 780 P Q G T W I G E D I F P P L L P P T E Q ENSG00000 2340 CCTCAGGGCACTTGGATTGGTGAAGACATATTCCCTCCTCTGCTGCCTCCCACTGAACAG ENSG00000 800 D L T K L L L E G Q G E S G G G S L G A ENSG00000 2400 GACCTCACTAAGCTTCTCCTGGAGGGGCAAGGGGAGTCGGGGGGAGGGTCCTTGGGGGCA ENSG00000 820 Q P L L Q P S H Y G Q S G I S M S H M D ENSG00000 2460 CAGCCCCTCCTGCAGCCCTCCCACTATGGGCAATCTGGGATCTCAATGTCCCACATGGAC ENSG00000 840 L R A N P S W 847 ENSG00000 2520 CTAAGGGCCAACCCCAGTTGG 2541 """, ) protein_record = protein_alignment.sequences[1] nucleotide_record = nucleotide_records[protein_record.id] self.assertEqual(nucleotide_record.id, protein_record.id) alignments = aligner.align(protein_record, nucleotide_record) self.assertEqual(len(alignments), 1) alignment = next(alignments) codon_alignments.append(alignment) self.assertTrue( np.array_equal(alignment.coordinates, np.array([[0, 847], [0, 2541]])) ) self.assertEqual( str(alignment), """\ ENSG00000 0 M S L W G L V S K M P P E K V Q R L Y V ENSG00000 0 ATGTCTCTGTGGGGTCTGGTCTCCAAGATGCCCCCAGAAAAAGTGCAGCGGCTCTATGTC ENSG00000 20 D F P Q H L R H L L G D W L E S Q P W E ENSG00000 60 GACTTTCCCCAACACCTGCGGCATCTTCTGGGTGACTGGCTGGAGAGCCAGCCCTGGGAG ENSG00000 40 F L V G S D A F C C N L A S A L L S D T ENSG00000 120 TTCCTGGTCGGCTCCGACGCCTTCTGCTGCAACTTGGCTAGTGCCCTACTTTCAGACACT ENSG00000 60 V Q H L Q A S V G E Q G E G S T I L Q H ENSG00000 180 GTCCAGCACCTTCAGGCCTCGGTGGGAGAGCAGGGGGAGGGGAGCACCATCTTGCAACAC ENSG00000 80 I S T L E S I Y Q R D P L K L V A T F R ENSG00000 240 ATCAGCACCCTTGAGAGCATATATCAGAGGGACCCCCTGAAGCTGGTGGCCACTTTCAGA ENSG00000 100 Q I L Q G E K K A V M E Q F R H L P M P ENSG00000 300 CAAATACTTCAAGGAGAGAAAAAAGCTGTTATGGAACAGTTCCGCCACTTGCCAATGCCT ENSG00000 120 F H W K Q E E L K F K T G L R R L Q H R ENSG00000 360 TTCCACTGGAAGCAGGAAGAACTCAAGTTTAAGACAGGCTTGCGGAGGCTGCAGCACCGA ENSG00000 140 V G E I H L L R E A L Q K G A E A G Q V ENSG00000 420 GTAGGGGAGATCCACCTTCTCCGAGAAGCCCTGCAGAAGGGGGCTGAGGCTGGCCAAGTG ENSG00000 160 S L H S L I E T P A N G T G P S E A L A ENSG00000 480 TCTCTGCACAGCTTGATAGAAACTCCTGCTAATGGGACTGGGCCAAGTGAGGCCCTGGCC ENSG00000 180 M L L Q E T T G E L E A A K A L V L K R ENSG00000 540 ATGCTACTGCAGGAGACCACTGGAGAGCTAGAGGCAGCCAAAGCCCTAGTGCTGAAGAGG ENSG00000 200 I Q I W K R Q Q Q L A G N G A P F E E S ENSG00000 600 ATCCAGATTTGGAAACGGCAGCAGCAGCTGGCAGGGAATGGCGCACCGTTTGAGGAGAGC ENSG00000 220 L A P L Q E R C E S L V D I Y S Q L Q Q ENSG00000 660 CTGGCCCCACTCCAGGAGAGGTGTGAAAGCCTGGTGGACATTTATTCCCAGCTACAGCAG ENSG00000 240 E V G A A G G E L E P K T R A S L T G R ENSG00000 720 GAGGTAGGGGCGGCTGGTGGGGAGCTTGAGCCCAAGACCCGGGCATCGCTGACTGGCCGG ENSG00000 260 L D E V L R T L V T S C F L V E K Q P P ENSG00000 780 CTGGATGAAGTCCTGAGAACCCTCGTCACCAGTTGCTTCCTGGTGGAGAAGCAGCCCCCC ENSG00000 280 Q V L K T Q T K F Q A G V R F L L G L R ENSG00000 840 CAGGTACTGAAGACTCAGACCAAGTTCCAGGCTGGAGTTCGATTCCTGTTGGGCTTGAGG ENSG00000 300 F L G A P A K P P L V R A D M V T E K Q ENSG00000 900 TTCCTGGGGGCCCCAGCCAAGCCTCCGCTGGTCAGGGCCGACATGGTGACAGAGAAGCAG ENSG00000 320 A R E L S V P Q G P G A G A E S T G E I ENSG00000 960 GCGCGGGAGCTGAGTGTGCCTCAGGGTCCTGGGGCTGGAGCAGAAAGCACTGGAGAAATC ENSG00000 340 I N N T V P L E N S I P G N C C S A L F ENSG00000 1020 ATCAACAACACTGTGCCCTTGGAGAACAGCATTCCTGGGAACTGCTGCTCTGCCCTGTTC ENSG00000 360 K N L L L K K I K R C E R K G T E S V T ENSG00000 1080 AAGAACCTGCTTCTCAAGAAGATCAAGCGGTGTGAGCGGAAGGGCACTGAGTCTGTCACA ENSG00000 380 E E K C A V L F S A S F T L G P G K L P ENSG00000 1140 GAGGAGAAGTGCGCTGTGCTCTTCTCTGCCAGCTTCACACTTGGCCCCGGCAAACTCCCC ENSG00000 400 I Q L Q A L S L P L V V I V H G N Q D N ENSG00000 1200 ATCCAGCTCCAGGCCCTGTCTCTGCCCCTGGTGGTCATCGTCCATGGCAACCAAGACAAC ENSG00000 420 N A K A T I L W D N A F S E M D R V P F ENSG00000 1260 AATGCCAAAGCCACTATCCTGTGGGACAATGCCTTCTCTGAGATGGACCGCGTGCCCTTT ENSG00000 440 V V A E R V P W E K M C E T L N L K F M ENSG00000 1320 GTGGTGGCTGAGCGGGTGCCCTGGGAGAAGATGTGTGAAACTCTGAACCTGAAGTTCATG ENSG00000 460 A E V G T N R G L L P E H F L F L A Q K ENSG00000 1380 GCTGAGGTGGGGACCAACCGGGGGCTGCTCCCAGAGCACTTCCTCTTCCTGGCCCAGAAG ENSG00000 480 I F N D N S L S M E A F Q H R S V S W S ENSG00000 1440 ATCTTCAATGACAACAGCCTCAGTATGGAGGCCTTCCAGCACCGTTCTGTGTCCTGGTCG ENSG00000 500 Q F N K E I L L G R G F T F W Q W F D G ENSG00000 1500 CAGTTCAACAAGGAGATCCTGCTGGGCCGTGGCTTCACCTTTTGGCAGTGGTTTGATGGT ENSG00000 520 V L D L T K R C L R S Y W S D R L I I G ENSG00000 1560 GTCCTGGACCTCACCAAACGCTGTCTCCGGAGCTACTGGTCTGACCGGCTGATCATTGGC ENSG00000 540 F I S K Q Y V T S L L L N E P D G T F L ENSG00000 1620 TTCATCAGCAAACAGTACGTTACTAGCCTTCTTCTCAATGAGCCCGACGGAACCTTTCTC ENSG00000 560 L R F S D S E I G G I T I A H V I R G Q ENSG00000 1680 CTCCGCTTCAGCGACTCAGAGATTGGGGGCATCACCATTGCCCATGTCATCCGGGGCCAG ENSG00000 580 D G S P Q I E N I Q P F S A K D L S I R ENSG00000 1740 GATGGCTCTCCACAGATAGAGAACATCCAGCCATTCTCTGCCAAAGACCTGTCCATTCGC ENSG00000 600 S L G D R I R D L A Q L K N L Y P K K P ENSG00000 1800 TCACTGGGGGACCGAATCCGGGATCTTGCTCAGCTCAAAAATCTCTATCCCAAGAAGCCC ENSG00000 620 K D E A F R S H Y K P E Q M G K D G R G ENSG00000 1860 AAGGATGAGGCTTTCCGGAGCCACTACAAGCCTGAACAGATGGGTAAGGATGGCAGGGGT ENSG00000 640 Y V P A T I K M T V E R D Q P L P T P E ENSG00000 1920 TATGTCCCAGCTACCATCAAGATGACCGTGGAAAGGGACCAACCACTTCCTACCCCAGAG ENSG00000 660 L Q M P T M V P S Y D L G M A P D S S M ENSG00000 1980 CTCCAGATGCCTACCATGGTGCCTTCTTATGACCTTGGAATGGCCCCTGATTCCTCCATG ENSG00000 680 S M Q L G P D M V P Q V Y P P H S H S I ENSG00000 2040 AGCATGCAGCTTGGCCCAGATATGGTGCCCCAGGTGTACCCACCACACTCTCACTCCATC ENSG00000 700 P P Y Q G L S P E E S V N V L S A F Q E ENSG00000 2100 CCCCCGTATCAAGGCCTCTCCCCAGAAGAATCAGTCAACGTGTTGTCAGCCTTCCAGGAG ENSG00000 720 P H L Q M P P S L G Q M S L P F D Q P H ENSG00000 2160 CCTCACCTGCAGATGCCCCCCAGCCTGGGCCAGATGAGCCTGCCCTTTGACCAGCCTCAC ENSG00000 740 P Q G L L P C Q P Q E H A V S S P D P L ENSG00000 2220 CCCCAGGGCCTGCTGCCGTGCCAGCCTCAGGAGCATGCTGTGTCCAGCCCTGACCCCCTG ENSG00000 760 L C S D V T M V E D S C L S Q P V T A F ENSG00000 2280 CTCTGCTCAGATGTGACCATGGTGGAAGACAGCTGCCTGAGCCAGCCAGTGACAGCGTTT ENSG00000 780 P Q G T W I G E D I F P P L L P P T E Q ENSG00000 2340 CCTCAGGGCACTTGGATTGGTGAAGACATATTCCCTCCTCTGCTGCCTCCCACTGAACAG ENSG00000 800 D L T K L L L E G Q G E S G G G S L G A ENSG00000 2400 GACCTCACTAAGCTTCTCCTGGAGGGGCAAGGGGAGTCGGGGGGAGGGTCCTTGGGGGCA ENSG00000 820 Q P L L Q P S H Y G Q S G I S M S H M D ENSG00000 2460 CAGCCCCTCCTGCAGCCCTCCCACTATGGGCAATCTGGGATCTCAATGTCCCACATGGAC ENSG00000 840 L R A N P S W 847 ENSG00000 2520 CTAAGGGCCAACCCCAGTTGG 2541 """, ) protein_record = protein_alignment.sequences[2] nucleotide_record = nucleotide_records[protein_record.id] self.assertEqual(nucleotide_record.id, protein_record.id) alignments = aligner.align(protein_record, nucleotide_record) self.assertEqual(len(alignments), 1) alignment = next(alignments) codon_alignments.append(alignment) self.assertTrue( np.array_equal(alignment.coordinates, np.array([[0, 847], [0, 2541]])) ) self.assertEqual( str(alignment), """\ ENSG00000 0 M S L W G L V S K M P P E K V Q R L Y V ENSG00000 0 ATGTCTCTGTGGGGTCTGGTCTCCAAGATGCCCCCAGAAAAAGTGCAGCGGCTCTATGTC ENSG00000 20 D F P Q H L R H L L G D W L E S Q P W E ENSG00000 60 GACTTTCCCCAACACCTGCGGCATCTTCTGGGTGACTGGCTGGAGAGCCAGCCCTGGGAG ENSG00000 40 F L V G S D A F C C N L A S A L L S D T ENSG00000 120 TTCCTGGTCGGCTCCGACGCCTTCTGCTGCAACTTGGCTAGTGCCCTACTTTCAGACACT ENSG00000 60 V Q H L Q A S V G E Q G E G S T I L Q H ENSG00000 180 GTCCAGCACCTTCAGGCCTCGGTGGGAGAGCAGGGGGAGGGGAGCACCATCTTGCAACAC ENSG00000 80 I S T L E S I Y Q R D P L K L V A T F R ENSG00000 240 ATCAGCACCCTTGAGAGCATATATCAGAGGGACCCCCTGAAGCTGGTGGCCACTTTCAGA ENSG00000 100 Q I L Q G E K K A V M E Q F R H L P M P ENSG00000 300 CAAATACTTCAAGGAGAGAAAAAAGCTGTTATGGAACAGTTCCGCCACTTGCCAATGCCT ENSG00000 120 F H W K Q E E L K F K T G L R R L Q H R ENSG00000 360 TTCCACTGGAAGCAGGAAGAACTCAAGTTTAAGACAGGCTTGCGGAGGCTGCAGCACCGA ENSG00000 140 V G E I H L L R E A L Q K G A E A G Q V ENSG00000 420 GTAGGGGAGATCCACCTTCTCCGAGAAGCCCTGCAGAAGGGGGCTGAGGCTGGCCAAGTG ENSG00000 160 S L H S L I E T P A N G T G P S E A L A ENSG00000 480 TCTCTGCACAGCTTGATAGAAACTCCTGCTAATGGGACTGGGCCAAGTGAGGCCCTGGCC ENSG00000 180 M L L Q E T T G E L E A A K A L V L K R ENSG00000 540 ATGCTACTGCAGGAGACCACTGGAGAGCTAGAGGCAGCCAAAGCCCTAGTGCTGAAGAGG ENSG00000 200 I Q I W K R Q Q Q L A G N G A P F E E S ENSG00000 600 ATCCAGATTTGGAAACGGCAGCAGCAGCTGGCAGGGAATGGCGCACCGTTTGAGGAGAGC ENSG00000 220 L A P L Q E R C E S L V D I Y S Q L Q Q ENSG00000 660 CTGGCCCCACTCCAGGAGAGGTGTGAAAGCCTGGTGGACATTTATTCCCAGCTACAGCAG ENSG00000 240 E V G A A G G E L E P K T R A S L T G R ENSG00000 720 GAGGTAGGGGCGGCTGGTGGGGAGCTTGAGCCCAAGACCCGGGCATCGCTGACTGGCCGG ENSG00000 260 L D E V L R T L V T S C F L V E K Q P P ENSG00000 780 CTGGATGAAGTCCTGAGAACCCTCGTCACCAGTTGCTTCCTGGTGGAGAAGCAGCCCCCC ENSG00000 280 Q V L K T Q T K F Q A G V R F L L G L R ENSG00000 840 CAGGTACTGAAGACTCAGACCAAGTTCCAGGCTGGAGTTCGATTCCTGTTGGGCTTGAGG ENSG00000 300 F L G A P A K P P L V R A D M V T E K Q ENSG00000 900 TTCCTGGGGGCCCCAGCCAAGCCTCCGCTGGTCAGGGCCGACATGGTGACAGAGAAGCAG ENSG00000 320 A R E L S V P Q G P G A G A E S T G E I ENSG00000 960 GCGCGGGAGCTGAGTGTGCCTCAGGGTCCTGGGGCTGGAGCAGAAAGCACTGGAGAAATC ENSG00000 340 I N N T V P L E N S I P G N C C S A L F ENSG00000 1020 ATCAACAACACTGTGCCCTTGGAGAACAGCATTCCTGGGAACTGCTGCTCTGCCCTGTTC ENSG00000 360 K N L L L K K I K R C E R K G T E S V T ENSG00000 1080 AAGAACCTGCTTCTCAAGAAGATCAAGCGGTGTGAGCGGAAGGGCACTGAGTCTGTCACA ENSG00000 380 E E K C A V L F S A S F T L G P G K L P ENSG00000 1140 GAGGAGAAGTGCGCTGTGCTCTTCTCTGCCAGCTTCACACTTGGCCCCGGCAAACTCCCC ENSG00000 400 I Q L Q A L S L P L V V I V H G N Q D N ENSG00000 1200 ATCCAGCTCCAGGCCCTGTCTCTGCCCCTGGTGGTCATCGTCCATGGCAACCAAGACAAC ENSG00000 420 N A K A T I L W D N A F S E M D R V P F ENSG00000 1260 AATGCCAAAGCCACTATCCTGTGGGACAATGCCTTCTCTGAGATGGACCGCGTGCCCTTT ENSG00000 440 V V A E R V P W E K M C E T L N L K F M ENSG00000 1320 GTGGTGGCTGAGCGGGTGCCCTGGGAGAAGATGTGTGAAACTCTGAACCTGAAGTTCATG ENSG00000 460 A E V G T N R G L L P E H F L F L A Q K ENSG00000 1380 GCTGAGGTGGGGACCAACCGGGGGCTGCTCCCAGAGCACTTCCTCTTCCTGGCCCAGAAG ENSG00000 480 I F N D N S L S M E A F Q H R S V S W S ENSG00000 1440 ATCTTCAATGACAACAGCCTCAGTATGGAGGCCTTCCAGCACCGTTCTGTGTCCTGGTCG ENSG00000 500 Q F N K E I L L G R G F T F W Q W F D G ENSG00000 1500 CAGTTCAACAAGGAGATCCTGCTGGGCCGTGGCTTCACCTTTTGGCAGTGGTTTGATGGT ENSG00000 520 V L D L T K R C L R S Y W S D R L I I G ENSG00000 1560 GTCCTGGACCTCACCAAACGCTGTCTCCGGAGCTACTGGTCTGACCGGCTGATCATTGGC ENSG00000 540 F I S K Q Y V T S L L L N E P D G T F L ENSG00000 1620 TTCATCAGCAAACAGTACGTTACTAGCCTTCTTCTCAATGAGCCCGACGGAACCTTTCTC ENSG00000 560 L R F S D S E I G G I T I A H V I R G Q ENSG00000 1680 CTCCGCTTCAGCGACTCAGAGATTGGGGGCATCACCATTGCCCATGTCATCCGGGGCCAG ENSG00000 580 D G S P Q I E N I Q P F S A K D L S I R ENSG00000 1740 GATGGCTCTCCACAGATAGAGAACATCCAGCCATTCTCTGCCAAAGACCTGTCCATTCGC ENSG00000 600 S L G D R I R D L A Q L K N L Y P K K P ENSG00000 1800 TCACTGGGGGACCGAATCCGGGATCTTGCTCAGCTCAAAAATCTCTATCCCAAGAAGCCC ENSG00000 620 K D E A F R S H Y K P E Q M G K D G R G ENSG00000 1860 AAGGATGAGGCTTTCCGGAGCCACTACAAGCCTGAACAGATGGGTAAGGATGGCAGGGGT ENSG00000 640 Y V P A T I K M T V E R D Q P L P T P E ENSG00000 1920 TATGTCCCAGCTACCATCAAGATGACCGTGGAAAGGGACCAACCACTTCCTACCCCAGAG ENSG00000 660 L Q M P T M V P S Y D L G M A P D S S M ENSG00000 1980 CTCCAGATGCCTACCATGGTGCCTTCTTATGACCTTGGAATGGCCCCTGATTCCTCCATG ENSG00000 680 S M Q L G P D M V P Q V Y P P H S H S I ENSG00000 2040 AGCATGCAGCTTGGCCCAGATATGGTGCCCCAGGTGTACCCACCACACTCTCACTCCATC ENSG00000 700 P P Y Q G L S P E E S V N V L S A F Q E ENSG00000 2100 CCCCCGTATCAAGGCCTCTCCCCAGAAGAATCAGTCAACGTGTTGTCAGCCTTCCAGGAG ENSG00000 720 P H L Q M P P S L G Q M S L P F D Q P H ENSG00000 2160 CCTCACCTGCAGATGCCCCCCAGCCTGGGCCAGATGAGCCTGCCCTTTGACCAGCCTCAC ENSG00000 740 P Q G L L P C Q P Q E H A V S S P D P L ENSG00000 2220 CCCCAGGGCCTGCTGCCGTGCCAGCCTCAGGAGCATGCTGTGTCCAGCCCTGACCCCCTG ENSG00000 760 L C S D V T M V E D S C L S Q P V T A F ENSG00000 2280 CTCTGCTCAGATGTGACCATGGTGGAAGACAGCTGCCTGAGCCAGCCAGTGACAGCGTTT ENSG00000 780 P Q G T W I G E D I F P P L L P P T E Q ENSG00000 2340 CCTCAGGGCACTTGGATTGGTGAAGACATATTCCCTCCTCTGCTGCCTCCCACTGAACAG ENSG00000 800 D L T K L L L E G Q G E S G G G S L G A ENSG00000 2400 GACCTCACTAAGCTTCTCCTGGAGGGGCAAGGGGAGTCGGGGGGAGGGTCCTTGGGGGCA ENSG00000 820 Q P L L Q P S H Y G Q S G I S M S H M D ENSG00000 2460 CAGCCCCTCCTGCAGCCCTCCCACTATGGGCAATCTGGGATCTCAATGTCCCACATGGAC ENSG00000 840 L R A N P S W 847 ENSG00000 2520 CTAAGGGCCAACCCCAGTTGG 2541 """, ) protein_record = protein_alignment.sequences[3] nucleotide_record = nucleotide_records[protein_record.id] self.assertEqual(nucleotide_record.id, protein_record.id) alignments = aligner.align(protein_record, nucleotide_record) self.assertEqual(len(alignments), 1) alignment = next(alignments) codon_alignments.append(alignment) self.assertTrue( np.array_equal(alignment.coordinates, np.array([[0, 847], [0, 2541]])) ) self.assertEqual( str(alignment), """\ ENSG00000 0 M S L W G L V S K M P P E K V Q R L Y V ENSG00000 0 ATGTCTCTGTGGGGTCTGGTCTCCAAGATGCCCCCAGAAAAAGTGCAGCGGCTCTATGTC ENSG00000 20 D F P Q H L R H L L G D W L E S Q P W E ENSG00000 60 GACTTTCCCCAACACCTGCGGCATCTTCTGGGTGACTGGCTGGAGAGCCAGCCCTGGGAG ENSG00000 40 F L V G S D A F C C N L A S A L L S D T ENSG00000 120 TTCCTGGTCGGCTCCGACGCCTTCTGCTGCAACTTGGCTAGTGCCCTACTTTCAGACACT ENSG00000 60 V Q H L Q A S V G E Q G E G S T I L Q H ENSG00000 180 GTCCAGCACCTTCAGGCCTCGGTGGGAGAGCAGGGGGAGGGGAGCACCATCTTGCAACAC ENSG00000 80 I S T L E S I Y Q R D P L K L V A T F R ENSG00000 240 ATCAGCACCCTTGAGAGCATATATCAGAGGGACCCCCTGAAGCTGGTGGCCACTTTCAGA ENSG00000 100 Q I L Q G E K K A V M E Q F R H L P M P ENSG00000 300 CAAATACTTCAAGGAGAGAAAAAAGCTGTTATGGAACAGTTCCGCCACTTGCCAATGCCT ENSG00000 120 F H W K Q E E L K F K T G L R R L Q H R ENSG00000 360 TTCCACTGGAAGCAGGAAGAACTCAAGTTTAAGACAGGCTTGCGGAGGCTGCAGCACCGA ENSG00000 140 V G E I H L L R E A L Q K G A E A G Q V ENSG00000 420 GTAGGGGAGATCCACCTTCTCCGAGAAGCCCTGCAGAAGGGGGCTGAGGCTGGCCAAGTG ENSG00000 160 S L H S L I E T P A N G T G P S E A L A ENSG00000 480 TCTCTGCACAGCTTGATAGAAACTCCTGCTAATGGGACTGGGCCAAGTGAGGCCCTGGCC ENSG00000 180 M L L Q E T T G E L E A A K A L V L K R ENSG00000 540 ATGCTACTGCAGGAGACCACTGGAGAGCTAGAGGCAGCCAAAGCCCTAGTGCTGAAGAGG ENSG00000 200 I Q I W K R Q Q Q L A G N G A P F E E S ENSG00000 600 ATCCAGATTTGGAAACGGCAGCAGCAGCTGGCAGGGAATGGCGCACCGTTTGAGGAGAGC ENSG00000 220 L A P L Q E R C E S L V D I Y S Q L Q Q ENSG00000 660 CTGGCCCCACTCCAGGAGAGGTGTGAAAGCCTGGTGGACATTTATTCCCAGCTACAGCAG ENSG00000 240 E V G A A G G E L E P K T R A S L T G R ENSG00000 720 GAGGTAGGGGCGGCTGGTGGGGAGCTTGAGCCCAAGACCCGGGCATCGCTGACTGGCCGG ENSG00000 260 L D E V L R T L V T S C F L V E K Q P P ENSG00000 780 CTGGATGAAGTCCTGAGAACCCTCGTCACCAGTTGCTTCCTGGTGGAGAAGCAGCCCCCC ENSG00000 280 Q V L K T Q T K F Q A G V R F L L G L R ENSG00000 840 CAGGTACTGAAGACTCAGACCAAGTTCCAGGCTGGAGTTCGATTCCTGTTGGGCTTGAGG ENSG00000 300 F L G A P A K P P L V R A D M V T E K Q ENSG00000 900 TTCCTGGGGGCCCCAGCCAAGCCTCCGCTGGTCAGGGCCGACATGGTGACAGAGAAGCAG ENSG00000 320 A R E L S V P Q G P G A G A E S T G E I ENSG00000 960 GCGCGGGAGCTGAGTGTGCCTCAGGGTCCTGGGGCTGGAGCAGAAAGCACTGGAGAAATC ENSG00000 340 I N N T V P L E N S I P G N C C S A L F ENSG00000 1020 ATCAACAACACTGTGCCCTTGGAGAACAGCATTCCTGGGAACTGCTGCTCTGCCCTGTTC ENSG00000 360 K N L L L K K I K R C E R K G T E S V T ENSG00000 1080 AAGAACCTGCTTCTCAAGAAGATCAAGCGGTGTGAGCGGAAGGGCACTGAGTCTGTCACA ENSG00000 380 E E K C A V L F S A S F T L G P G K L P ENSG00000 1140 GAGGAGAAGTGCGCTGTGCTCTTCTCTGCCAGCTTCACACTTGGCCCCGGCAAACTCCCC ENSG00000 400 I Q L Q A L S L P L V V I V H G N Q D N ENSG00000 1200 ATCCAGCTCCAGGCCCTGTCTCTGCCCCTGGTGGTCATCGTCCATGGCAACCAAGACAAC ENSG00000 420 N A K A T I L W D N A F S E M D R V P F ENSG00000 1260 AATGCCAAAGCCACTATCCTGTGGGACAATGCCTTCTCTGAGATGGACCGCGTGCCCTTT ENSG00000 440 V V A E R V P W E K M C E T L N L K F M ENSG00000 1320 GTGGTGGCTGAGCGGGTGCCCTGGGAGAAGATGTGTGAAACTCTGAACCTGAAGTTCATG ENSG00000 460 A E V G T N R G L L P E H F L F L A Q K ENSG00000 1380 GCTGAGGTGGGGACCAACCGGGGGCTGCTCCCAGAGCACTTCCTCTTCCTGGCCCAGAAG ENSG00000 480 I F N D N S L S M E A F Q H R S V S W S ENSG00000 1440 ATCTTCAATGACAACAGCCTCAGTATGGAGGCCTTCCAGCACCGTTCTGTGTCCTGGTCG ENSG00000 500 Q F N K E I L L G R G F T F W Q W F D G ENSG00000 1500 CAGTTCAACAAGGAGATCCTGCTGGGCCGTGGCTTCACCTTTTGGCAGTGGTTTGATGGT ENSG00000 520 V L D L T K R C L R S Y W S D R L I I G ENSG00000 1560 GTCCTGGACCTCACCAAACGCTGTCTCCGGAGCTACTGGTCTGACCGGCTGATCATTGGC ENSG00000 540 F I S K Q Y V T S L L L N E P D G T F L ENSG00000 1620 TTCATCAGCAAACAGTACGTTACTAGCCTTCTTCTCAATGAGCCCGACGGAACCTTTCTC ENSG00000 560 L R F S D S E I G G I T I A H V I R G Q ENSG00000 1680 CTCCGCTTCAGCGACTCAGAGATTGGGGGCATCACCATTGCCCATGTCATCCGGGGCCAG ENSG00000 580 D G S P Q I E N I Q P F S A K D L S I R ENSG00000 1740 GATGGCTCTCCACAGATAGAGAACATCCAGCCATTCTCTGCCAAAGACCTGTCCATTCGC ENSG00000 600 S L G D R I R D L A Q L K N L Y P K K P ENSG00000 1800 TCACTGGGGGACCGAATCCGGGATCTTGCTCAGCTCAAAAATCTCTATCCCAAGAAGCCC ENSG00000 620 K D E A F R S H Y K P E Q M G K D G R G ENSG00000 1860 AAGGATGAGGCTTTCCGGAGCCACTACAAGCCTGAACAGATGGGTAAGGATGGCAGGGGT ENSG00000 640 Y V P A T I K M T V E R D Q P L P T P E ENSG00000 1920 TATGTCCCAGCTACCATCAAGATGACCGTGGAAAGGGACCAACCACTTCCTACCCCAGAG ENSG00000 660 L Q M P T M V P S Y D L G M A P D S S M ENSG00000 1980 CTCCAGATGCCTACCATGGTGCCTTCTTATGACCTTGGAATGGCCCCTGATTCCTCCATG ENSG00000 680 S M Q L G P D M V P Q V Y P P H S H S I ENSG00000 2040 AGCATGCAGCTTGGCCCAGATATGGTGCCCCAGGTGTACCCACCACACTCTCACTCCATC ENSG00000 700 P P Y Q G L S P E E S V N V L S A F Q E ENSG00000 2100 CCCCCGTATCAAGGCCTCTCCCCAGAAGAATCAGTCAACGTGTTGTCAGCCTTCCAGGAG ENSG00000 720 P H L Q M P P S L G Q M S L P F D Q P H ENSG00000 2160 CCTCACCTGCAGATGCCCCCCAGCCTGGGCCAGATGAGCCTGCCCTTTGACCAGCCTCAC ENSG00000 740 P Q G L L P C Q P Q E H A V S S P D P L ENSG00000 2220 CCCCAGGGCCTGCTGCCGTGCCAGCCTCAGGAGCATGCTGTGTCCAGCCCTGACCCCCTG ENSG00000 760 L C S D V T M V E D S C L S Q P V T A F ENSG00000 2280 CTCTGCTCAGATGTGACCATGGTGGAAGACAGCTGCCTGAGCCAGCCAGTGACAGCGTTT ENSG00000 780 P Q G T W I G E D I F P P L L P P T E Q ENSG00000 2340 CCTCAGGGCACTTGGATTGGTGAAGACATATTCCCTCCTCTGCTGCCTCCCACTGAACAG ENSG00000 800 D L T K L L L E G Q G E S G G G S L G A ENSG00000 2400 GACCTCACTAAGCTTCTCCTGGAGGGGCAAGGGGAGTCGGGGGGAGGGTCCTTGGGGGCA ENSG00000 820 Q P L L Q P S H Y G Q S G I S M S H M D ENSG00000 2460 CAGCCCCTCCTGCAGCCCTCCCACTATGGGCAATCTGGGATCTCAATGTCCCACATGGAC ENSG00000 840 L R A N P S W 847 ENSG00000 2520 CTAAGGGCCAACCCCAGTTGG 2541 """, ) protein_record = protein_alignment.sequences[4] nucleotide_record = nucleotide_records[protein_record.id] self.assertEqual(nucleotide_record.id, protein_record.id) alignments = aligner.align(protein_record, nucleotide_record) self.assertEqual(len(alignments), 1) alignment = next(alignments) codon_alignments.append(alignment) self.assertTrue( np.array_equal(alignment.coordinates, np.array([[0, 737], [0, 2211]])) ) self.assertEqual( str(alignment), """\ ENSG00000 0 M E Q F R H L P M P F H W K Q E E L K F ENSG00000 0 ATGGAACAGTTCCGCCACTTGCCAATGCCTTTCCACTGGAAGCAGGAAGAACTCAAGTTT ENSG00000 20 K T G L R R L Q H R V G E I H L L R E A ENSG00000 60 AAGACAGGCTTGCGGAGGCTGCAGCACCGAGTAGGGGAGATCCACCTTCTCCGAGAAGCC ENSG00000 40 L Q K G A E A G Q V S L H S L I E T P A ENSG00000 120 CTGCAGAAGGGGGCTGAGGCTGGCCAAGTGTCTCTGCACAGCTTGATAGAAACTCCTGCT ENSG00000 60 N G T G P S E A L A M L L Q E T T G E L ENSG00000 180 AATGGGACTGGGCCAAGTGAGGCCCTGGCCATGCTACTGCAGGAGACCACTGGAGAGCTA ENSG00000 80 E A A K A L V L K R I Q I W K R Q Q Q L ENSG00000 240 GAGGCAGCCAAAGCCCTAGTGCTGAAGAGGATCCAGATTTGGAAACGGCAGCAGCAGCTG ENSG00000 100 A G N G A P F E E S L A P L Q E R C E S ENSG00000 300 GCAGGGAATGGCGCACCGTTTGAGGAGAGCCTGGCCCCACTCCAGGAGAGGTGTGAAAGC ENSG00000 120 L V D I Y S Q L Q Q E V G A A G G E L E ENSG00000 360 CTGGTGGACATTTATTCCCAGCTACAGCAGGAGGTAGGGGCGGCTGGTGGGGAGCTTGAG ENSG00000 140 P K T R A S L T G R L D E V L R T L V T ENSG00000 420 CCCAAGACCCGGGCATCGCTGACTGGCCGGCTGGATGAAGTCCTGAGAACCCTCGTCACC ENSG00000 160 S C F L V E K Q P P Q V L K T Q T K F Q ENSG00000 480 AGTTGCTTCCTGGTGGAGAAGCAGCCCCCCCAGGTACTGAAGACTCAGACCAAGTTCCAG ENSG00000 180 A G V R F L L G L R F L G A P A K P P L ENSG00000 540 GCTGGAGTTCGATTCCTGTTGGGCTTGAGGTTCCTGGGGGCCCCAGCCAAGCCTCCGCTG ENSG00000 200 V R A D M V T E K Q A R E L S V P Q G P ENSG00000 600 GTCAGGGCCGACATGGTGACAGAGAAGCAGGCGCGGGAGCTGAGTGTGCCTCAGGGTCCT ENSG00000 220 G A G A E S T G E I I N N T V P L E N S ENSG00000 660 GGGGCTGGAGCAGAAAGCACTGGAGAAATCATCAACAACACTGTGCCCTTGGAGAACAGC ENSG00000 240 I P G N C C S A L F K N L L L K K I K R ENSG00000 720 ATTCCTGGGAACTGCTGCTCTGCCCTGTTCAAGAACCTGCTTCTCAAGAAGATCAAGCGG ENSG00000 260 C E R K G T E S V T E E K C A V L F S A ENSG00000 780 TGTGAGCGGAAGGGCACTGAGTCTGTCACAGAGGAGAAGTGCGCTGTGCTCTTCTCTGCC ENSG00000 280 S F T L G P G K L P I Q L Q A L S L P L ENSG00000 840 AGCTTCACACTTGGCCCCGGCAAACTCCCCATCCAGCTCCAGGCCCTGTCTCTGCCCCTG ENSG00000 300 V V I V H G N Q D N N A K A T I L W D N ENSG00000 900 GTGGTCATCGTCCATGGCAACCAAGACAACAATGCCAAAGCCACTATCCTGTGGGACAAT ENSG00000 320 A F S E M D R V P F V V A E R V P W E K ENSG00000 960 GCCTTCTCTGAGATGGACCGCGTGCCCTTTGTGGTGGCTGAGCGGGTGCCCTGGGAGAAG ENSG00000 340 M C E T L N L K F M A E V G T N R G L L ENSG00000 1020 ATGTGTGAAACTCTGAACCTGAAGTTCATGGCTGAGGTGGGGACCAACCGGGGGCTGCTC ENSG00000 360 P E H F L F L A Q K I F N D N S L S M E ENSG00000 1080 CCAGAGCACTTCCTCTTCCTGGCCCAGAAGATCTTCAATGACAACAGCCTCAGTATGGAG ENSG00000 380 A F Q H R S V S W S Q F N K E I L L G R ENSG00000 1140 GCCTTCCAGCACCGTTCTGTGTCCTGGTCGCAGTTCAACAAGGAGATCCTGCTGGGCCGT ENSG00000 400 G F T F W Q W F D G V L D L T K R C L R ENSG00000 1200 GGCTTCACCTTTTGGCAGTGGTTTGATGGTGTCCTGGACCTCACCAAACGCTGTCTCCGG ENSG00000 420 S Y W S D R L I I G F I S K Q Y V T S L ENSG00000 1260 AGCTACTGGTCTGACCGGCTGATCATTGGCTTCATCAGCAAACAGTACGTTACTAGCCTT ENSG00000 440 L L N E P D G T F L L R F S D S E I G G ENSG00000 1320 CTTCTCAATGAGCCCGACGGAACCTTTCTCCTCCGCTTCAGCGACTCAGAGATTGGGGGC ENSG00000 460 I T I A H V I R G Q D G S P Q I E N I Q ENSG00000 1380 ATCACCATTGCCCATGTCATCCGGGGCCAGGATGGCTCTCCACAGATAGAGAACATCCAG ENSG00000 480 P F S A K D L S I R S L G D R I R D L A ENSG00000 1440 CCATTCTCTGCCAAAGACCTGTCCATTCGCTCACTGGGGGACCGAATCCGGGATCTTGCT ENSG00000 500 Q L K N L Y P K K P K D E A F R S H Y K ENSG00000 1500 CAGCTCAAAAATCTCTATCCCAAGAAGCCCAAGGATGAGGCTTTCCGGAGCCACTACAAG ENSG00000 520 P E Q M G K D G R G Y V P A T I K M T V ENSG00000 1560 CCTGAACAGATGGGTAAGGATGGCAGGGGTTATGTCCCAGCTACCATCAAGATGACCGTG ENSG00000 540 E R D Q P L P T P E L Q M P T M V P S Y ENSG00000 1620 GAAAGGGACCAACCACTTCCTACCCCAGAGCTCCAGATGCCTACCATGGTGCCTTCTTAT ENSG00000 560 D L G M A P D S S M S M Q L G P D M V P ENSG00000 1680 GACCTTGGAATGGCCCCTGATTCCTCCATGAGCATGCAGCTTGGCCCAGATATGGTGCCC ENSG00000 580 Q V Y P P H S H S I P P Y Q G L S P E E ENSG00000 1740 CAGGTGTACCCACCACACTCTCACTCCATCCCCCCGTATCAAGGCCTCTCCCCAGAAGAA ENSG00000 600 S V N V L S A F Q E P H L Q M P P S L G ENSG00000 1800 TCAGTCAACGTGTTGTCAGCCTTCCAGGAGCCTCACCTGCAGATGCCCCCCAGCCTGGGC ENSG00000 620 Q M S L P F D Q P H P Q G L L P C Q P Q ENSG00000 1860 CAGATGAGCCTGCCCTTTGACCAGCCTCACCCCCAGGGCCTGCTGCCGTGCCAGCCTCAG ENSG00000 640 E H A V S S P D P L L C S D V T M V E D ENSG00000 1920 GAGCATGCTGTGTCCAGCCCTGACCCCCTGCTCTGCTCAGATGTGACCATGGTGGAAGAC ENSG00000 660 S C L S Q P V T A F P Q G T W I G E D I ENSG00000 1980 AGCTGCCTGAGCCAGCCAGTGACAGCGTTTCCTCAGGGCACTTGGATTGGTGAAGACATA ENSG00000 680 F P P L L P P T E Q D L T K L L L E G Q ENSG00000 2040 TTCCCTCCTCTGCTGCCTCCCACTGAACAGGACCTCACTAAGCTTCTCCTGGAGGGGCAA ENSG00000 700 G E S G G G S L G A Q P L L Q P S H Y G ENSG00000 2100 GGGGAGTCGGGGGGAGGGTCCTTGGGGGCACAGCCCCTCCTGCAGCCCTCCCACTATGGG ENSG00000 720 Q S G I S M S H M D L R A N P S W 737 ENSG00000 2160 CAATCTGGGATCTCAATGTCCCACATGGACCTAAGGGCCAACCCCAGTTGG 2211 """, ) protein_record = protein_alignment.sequences[5] nucleotide_record = nucleotide_records[protein_record.id] self.assertEqual(nucleotide_record.id, protein_record.id) alignments = aligner.align(protein_record, nucleotide_record) self.assertEqual(len(alignments), 1) alignment = next(alignments) codon_alignments.append(alignment) self.assertTrue( np.array_equal(alignment.coordinates, np.array([[0, 737], [0, 2211]])) ) self.assertEqual( str(alignment), """\ ENSG00000 0 M E Q F R H L P M P F H W K Q E E L K F ENSG00000 0 ATGGAACAGTTCCGCCACTTGCCAATGCCTTTCCACTGGAAGCAGGAAGAACTCAAGTTT ENSG00000 20 K T G L R R L Q H R V G E I H L L R E A ENSG00000 60 AAGACAGGCTTGCGGAGGCTGCAGCACCGAGTAGGGGAGATCCACCTTCTCCGAGAAGCC ENSG00000 40 L Q K G A E A G Q V S L H S L I E T P A ENSG00000 120 CTGCAGAAGGGGGCTGAGGCTGGCCAAGTGTCTCTGCACAGCTTGATAGAAACTCCTGCT ENSG00000 60 N G T G P S E A L A M L L Q E T T G E L ENSG00000 180 AATGGGACTGGGCCAAGTGAGGCCCTGGCCATGCTACTGCAGGAGACCACTGGAGAGCTA ENSG00000 80 E A A K A L V L K R I Q I W K R Q Q Q L ENSG00000 240 GAGGCAGCCAAAGCCCTAGTGCTGAAGAGGATCCAGATTTGGAAACGGCAGCAGCAGCTG ENSG00000 100 A G N G A P F E E S L A P L Q E R C E S ENSG00000 300 GCAGGGAATGGCGCACCGTTTGAGGAGAGCCTGGCCCCACTCCAGGAGAGGTGTGAAAGC ENSG00000 120 L V D I Y S Q L Q Q E V G A A G G E L E ENSG00000 360 CTGGTGGACATTTATTCCCAGCTACAGCAGGAGGTAGGGGCGGCTGGTGGGGAGCTTGAG ENSG00000 140 P K T R A S L T G R L D E V L R T L V T ENSG00000 420 CCCAAGACCCGGGCATCGCTGACTGGCCGGCTGGATGAAGTCCTGAGAACCCTCGTCACC ENSG00000 160 S C F L V E K Q P P Q V L K T Q T K F Q ENSG00000 480 AGTTGCTTCCTGGTGGAGAAGCAGCCCCCCCAGGTACTGAAGACTCAGACCAAGTTCCAG ENSG00000 180 A G V R F L L G L R F L G A P A K P P L ENSG00000 540 GCTGGAGTTCGATTCCTGTTGGGCTTGAGGTTCCTGGGGGCCCCAGCCAAGCCTCCGCTG ENSG00000 200 V R A D M V T E K Q A R E L S V P Q G P ENSG00000 600 GTCAGGGCCGACATGGTGACAGAGAAGCAGGCGCGGGAGCTGAGTGTGCCTCAGGGTCCT ENSG00000 220 G A G A E S T G E I I N N T V P L E N S ENSG00000 660 GGGGCTGGAGCAGAAAGCACTGGAGAAATCATCAACAACACTGTGCCCTTGGAGAACAGC ENSG00000 240 I P G N C C S A L F K N L L L K K I K R ENSG00000 720 ATTCCTGGGAACTGCTGCTCTGCCCTGTTCAAGAACCTGCTTCTCAAGAAGATCAAGCGG ENSG00000 260 C E R K G T E S V T E E K C A V L F S A ENSG00000 780 TGTGAGCGGAAGGGCACTGAGTCTGTCACAGAGGAGAAGTGCGCTGTGCTCTTCTCTGCC ENSG00000 280 S F T L G P G K L P I Q L Q A L S L P L ENSG00000 840 AGCTTCACACTTGGCCCCGGCAAACTCCCCATCCAGCTCCAGGCCCTGTCTCTGCCCCTG ENSG00000 300 V V I V H G N Q D N N A K A T I L W D N ENSG00000 900 GTGGTCATCGTCCATGGCAACCAAGACAACAATGCCAAAGCCACTATCCTGTGGGACAAT ENSG00000 320 A F S E M D R V P F V V A E R V P W E K ENSG00000 960 GCCTTCTCTGAGATGGACCGCGTGCCCTTTGTGGTGGCTGAGCGGGTGCCCTGGGAGAAG ENSG00000 340 M C E T L N L K F M A E V G T N R G L L ENSG00000 1020 ATGTGTGAAACTCTGAACCTGAAGTTCATGGCTGAGGTGGGGACCAACCGGGGGCTGCTC ENSG00000 360 P E H F L F L A Q K I F N D N S L S M E ENSG00000 1080 CCAGAGCACTTCCTCTTCCTGGCCCAGAAGATCTTCAATGACAACAGCCTCAGTATGGAG ENSG00000 380 A F Q H R S V S W S Q F N K E I L L G R ENSG00000 1140 GCCTTCCAGCACCGTTCTGTGTCCTGGTCGCAGTTCAACAAGGAGATCCTGCTGGGCCGT ENSG00000 400 G F T F W Q W F D G V L D L T K R C L R ENSG00000 1200 GGCTTCACCTTTTGGCAGTGGTTTGATGGTGTCCTGGACCTCACCAAACGCTGTCTCCGG ENSG00000 420 S Y W S D R L I I G F I S K Q Y V T S L ENSG00000 1260 AGCTACTGGTCTGACCGGCTGATCATTGGCTTCATCAGCAAACAGTACGTTACTAGCCTT ENSG00000 440 L L N E P D G T F L L R F S D S E I G G ENSG00000 1320 CTTCTCAATGAGCCCGACGGAACCTTTCTCCTCCGCTTCAGCGACTCAGAGATTGGGGGC ENSG00000 460 I T I A H V I R G Q D G S P Q I E N I Q ENSG00000 1380 ATCACCATTGCCCATGTCATCCGGGGCCAGGATGGCTCTCCACAGATAGAGAACATCCAG ENSG00000 480 P F S A K D L S I R S L G D R I R D L A ENSG00000 1440 CCATTCTCTGCCAAAGACCTGTCCATTCGCTCACTGGGGGACCGAATCCGGGATCTTGCT ENSG00000 500 Q L K N L Y P K K P K D E A F R S H Y K ENSG00000 1500 CAGCTCAAAAATCTCTATCCCAAGAAGCCCAAGGATGAGGCTTTCCGGAGCCACTACAAG ENSG00000 520 P E Q M G K D G R G Y V P A T I K M T V ENSG00000 1560 CCTGAACAGATGGGTAAGGATGGCAGGGGTTATGTCCCAGCTACCATCAAGATGACCGTG ENSG00000 540 E R D Q P L P T P E L Q M P T M V P S Y ENSG00000 1620 GAAAGGGACCAACCACTTCCTACCCCAGAGCTCCAGATGCCTACCATGGTGCCTTCTTAT ENSG00000 560 D L G M A P D S S M S M Q L G P D M V P ENSG00000 1680 GACCTTGGAATGGCCCCTGATTCCTCCATGAGCATGCAGCTTGGCCCAGATATGGTGCCC ENSG00000 580 Q V Y P P H S H S I P P Y Q G L S P E E ENSG00000 1740 CAGGTGTACCCACCACACTCTCACTCCATCCCCCCGTATCAAGGCCTCTCCCCAGAAGAA ENSG00000 600 S V N V L S A F Q E P H L Q M P P S L G ENSG00000 1800 TCAGTCAACGTGTTGTCAGCCTTCCAGGAGCCTCACCTGCAGATGCCCCCCAGCCTGGGC ENSG00000 620 Q M S L P F D Q P H P Q G L L P C Q P Q ENSG00000 1860 CAGATGAGCCTGCCCTTTGACCAGCCTCACCCCCAGGGCCTGCTGCCGTGCCAGCCTCAG ENSG00000 640 E H A V S S P D P L L C S D V T M V E D ENSG00000 1920 GAGCATGCTGTGTCCAGCCCTGACCCCCTGCTCTGCTCAGATGTGACCATGGTGGAAGAC ENSG00000 660 S C L S Q P V T A F P Q G T W I G E D I ENSG00000 1980 AGCTGCCTGAGCCAGCCAGTGACAGCGTTTCCTCAGGGCACTTGGATTGGTGAAGACATA ENSG00000 680 F P P L L P P T E Q D L T K L L L E G Q ENSG00000 2040 TTCCCTCCTCTGCTGCCTCCCACTGAACAGGACCTCACTAAGCTTCTCCTGGAGGGGCAA ENSG00000 700 G E S G G G S L G A Q P L L Q P S H Y G ENSG00000 2100 GGGGAGTCGGGGGGAGGGTCCTTGGGGGCACAGCCCCTCCTGCAGCCCTCCCACTATGGG ENSG00000 720 Q S G I S M S H M D L R A N P S W 737 ENSG00000 2160 CAATCTGGGATCTCAATGTCCCACATGGACCTAAGGGCCAACCCCAGTTGG 2211 """, ) protein_record = protein_alignment.sequences[6] nucleotide_record = nucleotide_records[protein_record.id] self.assertEqual(nucleotide_record.id, protein_record.id) alignments = aligner.align(protein_record, nucleotide_record) self.assertEqual(len(alignments), 1) alignment = next(alignments) codon_alignments.append(alignment) self.assertTrue( np.array_equal(alignment.coordinates, np.array([[0, 737], [0, 2211]])) ) self.assertEqual( str(alignment), """\ ENSG00000 0 M E Q F R H L P M P F H W K Q E E L K F ENSG00000 0 ATGGAACAGTTCCGCCACTTGCCAATGCCTTTCCACTGGAAGCAGGAAGAACTCAAGTTT ENSG00000 20 K T G L R R L Q H R V G E I H L L R E A ENSG00000 60 AAGACAGGCTTGCGGAGGCTGCAGCACCGAGTAGGGGAGATCCACCTTCTCCGAGAAGCC ENSG00000 40 L Q K G A E A G Q V S L H S L I E T P A ENSG00000 120 CTGCAGAAGGGGGCTGAGGCTGGCCAAGTGTCTCTGCACAGCTTGATAGAAACTCCTGCT ENSG00000 60 N G T G P S E A L A M L L Q E T T G E L ENSG00000 180 AATGGGACTGGGCCAAGTGAGGCCCTGGCCATGCTACTGCAGGAGACCACTGGAGAGCTA ENSG00000 80 E A A K A L V L K R I Q I W K R Q Q Q L ENSG00000 240 GAGGCAGCCAAAGCCCTAGTGCTGAAGAGGATCCAGATTTGGAAACGGCAGCAGCAGCTG ENSG00000 100 A G N G A P F E E S L A P L Q E R C E S ENSG00000 300 GCAGGGAATGGCGCACCGTTTGAGGAGAGCCTGGCCCCACTCCAGGAGAGGTGTGAAAGC ENSG00000 120 L V D I Y S Q L Q Q E V G A A G G E L E ENSG00000 360 CTGGTGGACATTTATTCCCAGCTACAGCAGGAGGTAGGGGCGGCTGGTGGGGAGCTTGAG ENSG00000 140 P K T R A S L T G R L D E V L R T L V T ENSG00000 420 CCCAAGACCCGGGCATCGCTGACTGGCCGGCTGGATGAAGTCCTGAGAACCCTCGTCACC ENSG00000 160 S C F L V E K Q P P Q V L K T Q T K F Q ENSG00000 480 AGTTGCTTCCTGGTGGAGAAGCAGCCCCCCCAGGTACTGAAGACTCAGACCAAGTTCCAG ENSG00000 180 A G V R F L L G L R F L G A P A K P P L ENSG00000 540 GCTGGAGTTCGATTCCTGTTGGGCTTGAGGTTCCTGGGGGCCCCAGCCAAGCCTCCGCTG ENSG00000 200 V R A D M V T E K Q A R E L S V P Q G P ENSG00000 600 GTCAGGGCCGACATGGTGACAGAGAAGCAGGCGCGGGAGCTGAGTGTGCCTCAGGGTCCT ENSG00000 220 G A G A E S T G E I I N N T V P L E N S ENSG00000 660 GGGGCTGGAGCAGAAAGCACTGGAGAAATCATCAACAACACTGTGCCCTTGGAGAACAGC ENSG00000 240 I P G N C C S A L F K N L L L K K I K R ENSG00000 720 ATTCCTGGGAACTGCTGCTCTGCCCTGTTCAAGAACCTGCTTCTCAAGAAGATCAAGCGG ENSG00000 260 C E R K G T E S V T E E K C A V L F S A ENSG00000 780 TGTGAGCGGAAGGGCACTGAGTCTGTCACAGAGGAGAAGTGCGCTGTGCTCTTCTCTGCC ENSG00000 280 S F T L G P G K L P I Q L Q A L S L P L ENSG00000 840 AGCTTCACACTTGGCCCCGGCAAACTCCCCATCCAGCTCCAGGCCCTGTCTCTGCCCCTG ENSG00000 300 V V I V H G N Q D N N A K A T I L W D N ENSG00000 900 GTGGTCATCGTCCATGGCAACCAAGACAACAATGCCAAAGCCACTATCCTGTGGGACAAT ENSG00000 320 A F S E M D R V P F V V A E R V P W E K ENSG00000 960 GCCTTCTCTGAGATGGACCGCGTGCCCTTTGTGGTGGCTGAGCGGGTGCCCTGGGAGAAG ENSG00000 340 M C E T L N L K F M A E V G T N R G L L ENSG00000 1020 ATGTGTGAAACTCTGAACCTGAAGTTCATGGCTGAGGTGGGGACCAACCGGGGGCTGCTC ENSG00000 360 P E H F L F L A Q K I F N D N S L S M E ENSG00000 1080 CCAGAGCACTTCCTCTTCCTGGCCCAGAAGATCTTCAATGACAACAGCCTCAGTATGGAG ENSG00000 380 A F Q H R S V S W S Q F N K E I L L G R ENSG00000 1140 GCCTTCCAGCACCGTTCTGTGTCCTGGTCGCAGTTCAACAAGGAGATCCTGCTGGGCCGT ENSG00000 400 G F T F W Q W F D G V L D L T K R C L R ENSG00000 1200 GGCTTCACCTTTTGGCAGTGGTTTGATGGTGTCCTGGACCTCACCAAACGCTGTCTCCGG ENSG00000 420 S Y W S D R L I I G F I S K Q Y V T S L ENSG00000 1260 AGCTACTGGTCTGACCGGCTGATCATTGGCTTCATCAGCAAACAGTACGTTACTAGCCTT ENSG00000 440 L L N E P D G T F L L R F S D S E I G G ENSG00000 1320 CTTCTCAATGAGCCCGACGGAACCTTTCTCCTCCGCTTCAGCGACTCAGAGATTGGGGGC ENSG00000 460 I T I A H V I R G Q D G S P Q I E N I Q ENSG00000 1380 ATCACCATTGCCCATGTCATCCGGGGCCAGGATGGCTCTCCACAGATAGAGAACATCCAG ENSG00000 480 P F S A K D L S I R S L G D R I R D L A ENSG00000 1440 CCATTCTCTGCCAAAGACCTGTCCATTCGCTCACTGGGGGACCGAATCCGGGATCTTGCT ENSG00000 500 Q L K N L Y P K K P K D E A F R S H Y K ENSG00000 1500 CAGCTCAAAAATCTCTATCCCAAGAAGCCCAAGGATGAGGCTTTCCGGAGCCACTACAAG ENSG00000 520 P E Q M G K D G R G Y V P A T I K M T V ENSG00000 1560 CCTGAACAGATGGGTAAGGATGGCAGGGGTTATGTCCCAGCTACCATCAAGATGACCGTG ENSG00000 540 E R D Q P L P T P E L Q M P T M V P S Y ENSG00000 1620 GAAAGGGACCAACCACTTCCTACCCCAGAGCTCCAGATGCCTACCATGGTGCCTTCTTAT ENSG00000 560 D L G M A P D S S M S M Q L G P D M V P ENSG00000 1680 GACCTTGGAATGGCCCCTGATTCCTCCATGAGCATGCAGCTTGGCCCAGATATGGTGCCC ENSG00000 580 Q V Y P P H S H S I P P Y Q G L S P E E ENSG00000 1740 CAGGTGTACCCACCACACTCTCACTCCATCCCCCCGTATCAAGGCCTCTCCCCAGAAGAA ENSG00000 600 S V N V L S A F Q E P H L Q M P P S L G ENSG00000 1800 TCAGTCAACGTGTTGTCAGCCTTCCAGGAGCCTCACCTGCAGATGCCCCCCAGCCTGGGC ENSG00000 620 Q M S L P F D Q P H P Q G L L P C Q P Q ENSG00000 1860 CAGATGAGCCTGCCCTTTGACCAGCCTCACCCCCAGGGCCTGCTGCCGTGCCAGCCTCAG ENSG00000 640 E H A V S S P D P L L C S D V T M V E D ENSG00000 1920 GAGCATGCTGTGTCCAGCCCTGACCCCCTGCTCTGCTCAGATGTGACCATGGTGGAAGAC ENSG00000 660 S C L S Q P V T A F P Q G T W I G E D I ENSG00000 1980 AGCTGCCTGAGCCAGCCAGTGACAGCGTTTCCTCAGGGCACTTGGATTGGTGAAGACATA ENSG00000 680 F P P L L P P T E Q D L T K L L L E G Q ENSG00000 2040 TTCCCTCCTCTGCTGCCTCCCACTGAACAGGACCTCACTAAGCTTCTCCTGGAGGGGCAA ENSG00000 700 G E S G G G S L G A Q P L L Q P S H Y G ENSG00000 2100 GGGGAGTCGGGGGGAGGGTCCTTGGGGGCACAGCCCCTCCTGCAGCCCTCCCACTATGGG ENSG00000 720 Q S G I S M S H M D L R A N P S W 737 ENSG00000 2160 CAATCTGGGATCTCAATGTCCCACATGGACCTAAGGGCCAACCCCAGTTGG 2211 """, ) protein_record = protein_alignment.sequences[7] nucleotide_record = nucleotide_records[protein_record.id] self.assertEqual(nucleotide_record.id, protein_record.id) nucleotide_record = nucleotide_record.upper() alignments = aligner.align(protein_record, nucleotide_record) self.assertEqual(len(alignments), 1) alignment = next(alignments) codon_alignments.append(alignment) self.assertTrue( np.array_equal(alignment.coordinates, np.array([[0, 1021], [0, 3063]])) ) self.assertEqual( str(alignment), """\ isotig466 0 E V T Q S R R K P V R E G R P W E P S Q isotig466 0 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA isotig466 20 E L A Q T P E G G C P R Q E S R P E G G isotig466 60 GAGTTGGCCCAAACCCCTGAGGGAGGCTGTCCTCGGCAGGAGAGCAGACCTGAGGGAGGT isotig466 40 W C A G P G C P A L P S H P R A G S P E isotig466 120 TGGTGTGCCGGTCCTGGTTGTCCAGCCCTCCCGTCCCATCCCAGGGCTGGCTCACCAGAA isotig466 60 K S T G I P G P L G R E Q R V S S C P G isotig466 180 AAAAGTACAGGCATCCCAGGCCCTCTGGGGCGGGAGCAGAGGGTCTCCTCTTGTCCGGGG isotig466 80 E D K N K N K K R V C S P H W K S S G A isotig466 240 GAAGACAAAAACAAAAACAAAAAACGAGTGTGTAGCCCTCACTGGAAGTCTTCTGGTGCT isotig466 100 L G P F A L G S L A S G H G G R A P P G isotig466 300 CTGGGGCCGTTTGCACTTGGGAGCCTGGCTTCTGGGCATGGTGGCCGGGCTCCGCCGGGG isotig466 120 A S A L G K A F L E Q S G W E P T E V P isotig466 360 GCTTCAGCCCTCGGCAAAGCGTTTCTAGAACAGAGTGGGTGGGAGCCGACTGAAGTCCCA isotig466 140 E P R T L T H R K A S S G W R N A N P P isotig466 420 GAACCGCGAACACTGACGCACAGGAAAGCCTCGAGTGGGTGGAGAAATGCAAATCCCCCA isotig466 160 V A W P Q P L R T L T A D S D F G L E R isotig466 480 GTGGCATGGCCTCAGCCGCTGCGGACCCTGACGGCCGATTCTGACTTCGGACTTGAGCGG isotig466 180 D Q H P D P G R A S M S Q W N Q V Q Q L isotig466 540 GACCAGCACCCGGACCCAGGGCGAGCCAGCATGTCTCAGTGGAATCAAGTCCAACAGTTA isotig466 200 E I K F L E Q V D Q F Y D D N F P M E I isotig466 600 GAAATCAAGTTTTTGGAGCAAGTTGATCAGTTCTATGATGACAACTTTCCCATGGAAATC isotig466 220 R H L L A Q W I E H Q D W E V A S N N E isotig466 660 CGACATCTGCTGGCCCAGTGGATTGAGCATCAAGACTGGGAGGTGGCCTCTAACAATGAA isotig466 240 T M A T I L L Q N L L I Q L D E Q L G R isotig466 720 ACTATGGCAACAATTCTTCTTCAAAACTTATTAATACAATTGGATGAACAGTTAGGTCGT isotig466 260 V S K E K N L L L I H N L K R I R K V L isotig466 780 GTTTCCAAAGAGAAAAACCTGCTATTGATCCACAATCTAAAGAGAATTAGAAAAGTACTT isotig466 280 Q G K F H G N P M H V A V V I S N C L R isotig466 840 CAGGGGAAGTTTCATGGAAATCCAATGCATGTAGCCGTGGTAATCTCAAATTGTTTAAGG isotig466 300 E E R R I L A A A N M P I Q G P L E K S isotig466 900 GAAGAGAGGAGAATACTGGCTGCAGCGAACATGCCTATCCAGGGACCTCTGGAGAAATCC isotig466 320 L Q S S S V S E R Q R N V E H K V A A I isotig466 960 TTACAAAGTTCGTCGGTTTCAGAAAGACAGAGAAATGTGGAACACAAAGTGGCTGCCATT isotig466 340 K N S V Q M T E Q D T K Y L E D L Q D E isotig466 1020 AAAAACAGTGTGCAGATGACAGAACAAGACACCAAATACTTGGAAGATCTGCAAGATGAA isotig466 360 F D Y R Y K T I Q T M D Q G D K N S I L isotig466 1080 TTTGACTACAGGTATAAAACAATTCAGACAATGGACCAGGGTGACAAGAATAGCATCCTA isotig466 380 M N Q E V L T L Q E M L N S L D F K R K isotig466 1140 ATGAACCAGGAGGTTTTGACACTCCAAGAAATGCTTAATAGCCTGGACTTCAAGAGAAAG isotig466 400 E A L T K M T Q I V N E S D L L M S S M isotig466 1200 GAAGCACTCACTAAGATGACACAGATAGTGAACGAGTCGGACCTGCTGATGAGCAGCATG isotig466 420 L I E E L Q D W K R R Q Q I A C I G G P isotig466 1260 CTCATAGAAGAGCTGCAGGACTGGAAGAGGAGGCAGCAGATCGCCTGCATCGGTGGCCCA isotig466 440 L H N G L D Q L Q N C F T L L A E S L F isotig466 1320 CTCCACAACGGGCTGGACCAGCTTCAGAACTGCTTTACCCTGTTGGCAGAAAGTCTTTTC isotig466 460 Q L R R Q L E K L E E Q S S K M T Y E G isotig466 1380 CAACTCAGACGACAGCTGGAGAAATTAGAGGAGCAGTCTTCCAAGATGACTTACGAAGGA isotig466 480 D P I P T Q R A H L L E R A T F L I Y N isotig466 1440 GACCCCATCCCCACGCAGAGAGCACACCTGCTGGAGAGAGCCACCTTCCTGATCTACAAC isotig466 500 L F K N S F V V E R Q P C M P T H P Q R isotig466 1500 CTTTTCAAGAACTCATTTGTGGTTGAGCGACAGCCCTGCATGCCAACACACCCTCAGAGG isotig466 520 P L V L K T L I Q F T A K L R L L I K L isotig466 1560 CCGCTGGTACTCAAAACCCTCATTCAGTTCACCGCGAAACTGAGACTACTAATAAAATTG isotig466 540 P E L N Y Q V K V K A S I D K N V S T L isotig466 1620 CCGGAACTCAACTATCAGGTGAAAGTAAAGGCATCGATCGACAAGAATGTTTCAACGCTA isotig466 560 S N R R F V L C G T Q V K A M S I E E S isotig466 1680 AGCAATAGAAGATTTGTGCTTTGTGGAACTCAAGTCAAAGCCATGTCCATCGAGGAATCC isotig466 580 S N G S L S V E F R H L Q P K E M K S S isotig466 1740 TCCAATGGGAGCCTCTCAGTAGAATTTAGACATTTGCAACCGAAGGAAATGAAATCCAGT isotig466 600 A G S K G N E G C H M V T E E L H S I A isotig466 1800 GCCGGAAGTAAAGGAAATGAGGGCTGCCACATGGTGACGGAAGAGCTGCATTCCATAGCC isotig466 620 F E T Q I C L Y G L T I D L E T S S L P isotig466 1860 TTTGAGACCCAGATCTGCCTCTATGGCCTCACCATCGACTTGGAGACAAGCTCATTACCT isotig466 640 V V M I S N V S Q L P N A W A S I I W Y isotig466 1920 GTGGTGATGATTTCTAATGTCAGCCAACTGCCTAATGCTTGGGCATCCATCATTTGGTAC isotig466 660 N V S T N D C Q N L V F F N N P P P V T isotig466 1980 AATGTGTCAACCAACGATTGCCAGAACTTGGTTTTCTTTAATAATCCTCCGCCTGTCACT isotig466 680 L S Q L L E V M S W Q F S S Y V G R G L isotig466 2040 TTGAGTCAACTCCTGGAAGTGATGAGCTGGCAGTTTTCATCCTATGTTGGTCGTGGCCTT isotig466 700 N S D Q L N M L A E K L T V Q S N Y S D isotig466 2100 AATTCAGACCAGCTCAACATGCTGGCAGAGAAGCTCACAGTTCAGTCTAACTACAGCGAT isotig466 720 G H L T W A K F C K E H L P G K P F T F isotig466 2160 GGTCACCTCACCTGGGCCAAGTTCTGCAAGGAACACTTGCCTGGCAAACCATTTACCTTC isotig466 740 W T W L E A I L D L I K K H I L P L W I isotig466 2220 TGGACCTGGCTTGAAGCAATATTGGACCTAATTAAAAAACACATTCTTCCCCTCTGGATT isotig466 760 D G Y I M G F V S K E K E R F L L K D K isotig466 2280 GATGGGTACATCATGGGCTTCGTGAGCAAAGAGAAGGAGAGGTTTCTGCTCAAGGATAAA isotig466 780 M P G T F L L R F S E S H L G G I T F T isotig466 2340 ATGCCCGGGACATTTTTGTTACGATTCAGTGAGAGCCATCTCGGAGGGATCACCTTCACC isotig466 800 W V D H S E N G E V R F H S V E P Y N K isotig466 2400 TGGGTGGACCACTCTGAAAACGGAGAAGTGAGATTCCACTCCGTAGAACCCTACAACAAA isotig466 820 G R L S A L P F A D I L R D Y K V I M A isotig466 2460 GGGCGTCTGTCGGCCCTGCCATTTGCTGACATCCTGCGGGACTACAAGGTCATCATGGCT isotig466 840 E N I P E N P L K Y L Y P D I P K D K A isotig466 2520 GAGAACATTCCCGAGAACCCTCTCAAGTACCTCTACCCCGACATCCCCAAAGACAAAGCC isotig466 860 F G K H Y S S Q P C E V S R P T E R G D isotig466 2580 TTCGGTAAACACTACAGCTCCCAGCCTTGCGAAGTTTCAAGGCCAACAGAACGGGGAGAC isotig466 880 K G Y V P S V F I P I S T I R S D A M E isotig466 2640 AAAGGTTATGTTCCTTCAGTTTTTATCCCTATTTCAACAATCCGCAGCGACGCCATGGAG isotig466 900 P Q S P S D L L P M S P S V Y A V L R E isotig466 2700 CCGCAGTCTCCTTCAGACCTTCTCCCCATGTCTCCGAGTGTATACGCTGTGCTGAGAGAA isotig466 920 N L S P T T I E T A M K S P Y S E R Y K isotig466 2760 AACCTGAGCCCTACCACAATTGAAACAGCAATGAAGTCTCCATATTCTGAGCGGTACAAA isotig466 940 A T L Q G R E Q M K T E T A L C Q S P Q isotig466 2820 GCGACTCTTCAAGGAAGAGAGCAGATGAAAACGGAGACTGCTCTTTGCCAAAGTCCACAA isotig466 960 F I S S A L I L V S R K W H K S E A F L isotig466 2880 TTCATTTCTTCAGCTTTGATACTGGTTTCTAGAAAATGGCACAAATCCGAAGCTTTCCTC isotig466 980 S L G D I P Q L G V L L K C K P K L Q I isotig466 2940 TCACTAGGTGACATTCCCCAACTGGGAGTGCTGCTGAAATGCAAACCAAAGCTTCAGATA isotig466 1000 N T Q E K T A S R N L C S Q Y N R R L L isotig466 3000 AACACGCAGGAAAAGACAGCTTCGAGAAACCTATGTTCGCAATATAACAGAAGGCTGCTT isotig466 1020 C 1021 isotig466 3060 TGC 3063 """, ) protein_record = protein_alignment.sequences[8] nucleotide_record = nucleotide_records[protein_record.id] self.assertEqual(nucleotide_record.id, protein_record.id) nucleotide_record = nucleotide_record.upper() alignments = aligner.align(protein_record, nucleotide_record) self.assertEqual(len(alignments), 1) alignment = next(alignments) codon_alignments.append(alignment) self.assertTrue( np.array_equal(alignment.coordinates, np.array([[0, 806], [0, 2418]])) ) self.assertEqual( str(alignment), """\ isotig125 0 A R R G Q A A L G S P A A R T W S Q R S isotig125 0 GCTAGGAGAGGCCAGGCGGCCCTCGGGAGCCCAGCTGCTCGCACCTGGAGCCAGCGCAGC isotig125 20 P A S R A S A R E T V T P P D C G R M A isotig125 60 CCGGCCAGTCGGGCCTCAGCCCGGGAGACAGTTACGCCCCCTGATTGCGGCAGGATGGCC isotig125 40 Q W N Q L Q Q L D T R Y L E Q L H Q L Y isotig125 120 CAGTGGAACCAGCTGCAGCAGCTGGACACTCGGTACCTGGAGCAGCTGCACCAGCTGTAC isotig125 60 S D S F P M E L R Q F L A P W I E S Q D isotig125 180 AGCGACAGCTTCCCCATGGAGCTGCGGCAGTTCCTGGCACCTTGGATTGAGAGTCAAGAT isotig125 80 W A Y A A S K E S H A T L V F H N L L G isotig125 240 TGGGCATATGCAGCCAGCAAAGAGTCACATGCCACACTGGTGTTTCATAATCTCTTGGGT isotig125 100 E I D Q Q Y S R F L Q E S N V L Y Q H N isotig125 300 GAGATTGACCAGCAGTACAGCCGATTCCTGCAAGAGTCCAACGTCCTCTATCAGCACAAC isotig125 120 L R R I G Q F V Q S R Y L E K P M E I A isotig125 360 CTTCGGAGGATCAAGCAGTTCCTACAGAGCAGGTATCTTGAGAAGCCGATGGAAATCGCC isotig125 140 R I V A R C L W E E S R L L Q T A A T A isotig125 420 CGCATCGTGGCCCGATGCCTGTGGGAAGAGTCTCGCCTCCTCCAGACGGCAGCCACTGCA isotig125 160 A Q Q G G Q A N H P T A A V V T E K Q Q isotig125 480 GCCCAGCAAGGAGGCCAGGCCAACCACCCAACAGCTGCTGTGGTGACGGAGAAACAGCAG isotig125 180 M L E Q H L Q D V R K R V Q D L E Q K M isotig125 540 ATGCTGGAGCAGCATCTTCAGGATGTCCGGAAACGTGTGCAGGATCTAGAACAGAAAATG isotig125 200 K V V E N L Q D D F D F N Y K T L K S Q isotig125 600 AAAGTGGTAGAGAATCTCCAGGATGACTTTGATTTCAACTATAAAACCCTCAAGAGTCAA isotig125 220 G D M Q D L N G N N Q S V T R Q K M Q Q isotig125 660 GGAGACATGCAGGATCTGAATGGAAACAACCAGTCTGTGACCAGGCAGAAGATGCAGCAG isotig125 240 L E Q M L T A L D Q M R R S I V S E L A isotig125 720 CTGGAACAGATGCTCACGGCGCTGGACCAGATGCGGAGAAGCATTGTGAGTGAGCTGGCG isotig125 260 G L L S A M E Y V Q K T L T D E E L A D isotig125 780 GGGCTTTTGTCGGCAATGGAGTACGTGCAGAAAACACTCACAGACGAGGAGCTGGCTGAC isotig125 280 W K R R Q Q I A C I G G P P N I C L D R isotig125 840 TGGAAGAGGCGGCAGCAGATCGCGTGCATTGGAGGCCCTCCCAACATCTGCCTGGATCGC isotig125 300 L E N W I T S L A E S Q L Q T R Q Q I K isotig125 900 CTGGAAAACTGGATAACTTCGTTAGCAGAATCTCAACTTCAGACCCGCCAACAAATTAAG isotig125 320 K L E E L Q Q K V S Y K G D P I V Q H R isotig125 960 AAACTGGAGGAGCTACAGCAGAAGGTGTCCTACAAGGGGGACCCCATTGTGCAGCACCGG isotig125 340 P M L E E R I V E L F R N L M K S A F V isotig125 1020 CCGATGCTGGAGGAGCGGATCGTGGAGCTGTTCAGAAACTTGATGAAGAGTGCCTTCGTG isotig125 360 V E R Q P C M P M H P D R P L V I K T G isotig125 1080 GTGGAGCGACAGCCCTGCATGCCGATGCACCCCGACCGGCCCTTGGTCATCAAGACTGGT isotig125 380 V Q F T T K V R L L V K F P E L N Y Q L isotig125 1140 GTCCAGTTCACTACTAAAGTCAGGTTGTTGGTCAAGTTTCCCGAGTTGAATTATCAGCTT isotig125 400 K I K V C I D K D S G D V A A L R G S R isotig125 1200 AAAATTAAAGTGTGCATTGACAAAGATTCTGGGGACGTTGCTGCTCTCAGAGGATCTCGG isotig125 420 K F N I L G T N T K V M N M E E S N N G isotig125 1260 AAATTTAACATTCTGGGCACAAACACGAAGGTGATGAACATGGAAGAATCCAACAACGGC isotig125 440 S L S A E F K H L T L R E Q R C G N G G isotig125 1320 AGCCTGTCTGCGGAGTTCAAGCACTTGACCCTGAGGGAGCAGAGATGTGGGAATGGAGGC isotig125 460 R A N C D A S L I V T E E L H L I T F E isotig125 1380 CGTGCCAATTGTGATGCCTCCTTGATTGTGACCGAGGAGCTGCATCTGATCACCTTCGAG isotig125 480 T E V Y H Q G L K I D L E T H S L P V V isotig125 1440 ACTGAGGTGTACCACCAAGGCCTCAAGATTGACCTGGAGACCCATTCTTTGCCAGTTGTG isotig125 500 V I S N I C Q M P N A W A S I L W Y N M isotig125 1500 GTGATCTCCAACATCTGTCAGATGCCAAATGCCTGGGCATCCATCCTGTGGTATAACATG isotig125 520 L T N N P K N V N F F T K P P I G T W D isotig125 1560 CTGACCAACAACCCCAAGAACGTGAACTTCTTCACCAAGCCACCAATCGGAACCTGGGAC isotig125 540 Q V A E V L S W Q F S S T T K R G L S I isotig125 1620 CAGGTGGCCGAGGTGCTCAGCTGGCAGTTCTCATCCACCACAAAGCGAGGGCTGAGCATC isotig125 560 E Q L T T L A E K L L G P G V N Y S G C isotig125 1680 GAGCAGCTGACTACGCTGGCCGAGAAGCTCCTAGGACCTGGTGTCAACTACTCCGGGTGT isotig125 580 Q I T W A K F C K E N M A G K G F S F W isotig125 1740 CAGATCACATGGGCTAAATTTTGCAAAGAAAACATGGCTGGCAAGGGCTTCTCCTTCTGG isotig125 600 V W L D N I I D L V K K Y I L A L W N E isotig125 1800 GTGTGGCTAGACAATATCATTGACCTTGTGAAAAAGTATATCTTGGCCCTCTGGAATGAA isotig125 620 G Y I M G F I S K E R E R A I L S T K P isotig125 1860 GGGTACATCATGGGCTTCATTAGCAAGGAGCGGGAGCGGGCGATCCTGAGCACGAAACCC isotig125 640 P G T F L L R F S E S S K E G G V T F T isotig125 1920 CCGGGCACCTTCCTGCTGAGATTCAGCGAGAGCAGCAAAGAAGGAGGGGTCACTTTCACT isotig125 660 W V E K D I S G K T Q I Q S V E P Y T K isotig125 1980 TGGGTGGAAAAGGACATCAGTGGCAAGACCCAGATCCAGTCTGTAGAGCCGTACACCAAG isotig125 680 Q Q L N N M S F A E I I M G Y K I M D A isotig125 2040 CAGCAGCTGAACAACATGTCCTTTGCTGAAATCATCATGGGCTACAAGATCATGGATGCC isotig125 700 T N I L V S P L V Y L Y P D I P K E E A isotig125 2100 ACCAACATCCTGGTGTCCCCATTGGTCTACCTCTACCCTGACATTCCCAAGGAGGAGGCG isotig125 720 F G K Y C R P E S Q E H P E A D P G S A isotig125 2160 TTCGGGAAGTACTGTCGACCAGAGAGCCAGGAGCATCCTGAAGCTGACCCCGGTAGTGCC isotig125 740 A P Y L K T K F I C V T P T T C S N T I isotig125 2220 GCCCCTTACCTGAAGACCAAGTTCATCTGTGTGACACCAACGACCTGCAGCAATACCATT isotig125 760 D L P M S P P H F R F I D A V W K R R C isotig125 2280 GACCTGCCGATGTCCCCCCCGCACTTTAGATTCATTGATGCAGTTTGGAAACGGAGGTGC isotig125 780 A L G R R A V V T H V H G S D F G V R Y isotig125 2340 GCCCTCGGCAGGAGGGCAGTTGTCACTCACGTTCATGGATCTGACTTCGGAGTGCGCTAC isotig125 800 L P H V R S 806 isotig125 2400 CTCCCCCATGTGAGGAGC 2418 """, ) protein_record = protein_alignment.sequences[9] nucleotide_record = nucleotide_records[protein_record.id] self.assertEqual(nucleotide_record.id, protein_record.id) nucleotide_record = nucleotide_record.upper() alignments = aligner.align(protein_record, nucleotide_record) self.assertEqual(len(alignments), 1) alignment = next(alignments) codon_alignments.append(alignment) self.assertTrue( np.array_equal(alignment.coordinates, np.array([[0, 796], [0, 2388]])) ) self.assertEqual( str(alignment), """\ isotig125 0 A R R G Q A A L G S P A A R T W S Q R S isotig125 0 GCTAGGAGAGGCCAGGCGGCCCTCGGGAGCCCAGCTGCTCGCACCTGGAGCCAGCGCAGC isotig125 20 P A S R A S A R E T V T P P D C G R M A isotig125 60 CCGGCCAGTCGGGCCTCAGCCCGGGAGACAGTTACGCCCCCTGATTGCGGCAGGATGGCC isotig125 40 Q W N Q L Q Q L D T R Y L E Q L H Q L Y isotig125 120 CAGTGGAACCAGCTGCAGCAGCTGGACACTCGGTACCTGGAGCAGCTGCACCAGCTGTAC isotig125 60 S D S F P M E L R Q F L A P W I E S Q D isotig125 180 AGCGACAGCTTCCCCATGGAGCTGCGGCAGTTCCTGGCACCTTGGATTGAGAGTCAAGAT isotig125 80 W A Y A A S K E S H A T L V F H N L L G isotig125 240 TGGGCATATGCAGCCAGCAAAGAGTCACATGCCACACTGGTGTTTCATAATCTCTTGGGT isotig125 100 E I D Q Q Y S R F L Q E S N V L Y Q H N isotig125 300 GAGATTGACCAGCAGTACAGCCGATTCCTGCAAGAGTCCAACGTCCTCTATCAGCACAAC isotig125 120 L R R I K Q F L Q S R Y L E K P M E I A isotig125 360 CTTCGGAGGATCAAGCAGTTCCTACAGAGCAGGTATCTTGAGAAGCCGATGGAAATCGCC isotig125 140 R I V A R C L W E E S R L L Q T A A T A isotig125 420 CGCATCGTGGCCCGATGCCTGTGGGAAGAGTCTCGCCTCCTCCAGACGGCAGCCACTGCA isotig125 160 A Q Q G G Q A N H P T A A V V T E K Q Q isotig125 480 GCCCAGCAAGGAGGCCAGGCCAACCACCCAACAGCTGCTGTGGTGACGGAGAAACAGCAG isotig125 180 M L E Q H L Q D V R K R V Q D L E Q K M isotig125 540 ATGCTGGAGCAGCATCTTCAGGATGTCCGGAAACGTGTGCAGGATCTAGAACAGAAAATG isotig125 200 K V V E N L Q D D F D F N Y K T L K S Q isotig125 600 AAAGTGGTAGAGAATCTCCAGGATGACTTTGATTTCAACTATAAAACCCTCAAGAGTCAA isotig125 220 G D M Q D L N G N N Q S V T R Q K M Q Q isotig125 660 GGAGACATGCAGGATCTGAATGGAAACAACCAGTCTGTGACCAGGCAGAAGATGCAGCAG isotig125 240 L E Q M L T A L D Q M R R S I V S E L A isotig125 720 CTGGAACAGATGCTCACGGCGCTGGACCAGATGCGGAGAAGCATTGTGAGTGAGCTGGCG isotig125 260 G L L S A M E Y V Q K T L T D E E L A D isotig125 780 GGGCTTTTGTCGGCAATGGAGTACGTGCAGAAAACACTCACAGACGAGGAGCTGGCTGAC isotig125 280 W K R R Q Q I A C I G G P P N I C L D R isotig125 840 TGGAAGAGGCGGCAGCAGATCGCGTGCATTGGAGGCCCTCCCAACATCTGCCTGGATCGC isotig125 300 L E N W I T S L A E S Q L Q T R Q Q I K isotig125 900 CTGGAAAACTGGATAACTTCGTTAGCAGAATCTCAACTTCAGACCCGCCAACAAATTAAG isotig125 320 K L E E L Q Q K V S Y K G D P I V Q H R isotig125 960 AAACTGGAGGAGCTACAGCAGAAGGTGTCCTACAAGGGGGACCCCATTGTGCAGCACCGG isotig125 340 P M L E E R I V E L F R N L M K S A F V isotig125 1020 CCGATGCTGGAGGAGCGGATCGTGGAGCTGTTCAGAAACTTGATGAAGAGTGCCTTCGTG isotig125 360 V E R Q P C M P M H P D R P L V I K T G isotig125 1080 GTGGAGCGACAGCCCTGCATGCCGATGCACCCCGACCGGCCCTTGGTCATCAAGACTGGT isotig125 380 V Q F T T K V R L L V K F P E L N Y Q L isotig125 1140 GTCCAGTTCACTACTAAAGTCAGGTTGTTGGTCAAGTTTCCCGAGTTGAATTATCAGCTT isotig125 400 K I K V C I D K D S G D V A A L R G S R isotig125 1200 AAAATTAAAGTGTGCATTGACAAAGATTCTGGGGACGTTGCTGCTCTCAGAGGATCTCGG isotig125 420 K F N I L G T N T K V M N M E E S N N G isotig125 1260 AAATTTAACATTCTGGGCACAAACACGAAGGTGATGAACATGGAAGAATCCAACAACGGC isotig125 440 S L S A E F K H L T L R E Q R C G N G G isotig125 1320 AGCCTGTCTGCGGAGTTCAAGCACTTGACCCTGAGGGAGCAGAGATGTGGGAATGGAGGC isotig125 460 R A N C D A S L I V T E E L H L I T F E isotig125 1380 CGTGCCAATTGTGATGCCTCCTTGATTGTGACCGAGGAGCTGCATCTGATCACCTTCGAG isotig125 480 T E V Y H Q G L K I D L E T H S L P V V isotig125 1440 ACTGAGGTGTACCACCAAGGCCTCAAGATTGACCTGGAGACCCATTCTTTGCCAGTTGTG isotig125 500 V I S N I C Q M P N A W A S I L W Y N M isotig125 1500 GTGATCTCCAACATCTGTCAGATGCCAAATGCCTGGGCATCCATCCTGTGGTATAACATG isotig125 520 L T N N P K N V N F F T K P P I G T W D isotig125 1560 CTGACCAACAACCCCAAGAACGTGAACTTCTTCACCAAGCCACCAATCGGAACCTGGGAC isotig125 540 Q V A E V L S W Q F S S T T K R G L S I isotig125 1620 CAGGTGGCCGAGGTGCTCAGCTGGCAGTTCTCATCCACCACAAAGCGAGGGCTGAGCATC isotig125 560 E Q L T T L A E K L L G P G V N Y S G C isotig125 1680 GAGCAGCTGACTACGCTGGCCGAGAAGCTCCTAGGACCTGGTGTCAACTACTCCGGGTGT isotig125 580 Q I T W A K F C K E N M A G K G F S F W isotig125 1740 CAGATCACATGGGCTAAATTTTGCAAAGAAAACATGGCTGGCAAGGGCTTCTCCTTCTGG isotig125 600 V W L D N I I D L V K K Y I L A L W N E isotig125 1800 GTGTGGCTAGACAATATCATTGACCTTGTGAAAAAGTATATCTTGGCCCTCTGGAATGAA isotig125 620 G Y I M G F I S K E R E R A I L S T K P isotig125 1860 GGGTACATCATGGGCTTCATTAGCAAGGAGCGGGAGCGGGCGATCCTGAGCACGAAACCC isotig125 640 P G T F L L R F S E S S K E G G V T F T isotig125 1920 CCGGGCACCTTCCTGCTGAGATTCAGCGAGAGCAGCAAAGAAGGAGGGGTCACTTTCACT isotig125 660 W V E K D I S G K T Q I Q S V E P Y T K isotig125 1980 TGGGTGGAAAAGGACATCAGTGGCAAGACCCAGATCCAGTCTGTAGAGCCGTACACCAAG isotig125 680 Q Q L N N M S F A E I I M G Y K I M D A isotig125 2040 CAGCAGCTGAACAACATGTCCTTTGCTGAAATCATCATGGGCTACAAGATCATGGATGCC isotig125 700 T N I L V S P L V Y L Y P D I P K E E A isotig125 2100 ACCAACATCCTGGTGTCCCCATTGGTCTACCTCTACCCTGACATTCCCAAGGAGGAGGCG isotig125 720 F G K Y C R P E S Q E H P E A D P G S C isotig125 2160 TTCGGGAAGTACTGTCGACCAGAGAGCCAGGAGCATCCTGAAGCTGACCCCGGTAGTTGT isotig125 740 F S M V L V S L L G K G G Q C R S L E E isotig125 2220 TTTTCCATGGTTCTGGTTTCGCTGTTAGGGAAAGGGGGACAGTGCAGGTCCTTGGAGGAG isotig125 760 R Q G H D R V S G G E S C Y G R A V Y W isotig125 2280 AGACAAGGACATGACCGGGTGTCTGGTGGTGAGTCCTGCTATGGAAGAGCTGTTTATTGG isotig125 780 V L Q G D R D S R E D Q N Q A S 796 isotig125 2340 GTACTTCAGGGTGACCGGGATTCAAGAGAAGACCAGAATCAGGCCTCA 2388 """, ) alignment = protein_alignment.mapall(codon_alignments) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 36, 36, 63, 63, 213, 222, 240, 240, 330, 330, 330, 405, 405, 438, 450, 579, 579, 729, 729, 837, 837, 897, 912, 975, 987, 1020, 1026, 1074, 1077, 1107, 1107, 1116, 1119, 1182, 1188, 1302, 1302, 1392, 1398, 1455, 1458, 1470, 1695, 1695, 1824, 1824, 1887, 1887, 1896, 1902, 1956, 1980, 2022, 2025, 2043, 2046, 2061, 2106, 2187, 2220, 2232, 2253, 2271, 2331, 2334, 2352, 2364, 2373, 2382, 2424, 2463, 2484, 2517, 2541], [ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 36, 36, 63, 63, 213, 222, 240, 240, 330, 330, 330, 405, 405, 438, 450, 579, 579, 729, 729, 837, 837, 897, 912, 975, 987, 1020, 1026, 1074, 1077, 1107, 1107, 1116, 1119, 1182, 1188, 1302, 1302, 1392, 1398, 1455, 1458, 1470, 1695, 1695, 1824, 1824, 1887, 1887, 1896, 1902, 1956, 1980, 2022, 2025, 2043, 2046, 2061, 2106, 2187, 2220, 2232, 2253, 2271, 2331, 2334, 2352, 2364, 2373, 2382, 2424, 2463, 2484, 2517, 2541], [ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 36, 36, 63, 63, 213, 222, 240, 240, 330, 330, 330, 405, 405, 438, 450, 579, 579, 729, 729, 837, 837, 897, 912, 975, 987, 1020, 1026, 1074, 1077, 1107, 1107, 1116, 1119, 1182, 1188, 1302, 1302, 1392, 1398, 1455, 1458, 1470, 1695, 1695, 1824, 1824, 1887, 1887, 1896, 1902, 1956, 1980, 2022, 2025, 2043, 2046, 2061, 2106, 2187, 2220, 2232, 2253, 2271, 2331, 2334, 2352, 2364, 2373, 2382, 2424, 2463, 2484, 2517, 2541], [ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 36, 36, 63, 63, 213, 222, 240, 240, 330, 330, 330, 405, 405, 438, 450, 579, 579, 729, 729, 837, 837, 897, 912, 975, 987, 1020, 1026, 1074, 1077, 1107, 1107, 1116, 1119, 1182, 1188, 1302, 1302, 1392, 1398, 1455, 1458, 1470, 1695, 1695, 1824, 1824, 1887, 1887, 1896, 1902, 1956, 1980, 2022, 2025, 2043, 2046, 2061, 2106, 2187, 2220, 2232, 2253, 2271, 2331, 2334, 2352, 2364, 2373, 2382, 2424, 2463, 2484, 2517, 2541], [ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 75, 75, 108, 120, 249, 249, 399, 399, 507, 507, 567, 582, 645, 657, 690, 696, 744, 747, 777, 777, 786, 789, 852, 858, 972, 972, 1062, 1068, 1125, 1128, 1140, 1365, 1365, 1494, 1494, 1557, 1557, 1566, 1572, 1626, 1650, 1692, 1695, 1713, 1716, 1731, 1776, 1857, 1890, 1902, 1923, 1941, 2001, 2004, 2022, 2034, 2043, 2052, 2094, 2133, 2154, 2187, 2211], [ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 75, 75, 108, 120, 249, 249, 399, 399, 507, 507, 567, 582, 645, 657, 690, 696, 744, 747, 777, 777, 786, 789, 852, 858, 972, 972, 1062, 1068, 1125, 1128, 1140, 1365, 1365, 1494, 1494, 1557, 1557, 1566, 1572, 1626, 1650, 1692, 1695, 1713, 1716, 1731, 1776, 1857, 1890, 1902, 1923, 1941, 2001, 2004, 2022, 2034, 2043, 2052, 2094, 2133, 2154, 2187, 2211], [ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 75, 75, 108, 120, 249, 249, 399, 399, 507, 507, 567, 582, 645, 657, 690, 696, 744, 747, 777, 777, 786, 789, 852, 858, 972, 972, 1062, 1068, 1125, 1128, 1140, 1365, 1365, 1494, 1494, 1557, 1557, 1566, 1572, 1626, 1650, 1692, 1695, 1713, 1716, 1731, 1776, 1857, 1890, 1902, 1923, 1941, 2001, 2004, 2022, 2034, 2043, 2052, 2094, 2133, 2154, 2187, 2211], [ 0, 12, 21, 357, 378, 417, 444, 474, 516, 549, 564, 570, 606, 615, 642, 645, 795, 795, 813, 828, 918, 918, 999, 1074, 1077, 1110, 1110, 1239, 1251, 1401, 1428, 1536, 1560, 1620, 1620, 1683, 1683, 1716, 1716, 1764, 1764, 1794, 1809, 1818, 1818, 1881, 1881, 1995, 2001, 2091, 2091, 2148, 2148, 2148, 2373, 2373, 2502, 2532, 2595, 2619, 2628, 2628, 2682, 2706, 2706, 2709, 2727, 2727, 2727, 2772, 2772, 2805, 2817, 2817, 2835, 2895, 2898, 2916, 2928, 2937, 2946, 2946, 2985, 3006, 3039, 3063], [ 0, 0, 9, 9, 30, 30, 57, 57, 99, 99, 114, 114, 150, 159, 186, 189, 339, 339, 357, 372, 462, 465, 546, 621, 624, 657, 669, 798, 810, 960, 987, 1095, 1119, 1179, 1179, 1242, 1254, 1287, 1287, 1335, 1335, 1365, 1380, 1389, 1392, 1455, 1455, 1569, 1575, 1665, 1665, 1722, 1725, 1725, 1950, 1953, 2082, 2112, 2175, 2175, 2184, 2184, 2184, 2208, 2208, 2208, 2226, 2226, 2226, 2271, 2271, 2304, 2304, 2304, 2304, 2304, 2307, 2325, 2337, 2346, 2346, 2346, 2385, 2385, 2418, 2418], [ 0, 0, 9, 9, 30, 30, 57, 57, 99, 99, 114, 114, 150, 159, 186, 189, 339, 339, 357, 372, 462, 465, 546, 621, 624, 657, 669, 798, 810, 960, 987, 1095, 1119, 1179, 1179, 1242, 1254, 1287, 1287, 1335, 1335, 1365, 1380, 1389, 1392, 1455, 1455, 1569, 1575, 1665, 1665, 1722, 1725, 1725, 1950, 1953, 2082, 2112, 2175, 2175, 2184, 2184, 2184, 2208, 2208, 2208, 2226, 2229, 2229, 2229, 2229, 2262, 2274, 2274, 2274, 2334, 2337, 2337, 2349, 2349, 2349, 2349, 2388, 2388, 2388, 2388]]) # fmt: on ) ) self.assertEqual( format(alignment, "clustal"), """\ ENSG00000166888:ENST0000030013 -------------------------------------------------- ENSG00000166888:ENST0000054387 -------------------------------------------------- ENSG00000166888:ENST0000055615 -------------------------------------------------- ENSG00000166888:ENST0000045407 -------------------------------------------------- ENSG00000166888:ENST0000053891 -------------------------------------------------- ENSG00000166888:ENST0000053721 -------------------------------------------------- ENSG00000166888:ENST0000053520 -------------------------------------------------- isotig46679 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA isotig12565 ------------GCTAGGAGA----------------------------- isotig12566 ------------GCTAGGAGA----------------------------- ENSG00000166888:ENST0000030013 -------------------------------------------------- ENSG00000166888:ENST0000054387 -------------------------------------------------- ENSG00000166888:ENST0000055615 -------------------------------------------------- ENSG00000166888:ENST0000045407 -------------------------------------------------- ENSG00000166888:ENST0000053891 -------------------------------------------------- ENSG00000166888:ENST0000053721 -------------------------------------------------- ENSG00000166888:ENST0000053520 -------------------------------------------------- isotig46679 AAAAAAAAAAGAGTTGGCCCAAACCCCTGAGGGAGGCTGTCCTCGGCAGG isotig12565 -------------------------------------------------- isotig12566 -------------------------------------------------- ENSG00000166888:ENST0000030013 -------------------------------------------------- ENSG00000166888:ENST0000054387 -------------------------------------------------- ENSG00000166888:ENST0000055615 -------------------------------------------------- ENSG00000166888:ENST0000045407 -------------------------------------------------- ENSG00000166888:ENST0000053891 -------------------------------------------------- ENSG00000166888:ENST0000053721 -------------------------------------------------- ENSG00000166888:ENST0000053520 -------------------------------------------------- isotig46679 AGAGCAGACCTGAGGGAGGTTGGTGTGCCGGTCCTGGTTGTCCAGCCCTC isotig12565 -------------------------------------------------- isotig12566 -------------------------------------------------- ENSG00000166888:ENST0000030013 -------------------------------------------------- ENSG00000166888:ENST0000054387 -------------------------------------------------- ENSG00000166888:ENST0000055615 -------------------------------------------------- ENSG00000166888:ENST0000045407 -------------------------------------------------- ENSG00000166888:ENST0000053891 -------------------------------------------------- ENSG00000166888:ENST0000053721 -------------------------------------------------- ENSG00000166888:ENST0000053520 -------------------------------------------------- isotig46679 CCGTCCCATCCCAGGGCTGGCTCACCAGAAAAAAGTACAGGCATCCCAGG isotig12565 -------------------------------------------------- isotig12566 -------------------------------------------------- ENSG00000166888:ENST0000030013 -------------------------------------------------- ENSG00000166888:ENST0000054387 -------------------------------------------------- ENSG00000166888:ENST0000055615 -------------------------------------------------- ENSG00000166888:ENST0000045407 -------------------------------------------------- ENSG00000166888:ENST0000053891 -------------------------------------------------- ENSG00000166888:ENST0000053721 -------------------------------------------------- ENSG00000166888:ENST0000053520 -------------------------------------------------- isotig46679 CCCTCTGGGGCGGGAGCAGAGGGTCTCCTCTTGTCCGGGGGAAGACAAAA isotig12565 -------------------------------------------------- isotig12566 -------------------------------------------------- ENSG00000166888:ENST0000030013 -------------------------------------------------- ENSG00000166888:ENST0000054387 -------------------------------------------------- ENSG00000166888:ENST0000055615 -------------------------------------------------- ENSG00000166888:ENST0000045407 -------------------------------------------------- ENSG00000166888:ENST0000053891 -------------------------------------------------- ENSG00000166888:ENST0000053721 -------------------------------------------------- ENSG00000166888:ENST0000053520 -------------------------------------------------- isotig46679 ACAAAAACAAAAAACGAGTGTGTAGCCCTCACTGGAAGTCTTCTGGTGCT isotig12565 -------------------------------------------------- isotig12566 -------------------------------------------------- ENSG00000166888:ENST0000030013 -------------------------------------------------- ENSG00000166888:ENST0000054387 -------------------------------------------------- ENSG00000166888:ENST0000055615 -------------------------------------------------- ENSG00000166888:ENST0000045407 -------------------------------------------------- ENSG00000166888:ENST0000053891 -------------------------------------------------- ENSG00000166888:ENST0000053721 -------------------------------------------------- ENSG00000166888:ENST0000053520 -------------------------------------------------- isotig46679 CTGGGGCCGTTTGCACTTGGGAGCCTGGCTTCTGGGCATGGTGGCCGGGC isotig12565 -------------------------------------------------- isotig12566 -------------------------------------------------- ENSG00000166888:ENST0000030013 -------------------------------------------------- ENSG00000166888:ENST0000054387 -------------------------------------------------- ENSG00000166888:ENST0000055615 -------------------------------------------------- ENSG00000166888:ENST0000045407 -------------------------------------------------- ENSG00000166888:ENST0000053891 -------------------------------------------------- ENSG00000166888:ENST0000053721 -------------------------------------------------- ENSG00000166888:ENST0000053520 -------------------------------------------------- isotig46679 TCCGCCGGGGGCTTCAGCCCTCGGCAAAGCGTTTCTAGAACAGAGTGGGT isotig12565 -------GGCCAGGCGGCCCTCGGGAGC---------------------- isotig12566 -------GGCCAGGCGGCCCTCGGGAGC---------------------- ENSG00000166888:ENST0000030013 -------------------------------------------------- ENSG00000166888:ENST0000054387 -------------------------------------------------- ENSG00000166888:ENST0000055615 -------------------------------------------------- ENSG00000166888:ENST0000045407 -------------------------------------------------- ENSG00000166888:ENST0000053891 -------------------------------------------------- ENSG00000166888:ENST0000053721 -------------------------------------------------- ENSG00000166888:ENST0000053520 -------------------------------------------------- isotig46679 GGGAGCCGACTGAAGTCCCAGAACCGCGAACACTGACGCACAGGAAAGCC isotig12565 -----------------CCAGCTGCTCGCACCTGGAGCCAGCGC------ isotig12566 -----------------CCAGCTGCTCGCACCTGGAGCCAGCGC------ ENSG00000166888:ENST0000030013 -------------------------------------------------- ENSG00000166888:ENST0000054387 -------------------------------------------------- ENSG00000166888:ENST0000055615 -------------------------------------------------- ENSG00000166888:ENST0000045407 -------------------------------------------------- ENSG00000166888:ENST0000053891 -------------------------------------------------- ENSG00000166888:ENST0000053721 -------------------------------------------------- ENSG00000166888:ENST0000053520 -------------------------------------------------- isotig46679 TCGAGTGGGTGGAGAAATGCAAATCCCCCAGTGGCATGGCCTCAGCCGCT isotig12565 ------------------------AGCCCGGCCAGTCGGGCCTCAGCCCG isotig12566 ------------------------AGCCCGGCCAGTCGGGCCTCAGCCCG ENSG00000166888:ENST0000030013 -------------------------------------------------- ENSG00000166888:ENST0000054387 -------------------------------------------------- ENSG00000166888:ENST0000055615 -------------------------------------------------- ENSG00000166888:ENST0000045407 -------------------------------------------------- ENSG00000166888:ENST0000053891 -------------------------------------------------- ENSG00000166888:ENST0000053721 -------------------------------------------------- ENSG00000166888:ENST0000053520 -------------------------------------------------- isotig46679 GCGGACCCTGACGGCCGATTCTGACTTCGGACTTGAGCGGGACCAGCACC isotig12565 GGAGACAGTTACGCCC---------------------------------C isotig12566 GGAGACAGTTACGCCC---------------------------------C ENSG00000166888:ENST0000030013 --------------------ATGTCTCTGTGGGGTCTGGTCTCCAAGATG ENSG00000166888:ENST0000054387 --------------------ATGTCTCTGTGGGGTCTGGTCTCCAAGATG ENSG00000166888:ENST0000055615 --------------------ATGTCTCTGTGGGGTCTGGTCTCCAAGATG ENSG00000166888:ENST0000045407 --------------------ATGTCTCTGTGGGGTCTGGTCTCCAAGATG ENSG00000166888:ENST0000053891 -------------------------------------------------- ENSG00000166888:ENST0000053721 -------------------------------------------------- ENSG00000166888:ENST0000053520 -------------------------------------------------- isotig46679 CGGACCCAGGGCGAGCCAGCATGTCTCAGTGGAATCAAGTCCAACAGTTA isotig12565 CTGATTGCGGCAGG------ATGGCCCAGTGGAACCAGCTGCAGCAGCTG isotig12566 CTGATTGCGGCAGG------ATGGCCCAGTGGAACCAGCTGCAGCAGCTG ENSG00000166888:ENST0000030013 CCCCCA---------GAAAAAGTGCAGCGGCTCTATGTCGAC---TTTCC ENSG00000166888:ENST0000054387 CCCCCA---------GAAAAAGTGCAGCGGCTCTATGTCGAC---TTTCC ENSG00000166888:ENST0000055615 CCCCCA---------GAAAAAGTGCAGCGGCTCTATGTCGAC---TTTCC ENSG00000166888:ENST0000045407 CCCCCA---------GAAAAAGTGCAGCGGCTCTATGTCGAC---TTTCC ENSG00000166888:ENST0000053891 -------------------------------------------------- ENSG00000166888:ENST0000053721 -------------------------------------------------- ENSG00000166888:ENST0000053520 -------------------------------------------------- isotig46679 GAAATCAAGTTTTTGGAGCAAGTTGATCAGTTCTATGATGACAACTTTCC isotig12565 GACACTCGGTACCTGGAGCAGCTGCACCAGCTGTACAGCGACAGCTTCCC isotig12566 GACACTCGGTACCTGGAGCAGCTGCACCAGCTGTACAGCGACAGCTTCCC ENSG00000166888:ENST0000030013 CCAACACCTGCGGCATCTTCTGGGTGACTGGCTGGAGAGCCAGCCCTGGG ENSG00000166888:ENST0000054387 CCAACACCTGCGGCATCTTCTGGGTGACTGGCTGGAGAGCCAGCCCTGGG ENSG00000166888:ENST0000055615 CCAACACCTGCGGCATCTTCTGGGTGACTGGCTGGAGAGCCAGCCCTGGG ENSG00000166888:ENST0000045407 CCAACACCTGCGGCATCTTCTGGGTGACTGGCTGGAGAGCCAGCCCTGGG ENSG00000166888:ENST0000053891 -------------------------------------------------- ENSG00000166888:ENST0000053721 -------------------------------------------------- ENSG00000166888:ENST0000053520 -------------------------------------------------- isotig46679 CATGGAAATCCGACATCTGCTGGCCCAGTGGATTGAGCATCAAGACTGGG isotig12565 CATGGAGCTGCGGCAGTTCCTGGCACCTTGGATTGAGAGTCAAGATTGGG isotig12566 CATGGAGCTGCGGCAGTTCCTGGCACCTTGGATTGAGAGTCAAGATTGGG ENSG00000166888:ENST0000030013 AGTTCCTGGTCGGCTCCGACGCCTTCTGCTGCAACTTGGCTAGTGCCCTA ENSG00000166888:ENST0000054387 AGTTCCTGGTCGGCTCCGACGCCTTCTGCTGCAACTTGGCTAGTGCCCTA ENSG00000166888:ENST0000055615 AGTTCCTGGTCGGCTCCGACGCCTTCTGCTGCAACTTGGCTAGTGCCCTA ENSG00000166888:ENST0000045407 AGTTCCTGGTCGGCTCCGACGCCTTCTGCTGCAACTTGGCTAGTGCCCTA ENSG00000166888:ENST0000053891 -------------------------------------------------- ENSG00000166888:ENST0000053721 -------------------------------------------------- ENSG00000166888:ENST0000053520 -------------------------------------------------- isotig46679 AGGTGGCCTCTAACAATGAAACTATGGCAACAATTCTTCTTCAAAACTTA isotig12565 CATATGCAGCCAGCAAAGAGTCACATGCCACACTGGTGTTTCATAATCTC isotig12566 CATATGCAGCCAGCAAAGAGTCACATGCCACACTGGTGTTTCATAATCTC ENSG00000166888:ENST0000030013 CTTTCAGACACTGTCCAGCACCTTCAGGCCTCGGTGGGAGAGCAGGGGGA ENSG00000166888:ENST0000054387 CTTTCAGACACTGTCCAGCACCTTCAGGCCTCGGTGGGAGAGCAGGGGGA ENSG00000166888:ENST0000055615 CTTTCAGACACTGTCCAGCACCTTCAGGCCTCGGTGGGAGAGCAGGGGGA ENSG00000166888:ENST0000045407 CTTTCAGACACTGTCCAGCACCTTCAGGCCTCGGTGGGAGAGCAGGGGGA ENSG00000166888:ENST0000053891 -------------------------------------------------- ENSG00000166888:ENST0000053721 -------------------------------------------------- ENSG00000166888:ENST0000053520 -------------------------------------------------- isotig46679 TTAATACAATTGGATGAACAGTTAGGTCGTGTTTCCAAAGAGAAA----- isotig12565 TTGGGTGAGATTGACCAGCAGTACAGCCGATTCCTGCAAGAGTCC----- isotig12566 TTGGGTGAGATTGACCAGCAGTACAGCCGATTCCTGCAAGAGTCC----- ENSG00000166888:ENST0000030013 GGGGAGCACCATCTTGCAACAC---------------ATCAGCACCCTTG ENSG00000166888:ENST0000054387 GGGGAGCACCATCTTGCAACAC---------------ATCAGCACCCTTG ENSG00000166888:ENST0000055615 GGGGAGCACCATCTTGCAACAC---------------ATCAGCACCCTTG ENSG00000166888:ENST0000045407 GGGGAGCACCATCTTGCAACAC---------------ATCAGCACCCTTG ENSG00000166888:ENST0000053891 -------------------------------------------------- ENSG00000166888:ENST0000053721 -------------------------------------------------- ENSG00000166888:ENST0000053520 -------------------------------------------------- isotig46679 ----AACCTGCTATTGATCCACAATCTAAAGAGAATTAGAAAAGTACTTC isotig12565 ----AACGTCCTCTATCAGCACAACCTTCGGAGGATCAAGCAGTTCCTAC isotig12566 ----AACGTCCTCTATCAGCACAACCTTCGGAGGATCAAGCAGTTCCTAC ENSG00000166888:ENST0000030013 AGAGCATATATCAGAGGGACCCCCTGAAGCTGGTGGCCACTTTCAGACAA ENSG00000166888:ENST0000054387 AGAGCATATATCAGAGGGACCCCCTGAAGCTGGTGGCCACTTTCAGACAA ENSG00000166888:ENST0000055615 AGAGCATATATCAGAGGGACCCCCTGAAGCTGGTGGCCACTTTCAGACAA ENSG00000166888:ENST0000045407 AGAGCATATATCAGAGGGACCCCCTGAAGCTGGTGGCCACTTTCAGACAA ENSG00000166888:ENST0000053891 -------------------------------------------------- ENSG00000166888:ENST0000053721 -------------------------------------------------- ENSG00000166888:ENST0000053520 -------------------------------------------------- isotig46679 AGGGGAAGTTTCATGGAAATCCAATGCATGTAGCCGTGGTAATCTCAAAT isotig12565 AGAGCAGGTATCTTGAGAAGCCGATGGAAATCGCCCGCATCGTGGCCCGA isotig12566 AGAGCAGGTATCTTGAGAAGCCGATGGAAATCGCCCGCATCGTGGCCCGA ENSG00000166888:ENST0000030013 ATACTTCAAGGAGAGAAAAAAGCTGTT----------------------- ENSG00000166888:ENST0000054387 ATACTTCAAGGAGAGAAAAAAGCTGTT----------------------- ENSG00000166888:ENST0000055615 ATACTTCAAGGAGAGAAAAAAGCTGTT----------------------- ENSG00000166888:ENST0000045407 ATACTTCAAGGAGAGAAAAAAGCTGTT----------------------- ENSG00000166888:ENST0000053891 -------------------------------------------------- ENSG00000166888:ENST0000053721 -------------------------------------------------- ENSG00000166888:ENST0000053520 -------------------------------------------------- isotig46679 TGTTTAAGGGAAGAGAGGAGAATACTG---GCTGCAGCGAACATGCCTAT isotig12565 TGCCTGTGGGAAGAGTCTCGCCTCCTCCAGACGGCAGCCACTGCAGCCCA isotig12566 TGCCTGTGGGAAGAGTCTCGCCTCCTCCAGACGGCAGCCACTGCAGCCCA ENSG00000166888:ENST0000030013 -------------------------------------------------- ENSG00000166888:ENST0000054387 -------------------------------------------------- ENSG00000166888:ENST0000055615 -------------------------------------------------- ENSG00000166888:ENST0000045407 -------------------------------------------------- ENSG00000166888:ENST0000053891 -------------------------------------------------- ENSG00000166888:ENST0000053721 -------------------------------------------------- ENSG00000166888:ENST0000053520 -------------------------------------------------- isotig46679 CCAGGGACCTCTGGAGAAATCCTTACAAAGTTCGTCGGTTTCAGAAAGAC isotig12565 GCAAGGAGGCCAGGCCAACCACCCAACAGCTGCTGTGGTGACGGAGAAAC isotig12566 GCAAGGAGGCCAGGCCAACCACCCAACAGCTGCTGTGGTGACGGAGAAAC ENSG00000166888:ENST0000030013 -----------ATGGAACAGTTCCGCCACTTGCCAATGCCTTTCCACTGG ENSG00000166888:ENST0000054387 -----------ATGGAACAGTTCCGCCACTTGCCAATGCCTTTCCACTGG ENSG00000166888:ENST0000055615 -----------ATGGAACAGTTCCGCCACTTGCCAATGCCTTTCCACTGG ENSG00000166888:ENST0000045407 -----------ATGGAACAGTTCCGCCACTTGCCAATGCCTTTCCACTGG ENSG00000166888:ENST0000053891 -----------ATGGAACAGTTCCGCCACTTGCCAATGCCTTTCCACTGG ENSG00000166888:ENST0000053721 -----------ATGGAACAGTTCCGCCACTTGCCAATGCCTTTCCACTGG ENSG00000166888:ENST0000053520 -----------ATGGAACAGTTCCGCCACTTGCCAATGCCTTTCCACTGG isotig46679 AGAGAAATGTGGAACACAAAGTGGCTGCCATTAAAAACAGTGTGCAGATG isotig12565 AGCAGATGCTGGAGCAGCATCTTCAGGATGTCCGGAAACGTGTGCAGGAT isotig12566 AGCAGATGCTGGAGCAGCATCTTCAGGATGTCCGGAAACGTGTGCAGGAT ENSG00000166888:ENST0000030013 AAGCAGGAAGAACTCAAGTTTAAGACAGGCTTGCGG---AGGCTGCAGCA ENSG00000166888:ENST0000054387 AAGCAGGAAGAACTCAAGTTTAAGACAGGCTTGCGG---AGGCTGCAGCA ENSG00000166888:ENST0000055615 AAGCAGGAAGAACTCAAGTTTAAGACAGGCTTGCGG---AGGCTGCAGCA ENSG00000166888:ENST0000045407 AAGCAGGAAGAACTCAAGTTTAAGACAGGCTTGCGG---AGGCTGCAGCA ENSG00000166888:ENST0000053891 AAGCAGGAAGAACTCAAGTTTAAGACAGGCTTGCGG---AGGCTGCAGCA ENSG00000166888:ENST0000053721 AAGCAGGAAGAACTCAAGTTTAAGACAGGCTTGCGG---AGGCTGCAGCA ENSG00000166888:ENST0000053520 AAGCAGGAAGAACTCAAGTTTAAGACAGGCTTGCGG---AGGCTGCAGCA isotig46679 ACAGAACAAGACACCAAATACTTGGAAGATCTGCAAGATGAATTTGACTA isotig12565 CTAGAACAGAAAATGAAAGTGGTAGAGAATCTCCAGGATGACTTTGATTT isotig12566 CTAGAACAGAAAATGAAAGTGGTAGAGAATCTCCAGGATGACTTTGATTT ENSG00000166888:ENST0000030013 CCGAGTAGGGGAGATCCACCTTCTCCGAGAAGCCCTGCAGAAGGGGGCTG ENSG00000166888:ENST0000054387 CCGAGTAGGGGAGATCCACCTTCTCCGAGAAGCCCTGCAGAAGGGGGCTG ENSG00000166888:ENST0000055615 CCGAGTAGGGGAGATCCACCTTCTCCGAGAAGCCCTGCAGAAGGGGGCTG ENSG00000166888:ENST0000045407 CCGAGTAGGGGAGATCCACCTTCTCCGAGAAGCCCTGCAGAAGGGGGCTG ENSG00000166888:ENST0000053891 CCGAGTAGGGGAGATCCACCTTCTCCGAGAAGCCCTGCAGAAGGGGGCTG ENSG00000166888:ENST0000053721 CCGAGTAGGGGAGATCCACCTTCTCCGAGAAGCCCTGCAGAAGGGGGCTG ENSG00000166888:ENST0000053520 CCGAGTAGGGGAGATCCACCTTCTCCGAGAAGCCCTGCAGAAGGGGGCTG isotig46679 CAGGTATAAAACAATTCAGACA------------ATGGACCAGGGTGACA isotig12565 CAACTATAAAACCCTCAAGAGTCAAGGAGACATGCAGGATCTGAATGGAA isotig12566 CAACTATAAAACCCTCAAGAGTCAAGGAGACATGCAGGATCTGAATGGAA ENSG00000166888:ENST0000030013 AGGCTGGCCAAGTGTCTCTGCACAGCTTGATAGAAACTCCTGCTAATGGG ENSG00000166888:ENST0000054387 AGGCTGGCCAAGTGTCTCTGCACAGCTTGATAGAAACTCCTGCTAATGGG ENSG00000166888:ENST0000055615 AGGCTGGCCAAGTGTCTCTGCACAGCTTGATAGAAACTCCTGCTAATGGG ENSG00000166888:ENST0000045407 AGGCTGGCCAAGTGTCTCTGCACAGCTTGATAGAAACTCCTGCTAATGGG ENSG00000166888:ENST0000053891 AGGCTGGCCAAGTGTCTCTGCACAGCTTGATAGAAACTCCTGCTAATGGG ENSG00000166888:ENST0000053721 AGGCTGGCCAAGTGTCTCTGCACAGCTTGATAGAAACTCCTGCTAATGGG ENSG00000166888:ENST0000053520 AGGCTGGCCAAGTGTCTCTGCACAGCTTGATAGAAACTCCTGCTAATGGG isotig46679 AGAATAGCATCCTAATGAACCAGGAGGTTTTGACACTCCAAGAAATGCTT isotig12565 ACAACCAGTCTGTGACCAGGCAGAAGATGCAGCAGCTGGAACAGATGCTC isotig12566 ACAACCAGTCTGTGACCAGGCAGAAGATGCAGCAGCTGGAACAGATGCTC ENSG00000166888:ENST0000030013 ACTGGGCCAAGTGAGGCCCTGGCCATGCTACTGCAGGAGACCACTGGAGA ENSG00000166888:ENST0000054387 ACTGGGCCAAGTGAGGCCCTGGCCATGCTACTGCAGGAGACCACTGGAGA ENSG00000166888:ENST0000055615 ACTGGGCCAAGTGAGGCCCTGGCCATGCTACTGCAGGAGACCACTGGAGA ENSG00000166888:ENST0000045407 ACTGGGCCAAGTGAGGCCCTGGCCATGCTACTGCAGGAGACCACTGGAGA ENSG00000166888:ENST0000053891 ACTGGGCCAAGTGAGGCCCTGGCCATGCTACTGCAGGAGACCACTGGAGA ENSG00000166888:ENST0000053721 ACTGGGCCAAGTGAGGCCCTGGCCATGCTACTGCAGGAGACCACTGGAGA ENSG00000166888:ENST0000053520 ACTGGGCCAAGTGAGGCCCTGGCCATGCTACTGCAGGAGACCACTGGAGA isotig46679 AATAGCCTGGACTTCAAGAGAAAGGAAGCACTCACTAAGATGACACAGAT isotig12565 ACGGCGCTGGACCAGATGCGGAGAAGCATTGTGAGTGAGCTGGCGGGGCT isotig12566 ACGGCGCTGGACCAGATGCGGAGAAGCATTGTGAGTGAGCTGGCGGGGCT ENSG00000166888:ENST0000030013 GCTAGAGGCAGCC------------AAAGCCCTAGTGCTGAAGAGGATCC ENSG00000166888:ENST0000054387 GCTAGAGGCAGCC------------AAAGCCCTAGTGCTGAAGAGGATCC ENSG00000166888:ENST0000055615 GCTAGAGGCAGCC------------AAAGCCCTAGTGCTGAAGAGGATCC ENSG00000166888:ENST0000045407 GCTAGAGGCAGCC------------AAAGCCCTAGTGCTGAAGAGGATCC ENSG00000166888:ENST0000053891 GCTAGAGGCAGCC------------AAAGCCCTAGTGCTGAAGAGGATCC ENSG00000166888:ENST0000053721 GCTAGAGGCAGCC------------AAAGCCCTAGTGCTGAAGAGGATCC ENSG00000166888:ENST0000053520 GCTAGAGGCAGCC------------AAAGCCCTAGTGCTGAAGAGGATCC isotig46679 AGTGAACGAGTCGGACCTGCTGATGAGCAGCATGCTCATAGAAGAGCTGC isotig12565 TTTGTCGGCAATGGAGTACGTGCAGAAAACACTCACAGACGAGGAGCTGG isotig12566 TTTGTCGGCAATGGAGTACGTGCAGAAAACACTCACAGACGAGGAGCTGG ENSG00000166888:ENST0000030013 AGATTTGGAAACGGCAGCAGCAGCTGGCAGGGAATGGCGCACCGTTTGAG ENSG00000166888:ENST0000054387 AGATTTGGAAACGGCAGCAGCAGCTGGCAGGGAATGGCGCACCGTTTGAG ENSG00000166888:ENST0000055615 AGATTTGGAAACGGCAGCAGCAGCTGGCAGGGAATGGCGCACCGTTTGAG ENSG00000166888:ENST0000045407 AGATTTGGAAACGGCAGCAGCAGCTGGCAGGGAATGGCGCACCGTTTGAG ENSG00000166888:ENST0000053891 AGATTTGGAAACGGCAGCAGCAGCTGGCAGGGAATGGCGCACCGTTTGAG ENSG00000166888:ENST0000053721 AGATTTGGAAACGGCAGCAGCAGCTGGCAGGGAATGGCGCACCGTTTGAG ENSG00000166888:ENST0000053520 AGATTTGGAAACGGCAGCAGCAGCTGGCAGGGAATGGCGCACCGTTTGAG isotig46679 AGGACTGGAAGAGGAGGCAGCAGATCGCCTGCATCGGTGGCCCACTCCAC isotig12565 CTGACTGGAAGAGGCGGCAGCAGATCGCGTGCATTGGAGGCCCTCCCAAC isotig12566 CTGACTGGAAGAGGCGGCAGCAGATCGCGTGCATTGGAGGCCCTCCCAAC ENSG00000166888:ENST0000030013 GAGAGCCTGGCCCCACTCCAGGAGAGGTGTGAAAGCCTGGTGGACATTTA ENSG00000166888:ENST0000054387 GAGAGCCTGGCCCCACTCCAGGAGAGGTGTGAAAGCCTGGTGGACATTTA ENSG00000166888:ENST0000055615 GAGAGCCTGGCCCCACTCCAGGAGAGGTGTGAAAGCCTGGTGGACATTTA ENSG00000166888:ENST0000045407 GAGAGCCTGGCCCCACTCCAGGAGAGGTGTGAAAGCCTGGTGGACATTTA ENSG00000166888:ENST0000053891 GAGAGCCTGGCCCCACTCCAGGAGAGGTGTGAAAGCCTGGTGGACATTTA ENSG00000166888:ENST0000053721 GAGAGCCTGGCCCCACTCCAGGAGAGGTGTGAAAGCCTGGTGGACATTTA ENSG00000166888:ENST0000053520 GAGAGCCTGGCCCCACTCCAGGAGAGGTGTGAAAGCCTGGTGGACATTTA isotig46679 AACGGGCTGGACCAGCTTCAGAACTGCTTTACCCTGTTGGCAGAAAGTCT isotig12565 ATCTGCCTGGATCGCCTGGAAAACTGGATAACTTCGTTAGCAGAATCTCA isotig12566 ATCTGCCTGGATCGCCTGGAAAACTGGATAACTTCGTTAGCAGAATCTCA ENSG00000166888:ENST0000030013 TTCCCAGCTACAGCAGGAGGTAGGG------------------------- ENSG00000166888:ENST0000054387 TTCCCAGCTACAGCAGGAGGTAGGG------------------------- ENSG00000166888:ENST0000055615 TTCCCAGCTACAGCAGGAGGTAGGG------------------------- ENSG00000166888:ENST0000045407 TTCCCAGCTACAGCAGGAGGTAGGG------------------------- ENSG00000166888:ENST0000053891 TTCCCAGCTACAGCAGGAGGTAGGG------------------------- ENSG00000166888:ENST0000053721 TTCCCAGCTACAGCAGGAGGTAGGG------------------------- ENSG00000166888:ENST0000053520 TTCCCAGCTACAGCAGGAGGTAGGG------------------------- isotig46679 TTTCCAACTCAGACGACAGCTGGAGAAATTAGAGGAGCAGTCTTCCAAGA isotig12565 ACTTCAGACCCGCCAACAAATTAAGAAACTGGAGGAGCTACAGCAGAAGG isotig12566 ACTTCAGACCCGCCAACAAATTAAGAAACTGGAGGAGCTACAGCAGAAGG ENSG00000166888:ENST0000030013 --GCGGCTGGTGGGGAGCTTGAGCCCAAGACCCGGGCATCGCTGACTGGC ENSG00000166888:ENST0000054387 --GCGGCTGGTGGGGAGCTTGAGCCCAAGACCCGGGCATCGCTGACTGGC ENSG00000166888:ENST0000055615 --GCGGCTGGTGGGGAGCTTGAGCCCAAGACCCGGGCATCGCTGACTGGC ENSG00000166888:ENST0000045407 --GCGGCTGGTGGGGAGCTTGAGCCCAAGACCCGGGCATCGCTGACTGGC ENSG00000166888:ENST0000053891 --GCGGCTGGTGGGGAGCTTGAGCCCAAGACCCGGGCATCGCTGACTGGC ENSG00000166888:ENST0000053721 --GCGGCTGGTGGGGAGCTTGAGCCCAAGACCCGGGCATCGCTGACTGGC ENSG00000166888:ENST0000053520 --GCGGCTGGTGGGGAGCTTGAGCCCAAGACCCGGGCATCGCTGACTGGC isotig46679 TGACTTACGAAGGAGACCCCATCCCCACGCAGAGAGCACACCTGCTGGAG isotig12565 TGTCCTACAAGGGGGACCCCATTGTGCAGCACCGGCCGATGCTGGAGGAG isotig12566 TGTCCTACAAGGGGGACCCCATTGTGCAGCACCGGCCGATGCTGGAGGAG ENSG00000166888:ENST0000030013 CGGCTGGATGAAGTCCTGAGAACCCTCGTCACCAGTTGCTTCCTGGTGGA ENSG00000166888:ENST0000054387 CGGCTGGATGAAGTCCTGAGAACCCTCGTCACCAGTTGCTTCCTGGTGGA ENSG00000166888:ENST0000055615 CGGCTGGATGAAGTCCTGAGAACCCTCGTCACCAGTTGCTTCCTGGTGGA ENSG00000166888:ENST0000045407 CGGCTGGATGAAGTCCTGAGAACCCTCGTCACCAGTTGCTTCCTGGTGGA ENSG00000166888:ENST0000053891 CGGCTGGATGAAGTCCTGAGAACCCTCGTCACCAGTTGCTTCCTGGTGGA ENSG00000166888:ENST0000053721 CGGCTGGATGAAGTCCTGAGAACCCTCGTCACCAGTTGCTTCCTGGTGGA ENSG00000166888:ENST0000053520 CGGCTGGATGAAGTCCTGAGAACCCTCGTCACCAGTTGCTTCCTGGTGGA isotig46679 AGAGCCACCTTCCTGATCTACAACCTTTTCAAGAACTCATTTGTGGTTGA isotig12565 CGGATCGTGGAGCTGTTCAGAAACTTGATGAAGAGTGCCTTCGTGGTGGA isotig12566 CGGATCGTGGAGCTGTTCAGAAACTTGATGAAGAGTGCCTTCGTGGTGGA ENSG00000166888:ENST0000030013 GAAGCAGCCC------------------------CCCCAGGTACTGAAGA ENSG00000166888:ENST0000054387 GAAGCAGCCC------------------------CCCCAGGTACTGAAGA ENSG00000166888:ENST0000055615 GAAGCAGCCC------------------------CCCCAGGTACTGAAGA ENSG00000166888:ENST0000045407 GAAGCAGCCC------------------------CCCCAGGTACTGAAGA ENSG00000166888:ENST0000053891 GAAGCAGCCC------------------------CCCCAGGTACTGAAGA ENSG00000166888:ENST0000053721 GAAGCAGCCC------------------------CCCCAGGTACTGAAGA ENSG00000166888:ENST0000053520 GAAGCAGCCC------------------------CCCCAGGTACTGAAGA isotig46679 GCGACAGCCCTGCATGCCAACACACCCTCAGAGGCCGCTGGTACTCAAAA isotig12565 GCGACAGCCCTGCATGCCGATGCACCCCGACCGGCCCTTGGTCATCAAGA isotig12566 GCGACAGCCCTGCATGCCGATGCACCCCGACCGGCCCTTGGTCATCAAGA ENSG00000166888:ENST0000030013 CTCAGACCAAGTTCCAGGCTGGAGTTCGATTCCTGTTGGGCTTGAGGTTC ENSG00000166888:ENST0000054387 CTCAGACCAAGTTCCAGGCTGGAGTTCGATTCCTGTTGGGCTTGAGGTTC ENSG00000166888:ENST0000055615 CTCAGACCAAGTTCCAGGCTGGAGTTCGATTCCTGTTGGGCTTGAGGTTC ENSG00000166888:ENST0000045407 CTCAGACCAAGTTCCAGGCTGGAGTTCGATTCCTGTTGGGCTTGAGGTTC ENSG00000166888:ENST0000053891 CTCAGACCAAGTTCCAGGCTGGAGTTCGATTCCTGTTGGGCTTGAGGTTC ENSG00000166888:ENST0000053721 CTCAGACCAAGTTCCAGGCTGGAGTTCGATTCCTGTTGGGCTTGAGGTTC ENSG00000166888:ENST0000053520 CTCAGACCAAGTTCCAGGCTGGAGTTCGATTCCTGTTGGGCTTGAGGTTC isotig46679 CCCTCATTCAGTTCACCGCGAAACTGAGACTACTAATAAAATTG------ isotig12565 CTGGTGTCCAGTTCACTACTAAAGTCAGGTTGTTGGTCAAGTTT------ isotig12566 CTGGTGTCCAGTTCACTACTAAAGTCAGGTTGTTGGTCAAGTTT------ ENSG00000166888:ENST0000030013 CTGGGGGCCCCAGCCAAGCCTCCGCTGGTCAGGGCCGACATGGTGACAGA ENSG00000166888:ENST0000054387 CTGGGGGCCCCAGCCAAGCCTCCGCTGGTCAGGGCCGACATGGTGACAGA ENSG00000166888:ENST0000055615 CTGGGGGCCCCAGCCAAGCCTCCGCTGGTCAGGGCCGACATGGTGACAGA ENSG00000166888:ENST0000045407 CTGGGGGCCCCAGCCAAGCCTCCGCTGGTCAGGGCCGACATGGTGACAGA ENSG00000166888:ENST0000053891 CTGGGGGCCCCAGCCAAGCCTCCGCTGGTCAGGGCCGACATGGTGACAGA ENSG00000166888:ENST0000053721 CTGGGGGCCCCAGCCAAGCCTCCGCTGGTCAGGGCCGACATGGTGACAGA ENSG00000166888:ENST0000053520 CTGGGGGCCCCAGCCAAGCCTCCGCTGGTCAGGGCCGACATGGTGACAGA isotig46679 ---------CCGGAACTCAACTATCAGGTGAAAGTAAAGGCATCGATCGA isotig12565 ---------CCCGAGTTGAATTATCAGCTTAAAATTAAAGTGTGCATTGA isotig12566 ---------CCCGAGTTGAATTATCAGCTTAAAATTAAAGTGTGCATTGA ENSG00000166888:ENST0000030013 GAAGCAGGCGCGGGAGCTGAGTGTGCCTCAGGGTCCTGGGGCTGGAGCAG ENSG00000166888:ENST0000054387 GAAGCAGGCGCGGGAGCTGAGTGTGCCTCAGGGTCCTGGGGCTGGAGCAG ENSG00000166888:ENST0000055615 GAAGCAGGCGCGGGAGCTGAGTGTGCCTCAGGGTCCTGGGGCTGGAGCAG ENSG00000166888:ENST0000045407 GAAGCAGGCGCGGGAGCTGAGTGTGCCTCAGGGTCCTGGGGCTGGAGCAG ENSG00000166888:ENST0000053891 GAAGCAGGCGCGGGAGCTGAGTGTGCCTCAGGGTCCTGGGGCTGGAGCAG ENSG00000166888:ENST0000053721 GAAGCAGGCGCGGGAGCTGAGTGTGCCTCAGGGTCCTGGGGCTGGAGCAG ENSG00000166888:ENST0000053520 GAAGCAGGCGCGGGAGCTGAGTGTGCCTCAGGGTCCTGGGGCTGGAGCAG isotig46679 CAAGAATGTTTCAACGCTAAGC------------AATAGAAGATTTGTGC isotig12565 CAAAGATTCTGGGGACGTTGCTGCTCTCAGAGGATCTCGGAAATTTAACA isotig12566 CAAAGATTCTGGGGACGTTGCTGCTCTCAGAGGATCTCGGAAATTTAACA ENSG00000166888:ENST0000030013 AAAGCACTGGAGAAATCATCAACAACACTGTGCCCTTGGAGAACAGCATT ENSG00000166888:ENST0000054387 AAAGCACTGGAGAAATCATCAACAACACTGTGCCCTTGGAGAACAGCATT ENSG00000166888:ENST0000055615 AAAGCACTGGAGAAATCATCAACAACACTGTGCCCTTGGAGAACAGCATT ENSG00000166888:ENST0000045407 AAAGCACTGGAGAAATCATCAACAACACTGTGCCCTTGGAGAACAGCATT ENSG00000166888:ENST0000053891 AAAGCACTGGAGAAATCATCAACAACACTGTGCCCTTGGAGAACAGCATT ENSG00000166888:ENST0000053721 AAAGCACTGGAGAAATCATCAACAACACTGTGCCCTTGGAGAACAGCATT ENSG00000166888:ENST0000053520 AAAGCACTGGAGAAATCATCAACAACACTGTGCCCTTGGAGAACAGCATT isotig46679 TTTGTGGAACTCAAGTC------AAAGCCATGTCCATCGAGGAATCCTCC isotig12565 TTCTGGGCACAAACACG------AAGGTGATGAACATGGAAGAATCCAAC isotig12566 TTCTGGGCACAAACACG------AAGGTGATGAACATGGAAGAATCCAAC ENSG00000166888:ENST0000030013 CCTGGGAACTGCTGCTCTGCCCTGTTCAAGAACCTGCTTCTCAAGAAGAT ENSG00000166888:ENST0000054387 CCTGGGAACTGCTGCTCTGCCCTGTTCAAGAACCTGCTTCTCAAGAAGAT ENSG00000166888:ENST0000055615 CCTGGGAACTGCTGCTCTGCCCTGTTCAAGAACCTGCTTCTCAAGAAGAT ENSG00000166888:ENST0000045407 CCTGGGAACTGCTGCTCTGCCCTGTTCAAGAACCTGCTTCTCAAGAAGAT ENSG00000166888:ENST0000053891 CCTGGGAACTGCTGCTCTGCCCTGTTCAAGAACCTGCTTCTCAAGAAGAT ENSG00000166888:ENST0000053721 CCTGGGAACTGCTGCTCTGCCCTGTTCAAGAACCTGCTTCTCAAGAAGAT ENSG00000166888:ENST0000053520 CCTGGGAACTGCTGCTCTGCCCTGTTCAAGAACCTGCTTCTCAAGAAGAT isotig46679 AATGGGAGCCTCTCAGTAGAA---TTTAGACATTTGCAACCGAAGGAAAT isotig12565 AACGGCAGCCTGTCTGCGGAG---TTCAAGCACTTGACCCTGAGGGAGCA isotig12566 AACGGCAGCCTGTCTGCGGAG---TTCAAGCACTTGACCCTGAGGGAGCA ENSG00000166888:ENST0000030013 CAAG---------------CGGTGTGAGCGGAAGGGCACTGAGTCTGTCA ENSG00000166888:ENST0000054387 CAAG---------------CGGTGTGAGCGGAAGGGCACTGAGTCTGTCA ENSG00000166888:ENST0000055615 CAAG---------------CGGTGTGAGCGGAAGGGCACTGAGTCTGTCA ENSG00000166888:ENST0000045407 CAAG---------------CGGTGTGAGCGGAAGGGCACTGAGTCTGTCA ENSG00000166888:ENST0000053891 CAAG---------------CGGTGTGAGCGGAAGGGCACTGAGTCTGTCA ENSG00000166888:ENST0000053721 CAAG---------------CGGTGTGAGCGGAAGGGCACTGAGTCTGTCA ENSG00000166888:ENST0000053520 CAAG---------------CGGTGTGAGCGGAAGGGCACTGAGTCTGTCA isotig46679 GAAATCCAGTGCCGGAAGTAAAGGAAAT---GAGGGCTGCCACATGGTGA isotig12565 GAGATGTGGGAATGGAGGCCGTGCCAATTGTGATGCCTCCTTGATTGTGA isotig12566 GAGATGTGGGAATGGAGGCCGTGCCAATTGTGATGCCTCCTTGATTGTGA ENSG00000166888:ENST0000030013 CAGAGGAGAAGTGCGCTGTGCTCTTCTCTGCCAGCTTCACACTTGGCCCC ENSG00000166888:ENST0000054387 CAGAGGAGAAGTGCGCTGTGCTCTTCTCTGCCAGCTTCACACTTGGCCCC ENSG00000166888:ENST0000055615 CAGAGGAGAAGTGCGCTGTGCTCTTCTCTGCCAGCTTCACACTTGGCCCC ENSG00000166888:ENST0000045407 CAGAGGAGAAGTGCGCTGTGCTCTTCTCTGCCAGCTTCACACTTGGCCCC ENSG00000166888:ENST0000053891 CAGAGGAGAAGTGCGCTGTGCTCTTCTCTGCCAGCTTCACACTTGGCCCC ENSG00000166888:ENST0000053721 CAGAGGAGAAGTGCGCTGTGCTCTTCTCTGCCAGCTTCACACTTGGCCCC ENSG00000166888:ENST0000053520 CAGAGGAGAAGTGCGCTGTGCTCTTCTCTGCCAGCTTCACACTTGGCCCC isotig46679 CGGAAGAGCTGCATTCCATAGCCTTTGAGACCCAGATCTGCCTC------ isotig12565 CCGAGGAGCTGCATCTGATCACCTTCGAGACTGAGGTGTACCAC------ isotig12566 CCGAGGAGCTGCATCTGATCACCTTCGAGACTGAGGTGTACCAC------ ENSG00000166888:ENST0000030013 GGCAAACTCCCCATCCAGCTCCAGGCCCTGTCTCTGCCCCTGGTGGTCAT ENSG00000166888:ENST0000054387 GGCAAACTCCCCATCCAGCTCCAGGCCCTGTCTCTGCCCCTGGTGGTCAT ENSG00000166888:ENST0000055615 GGCAAACTCCCCATCCAGCTCCAGGCCCTGTCTCTGCCCCTGGTGGTCAT ENSG00000166888:ENST0000045407 GGCAAACTCCCCATCCAGCTCCAGGCCCTGTCTCTGCCCCTGGTGGTCAT ENSG00000166888:ENST0000053891 GGCAAACTCCCCATCCAGCTCCAGGCCCTGTCTCTGCCCCTGGTGGTCAT ENSG00000166888:ENST0000053721 GGCAAACTCCCCATCCAGCTCCAGGCCCTGTCTCTGCCCCTGGTGGTCAT ENSG00000166888:ENST0000053520 GGCAAACTCCCCATCCAGCTCCAGGCCCTGTCTCTGCCCCTGGTGGTCAT isotig46679 TATGGCCTCACCATCGACTTGGAGACAAGCTCATTACCTGTGGTGATGAT isotig12565 CAAGGCCTCAAGATTGACCTGGAGACCCATTCTTTGCCAGTTGTGGTGAT isotig12566 CAAGGCCTCAAGATTGACCTGGAGACCCATTCTTTGCCAGTTGTGGTGAT ENSG00000166888:ENST0000030013 CGTCCATGGCAACCAAGACAACAATGCCAAAGCCACTATCCTGTGGGACA ENSG00000166888:ENST0000054387 CGTCCATGGCAACCAAGACAACAATGCCAAAGCCACTATCCTGTGGGACA ENSG00000166888:ENST0000055615 CGTCCATGGCAACCAAGACAACAATGCCAAAGCCACTATCCTGTGGGACA ENSG00000166888:ENST0000045407 CGTCCATGGCAACCAAGACAACAATGCCAAAGCCACTATCCTGTGGGACA ENSG00000166888:ENST0000053891 CGTCCATGGCAACCAAGACAACAATGCCAAAGCCACTATCCTGTGGGACA ENSG00000166888:ENST0000053721 CGTCCATGGCAACCAAGACAACAATGCCAAAGCCACTATCCTGTGGGACA ENSG00000166888:ENST0000053520 CGTCCATGGCAACCAAGACAACAATGCCAAAGCCACTATCCTGTGGGACA isotig46679 TTCTAATGTCAGCCAACTGCCTAATGCTTGGGCATCCATCATTTGGTACA isotig12565 CTCCAACATCTGTCAGATGCCAAATGCCTGGGCATCCATCCTGTGGTATA isotig12566 CTCCAACATCTGTCAGATGCCAAATGCCTGGGCATCCATCCTGTGGTATA ENSG00000166888:ENST0000030013 ATGCCTTCTCTGAG------ATGGACCGCGTGCCCTTTGTGGTGGCTGAG ENSG00000166888:ENST0000054387 ATGCCTTCTCTGAG------ATGGACCGCGTGCCCTTTGTGGTGGCTGAG ENSG00000166888:ENST0000055615 ATGCCTTCTCTGAG------ATGGACCGCGTGCCCTTTGTGGTGGCTGAG ENSG00000166888:ENST0000045407 ATGCCTTCTCTGAG------ATGGACCGCGTGCCCTTTGTGGTGGCTGAG ENSG00000166888:ENST0000053891 ATGCCTTCTCTGAG------ATGGACCGCGTGCCCTTTGTGGTGGCTGAG ENSG00000166888:ENST0000053721 ATGCCTTCTCTGAG------ATGGACCGCGTGCCCTTTGTGGTGGCTGAG ENSG00000166888:ENST0000053520 ATGCCTTCTCTGAG------ATGGACCGCGTGCCCTTTGTGGTGGCTGAG isotig46679 ATGTGTCAACCAACGATTGCCAGAACTTGGTTTTCTTTAATAATCCTCCG isotig12565 ACATGCTGACCAACAACCCCAAGAACGTGAACTTCTTCACCAAGCCACCA isotig12566 ACATGCTGACCAACAACCCCAAGAACGTGAACTTCTTCACCAAGCCACCA ENSG00000166888:ENST0000030013 CGGGTGCCCTGGGAGAAGATGTGTGAAACTCTGAACCTGAAGTTCATGGC ENSG00000166888:ENST0000054387 CGGGTGCCCTGGGAGAAGATGTGTGAAACTCTGAACCTGAAGTTCATGGC ENSG00000166888:ENST0000055615 CGGGTGCCCTGGGAGAAGATGTGTGAAACTCTGAACCTGAAGTTCATGGC ENSG00000166888:ENST0000045407 CGGGTGCCCTGGGAGAAGATGTGTGAAACTCTGAACCTGAAGTTCATGGC ENSG00000166888:ENST0000053891 CGGGTGCCCTGGGAGAAGATGTGTGAAACTCTGAACCTGAAGTTCATGGC ENSG00000166888:ENST0000053721 CGGGTGCCCTGGGAGAAGATGTGTGAAACTCTGAACCTGAAGTTCATGGC ENSG00000166888:ENST0000053520 CGGGTGCCCTGGGAGAAGATGTGTGAAACTCTGAACCTGAAGTTCATGGC isotig46679 CCTGTCACTTTGAGTCAACTCCTGGAAGTGATGAGCTGGCAGTTTTCATC isotig12565 ATCGGAACCTGGGACCAGGTGGCCGAGGTGCTCAGCTGGCAGTTCTCATC isotig12566 ATCGGAACCTGGGACCAGGTGGCCGAGGTGCTCAGCTGGCAGTTCTCATC ENSG00000166888:ENST0000030013 TGAGGTGGGGACCAACCGGGGGCTGCTCCCAGAGCACTTCCTCTTCCTGG ENSG00000166888:ENST0000054387 TGAGGTGGGGACCAACCGGGGGCTGCTCCCAGAGCACTTCCTCTTCCTGG ENSG00000166888:ENST0000055615 TGAGGTGGGGACCAACCGGGGGCTGCTCCCAGAGCACTTCCTCTTCCTGG ENSG00000166888:ENST0000045407 TGAGGTGGGGACCAACCGGGGGCTGCTCCCAGAGCACTTCCTCTTCCTGG ENSG00000166888:ENST0000053891 TGAGGTGGGGACCAACCGGGGGCTGCTCCCAGAGCACTTCCTCTTCCTGG ENSG00000166888:ENST0000053721 TGAGGTGGGGACCAACCGGGGGCTGCTCCCAGAGCACTTCCTCTTCCTGG ENSG00000166888:ENST0000053520 TGAGGTGGGGACCAACCGGGGGCTGCTCCCAGAGCACTTCCTCTTCCTGG isotig46679 CTATGTTGGT------CGTGGCCTTAATTCAGACCAGCTCAACATGCTGG isotig12565 CACCACAAAG------CGAGGGCTGAGCATCGAGCAGCTGACTACGCTGG isotig12566 CACCACAAAG------CGAGGGCTGAGCATCGAGCAGCTGACTACGCTGG ENSG00000166888:ENST0000030013 CCCAGAAGATCTTCAATGACAACAGCCTCAGTATGGAGGCCTTCCAGCAC ENSG00000166888:ENST0000054387 CCCAGAAGATCTTCAATGACAACAGCCTCAGTATGGAGGCCTTCCAGCAC ENSG00000166888:ENST0000055615 CCCAGAAGATCTTCAATGACAACAGCCTCAGTATGGAGGCCTTCCAGCAC ENSG00000166888:ENST0000045407 CCCAGAAGATCTTCAATGACAACAGCCTCAGTATGGAGGCCTTCCAGCAC ENSG00000166888:ENST0000053891 CCCAGAAGATCTTCAATGACAACAGCCTCAGTATGGAGGCCTTCCAGCAC ENSG00000166888:ENST0000053721 CCCAGAAGATCTTCAATGACAACAGCCTCAGTATGGAGGCCTTCCAGCAC ENSG00000166888:ENST0000053520 CCCAGAAGATCTTCAATGACAACAGCCTCAGTATGGAGGCCTTCCAGCAC isotig46679 CAGAGAAGCTCACAGTTCAGTCT---------------AACTACAGCGAT isotig12565 CCGAGAAGCTCCTAGGACCTGGTGTC------------AACTACTCCGGG isotig12566 CCGAGAAGCTCCTAGGACCTGGTGTC------------AACTACTCCGGG ENSG00000166888:ENST0000030013 CGTTCTGTGTCCTGGTCGCAGTTCAACAAGGAGATCCTGCTGGGCCGTGG ENSG00000166888:ENST0000054387 CGTTCTGTGTCCTGGTCGCAGTTCAACAAGGAGATCCTGCTGGGCCGTGG ENSG00000166888:ENST0000055615 CGTTCTGTGTCCTGGTCGCAGTTCAACAAGGAGATCCTGCTGGGCCGTGG ENSG00000166888:ENST0000045407 CGTTCTGTGTCCTGGTCGCAGTTCAACAAGGAGATCCTGCTGGGCCGTGG ENSG00000166888:ENST0000053891 CGTTCTGTGTCCTGGTCGCAGTTCAACAAGGAGATCCTGCTGGGCCGTGG ENSG00000166888:ENST0000053721 CGTTCTGTGTCCTGGTCGCAGTTCAACAAGGAGATCCTGCTGGGCCGTGG ENSG00000166888:ENST0000053520 CGTTCTGTGTCCTGGTCGCAGTTCAACAAGGAGATCCTGCTGGGCCGTGG isotig46679 GGTCACCTCACCTGGGCCAAGTTCTGCAAGGAACACTTGCCTGGCAAACC isotig12565 TGTCAGATCACATGGGCTAAATTTTGCAAAGAAAACATGGCTGGCAAGGG isotig12566 TGTCAGATCACATGGGCTAAATTTTGCAAAGAAAACATGGCTGGCAAGGG ENSG00000166888:ENST0000030013 CTTCACCTTTTGGCAGTGGTTTGATGGTGTCCTGGACCTCACCAAACGCT ENSG00000166888:ENST0000054387 CTTCACCTTTTGGCAGTGGTTTGATGGTGTCCTGGACCTCACCAAACGCT ENSG00000166888:ENST0000055615 CTTCACCTTTTGGCAGTGGTTTGATGGTGTCCTGGACCTCACCAAACGCT ENSG00000166888:ENST0000045407 CTTCACCTTTTGGCAGTGGTTTGATGGTGTCCTGGACCTCACCAAACGCT ENSG00000166888:ENST0000053891 CTTCACCTTTTGGCAGTGGTTTGATGGTGTCCTGGACCTCACCAAACGCT ENSG00000166888:ENST0000053721 CTTCACCTTTTGGCAGTGGTTTGATGGTGTCCTGGACCTCACCAAACGCT ENSG00000166888:ENST0000053520 CTTCACCTTTTGGCAGTGGTTTGATGGTGTCCTGGACCTCACCAAACGCT isotig46679 ATTTACCTTCTGGACCTGGCTTGAAGCAATATTGGACCTAATTAAAAAAC isotig12565 CTTCTCCTTCTGGGTGTGGCTAGACAATATCATTGACCTTGTGAAAAAGT isotig12566 CTTCTCCTTCTGGGTGTGGCTAGACAATATCATTGACCTTGTGAAAAAGT ENSG00000166888:ENST0000030013 GTCTCCGGAGCTACTGGTCTGACCGGCTGATCATTGGCTTCATCAGCAAA ENSG00000166888:ENST0000054387 GTCTCCGGAGCTACTGGTCTGACCGGCTGATCATTGGCTTCATCAGCAAA ENSG00000166888:ENST0000055615 GTCTCCGGAGCTACTGGTCTGACCGGCTGATCATTGGCTTCATCAGCAAA ENSG00000166888:ENST0000045407 GTCTCCGGAGCTACTGGTCTGACCGGCTGATCATTGGCTTCATCAGCAAA ENSG00000166888:ENST0000053891 GTCTCCGGAGCTACTGGTCTGACCGGCTGATCATTGGCTTCATCAGCAAA ENSG00000166888:ENST0000053721 GTCTCCGGAGCTACTGGTCTGACCGGCTGATCATTGGCTTCATCAGCAAA ENSG00000166888:ENST0000053520 GTCTCCGGAGCTACTGGTCTGACCGGCTGATCATTGGCTTCATCAGCAAA isotig46679 ACATTCTTCCCCTCTGGATTGATGGGTACATCATGGGCTTCGTGAGCAAA isotig12565 ATATCTTGGCCCTCTGGAATGAAGGGTACATCATGGGCTTCATTAGCAAG isotig12566 ATATCTTGGCCCTCTGGAATGAAGGGTACATCATGGGCTTCATTAGCAAG ENSG00000166888:ENST0000030013 CAGTACGTTACTAGCCTTCTTCTCAATGAGCCCGACGGAACCTTTCTCCT ENSG00000166888:ENST0000054387 CAGTACGTTACTAGCCTTCTTCTCAATGAGCCCGACGGAACCTTTCTCCT ENSG00000166888:ENST0000055615 CAGTACGTTACTAGCCTTCTTCTCAATGAGCCCGACGGAACCTTTCTCCT ENSG00000166888:ENST0000045407 CAGTACGTTACTAGCCTTCTTCTCAATGAGCCCGACGGAACCTTTCTCCT ENSG00000166888:ENST0000053891 CAGTACGTTACTAGCCTTCTTCTCAATGAGCCCGACGGAACCTTTCTCCT ENSG00000166888:ENST0000053721 CAGTACGTTACTAGCCTTCTTCTCAATGAGCCCGACGGAACCTTTCTCCT ENSG00000166888:ENST0000053520 CAGTACGTTACTAGCCTTCTTCTCAATGAGCCCGACGGAACCTTTCTCCT isotig46679 GAGAAGGAGAGGTTTCTGCTCAAGGATAAAATGCCCGGGACATTTTTGTT isotig12565 GAGCGGGAGCGGGCGATCCTGAGCACGAAACCCCCGGGCACCTTCCTGCT isotig12566 GAGCGGGAGCGGGCGATCCTGAGCACGAAACCCCCGGGCACCTTCCTGCT ENSG00000166888:ENST0000030013 CCGCTTCAGCGAC---TCAGAGATTGGGGGCATCACCATTGCCCATGTCA ENSG00000166888:ENST0000054387 CCGCTTCAGCGAC---TCAGAGATTGGGGGCATCACCATTGCCCATGTCA ENSG00000166888:ENST0000055615 CCGCTTCAGCGAC---TCAGAGATTGGGGGCATCACCATTGCCCATGTCA ENSG00000166888:ENST0000045407 CCGCTTCAGCGAC---TCAGAGATTGGGGGCATCACCATTGCCCATGTCA ENSG00000166888:ENST0000053891 CCGCTTCAGCGAC---TCAGAGATTGGGGGCATCACCATTGCCCATGTCA ENSG00000166888:ENST0000053721 CCGCTTCAGCGAC---TCAGAGATTGGGGGCATCACCATTGCCCATGTCA ENSG00000166888:ENST0000053520 CCGCTTCAGCGAC---TCAGAGATTGGGGGCATCACCATTGCCCATGTCA isotig46679 ACGATTCAGTGAG---AGCCATCTCGGAGGGATCACCTTCACCTGGGTGG isotig12565 GAGATTCAGCGAGAGCAGCAAAGAAGGAGGGGTCACTTTCACTTGGGTGG isotig12566 GAGATTCAGCGAGAGCAGCAAAGAAGGAGGGGTCACTTTCACTTGGGTGG ENSG00000166888:ENST0000030013 TCCGGGGCCAGGATGGCTCTCCACAGATAGAGAACATCCAGCCATTCTCT ENSG00000166888:ENST0000054387 TCCGGGGCCAGGATGGCTCTCCACAGATAGAGAACATCCAGCCATTCTCT ENSG00000166888:ENST0000055615 TCCGGGGCCAGGATGGCTCTCCACAGATAGAGAACATCCAGCCATTCTCT ENSG00000166888:ENST0000045407 TCCGGGGCCAGGATGGCTCTCCACAGATAGAGAACATCCAGCCATTCTCT ENSG00000166888:ENST0000053891 TCCGGGGCCAGGATGGCTCTCCACAGATAGAGAACATCCAGCCATTCTCT ENSG00000166888:ENST0000053721 TCCGGGGCCAGGATGGCTCTCCACAGATAGAGAACATCCAGCCATTCTCT ENSG00000166888:ENST0000053520 TCCGGGGCCAGGATGGCTCTCCACAGATAGAGAACATCCAGCCATTCTCT isotig46679 ACCACTCTGAAAACGGAGAAGTGAGATTCCACTCCGTAGAACCCTACAAC isotig12565 AAAAGGACATCAGTGGCAAGACCCAGATCCAGTCTGTAGAGCCGTACACC isotig12566 AAAAGGACATCAGTGGCAAGACCCAGATCCAGTCTGTAGAGCCGTACACC ENSG00000166888:ENST0000030013 GCCAAAGACCTGTCCATTCGCTCACTGGGGGACCGAATCCGGGAT----- ENSG00000166888:ENST0000054387 GCCAAAGACCTGTCCATTCGCTCACTGGGGGACCGAATCCGGGAT----- ENSG00000166888:ENST0000055615 GCCAAAGACCTGTCCATTCGCTCACTGGGGGACCGAATCCGGGAT----- ENSG00000166888:ENST0000045407 GCCAAAGACCTGTCCATTCGCTCACTGGGGGACCGAATCCGGGAT----- ENSG00000166888:ENST0000053891 GCCAAAGACCTGTCCATTCGCTCACTGGGGGACCGAATCCGGGAT----- ENSG00000166888:ENST0000053721 GCCAAAGACCTGTCCATTCGCTCACTGGGGGACCGAATCCGGGAT----- ENSG00000166888:ENST0000053520 GCCAAAGACCTGTCCATTCGCTCACTGGGGGACCGAATCCGGGAT----- isotig46679 AAAGGGCGTCTGTCGGCCCTGCCATTTGCTGACATCCTGCGGGACTACAA isotig12565 AAGCAGCAGCTGAACAACATGTCCTTTGCTGAAATCATCATGGGCTACAA isotig12566 AAGCAGCAGCTGAACAACATGTCCTTTGCTGAAATCATCATGGGCTACAA ENSG00000166888:ENST0000030013 -------------------------CTTGCTCAGCTCAAAAATCTCTATC ENSG00000166888:ENST0000054387 -------------------------CTTGCTCAGCTCAAAAATCTCTATC ENSG00000166888:ENST0000055615 -------------------------CTTGCTCAGCTCAAAAATCTCTATC ENSG00000166888:ENST0000045407 -------------------------CTTGCTCAGCTCAAAAATCTCTATC ENSG00000166888:ENST0000053891 -------------------------CTTGCTCAGCTCAAAAATCTCTATC ENSG00000166888:ENST0000053721 -------------------------CTTGCTCAGCTCAAAAATCTCTATC ENSG00000166888:ENST0000053520 -------------------------CTTGCTCAGCTCAAAAATCTCTATC isotig46679 GGTCATCATGGCTGAGAACATTCCCGAGAACCCTCTCAAGTACCTCTACC isotig12565 GATCATGGATGCCACCAACATCCTGGTGTCCCCATTGGTCTACCTCTACC isotig12566 GATCATGGATGCCACCAACATCCTGGTGTCCCCATTGGTCTACCTCTACC ENSG00000166888:ENST0000030013 CCAAGAAGCCCAAGGATGAGGCTTTCCGGAGCCACTAC------------ ENSG00000166888:ENST0000054387 CCAAGAAGCCCAAGGATGAGGCTTTCCGGAGCCACTAC------------ ENSG00000166888:ENST0000055615 CCAAGAAGCCCAAGGATGAGGCTTTCCGGAGCCACTAC------------ ENSG00000166888:ENST0000045407 CCAAGAAGCCCAAGGATGAGGCTTTCCGGAGCCACTAC------------ ENSG00000166888:ENST0000053891 CCAAGAAGCCCAAGGATGAGGCTTTCCGGAGCCACTAC------------ ENSG00000166888:ENST0000053721 CCAAGAAGCCCAAGGATGAGGCTTTCCGGAGCCACTAC------------ ENSG00000166888:ENST0000053520 CCAAGAAGCCCAAGGATGAGGCTTTCCGGAGCCACTAC------------ isotig46679 CCGACATCCCCAAAGACAAAGCCTTCGGTAAACACTACAGCTCCCAGCCT isotig12565 CTGACATTCCCAAGGAGGAGGCGTTCGGGAAGTACTGT------------ isotig12566 CTGACATTCCCAAGGAGGAGGCGTTCGGGAAGTACTGT------------ ENSG00000166888:ENST0000030013 ------------AAGCCTGAACAGATGGGTAAGGATGGCAGGGGTTATGT ENSG00000166888:ENST0000054387 ------------AAGCCTGAACAGATGGGTAAGGATGGCAGGGGTTATGT ENSG00000166888:ENST0000055615 ------------AAGCCTGAACAGATGGGTAAGGATGGCAGGGGTTATGT ENSG00000166888:ENST0000045407 ------------AAGCCTGAACAGATGGGTAAGGATGGCAGGGGTTATGT ENSG00000166888:ENST0000053891 ------------AAGCCTGAACAGATGGGTAAGGATGGCAGGGGTTATGT ENSG00000166888:ENST0000053721 ------------AAGCCTGAACAGATGGGTAAGGATGGCAGGGGTTATGT ENSG00000166888:ENST0000053520 ------------AAGCCTGAACAGATGGGTAAGGATGGCAGGGGTTATGT isotig46679 TGCGAAGTTTCAAGGCCAACA------GAACGGGGAGACAAAGGTTATGT isotig12565 ------------CGACCAGAG----------------------------- isotig12566 ------------CGACCAGAG----------------------------- ENSG00000166888:ENST0000030013 CCCAGCTACCATCAAGATGACCGTGGAAAGGGACCAACCACTTCCTACCC ENSG00000166888:ENST0000054387 CCCAGCTACCATCAAGATGACCGTGGAAAGGGACCAACCACTTCCTACCC ENSG00000166888:ENST0000055615 CCCAGCTACCATCAAGATGACCGTGGAAAGGGACCAACCACTTCCTACCC ENSG00000166888:ENST0000045407 CCCAGCTACCATCAAGATGACCGTGGAAAGGGACCAACCACTTCCTACCC ENSG00000166888:ENST0000053891 CCCAGCTACCATCAAGATGACCGTGGAAAGGGACCAACCACTTCCTACCC ENSG00000166888:ENST0000053721 CCCAGCTACCATCAAGATGACCGTGGAAAGGGACCAACCACTTCCTACCC ENSG00000166888:ENST0000053520 CCCAGCTACCATCAAGATGACCGTGGAAAGGGACCAACCACTTCCTACCC isotig46679 TCCTTCAGTTTTTATCCCTATTTCAACAATCCGCAGCGACGCCATGGAGC isotig12565 -------------------------------AGCCAGGAGCATCCTGAAG isotig12566 -------------------------------AGCCAGGAGCATCCTGAAG ENSG00000166888:ENST0000030013 CAGAGCTCCAGATGCCTACCATGGTGCCTTCTTATGACCTTGGAATGGCC ENSG00000166888:ENST0000054387 CAGAGCTCCAGATGCCTACCATGGTGCCTTCTTATGACCTTGGAATGGCC ENSG00000166888:ENST0000055615 CAGAGCTCCAGATGCCTACCATGGTGCCTTCTTATGACCTTGGAATGGCC ENSG00000166888:ENST0000045407 CAGAGCTCCAGATGCCTACCATGGTGCCTTCTTATGACCTTGGAATGGCC ENSG00000166888:ENST0000053891 CAGAGCTCCAGATGCCTACCATGGTGCCTTCTTATGACCTTGGAATGGCC ENSG00000166888:ENST0000053721 CAGAGCTCCAGATGCCTACCATGGTGCCTTCTTATGACCTTGGAATGGCC ENSG00000166888:ENST0000053520 CAGAGCTCCAGATGCCTACCATGGTGCCTTCTTATGACCTTGGAATGGCC isotig46679 CGCAG------------------------------------------TCT isotig12565 CTGAC--------------------------------------------- isotig12566 CTGAC--------------------------------------------- ENSG00000166888:ENST0000030013 CCTGATTCCTCCATGAGCATGCAGCTTGGCCCAGATATGGTGCCCCAGGT ENSG00000166888:ENST0000054387 CCTGATTCCTCCATGAGCATGCAGCTTGGCCCAGATATGGTGCCCCAGGT ENSG00000166888:ENST0000055615 CCTGATTCCTCCATGAGCATGCAGCTTGGCCCAGATATGGTGCCCCAGGT ENSG00000166888:ENST0000045407 CCTGATTCCTCCATGAGCATGCAGCTTGGCCCAGATATGGTGCCCCAGGT ENSG00000166888:ENST0000053891 CCTGATTCCTCCATGAGCATGCAGCTTGGCCCAGATATGGTGCCCCAGGT ENSG00000166888:ENST0000053721 CCTGATTCCTCCATGAGCATGCAGCTTGGCCCAGATATGGTGCCCCAGGT ENSG00000166888:ENST0000053520 CCTGATTCCTCCATGAGCATGCAGCTTGGCCCAGATATGGTGCCCCAGGT isotig46679 CCTTCAGACCTTCTCCCC------------------ATGTCTCCGAGTGT isotig12565 CCCGGTAGTGCCGCCCCT------------------TACCTGAAGACCAA isotig12566 CCCGGTAGTTGTTTTTCCATG----------------------------- ENSG00000166888:ENST0000030013 GTACCCACCACACTCTCACTCCATCCCCCCGTATCAAGGCCTCTCCCCAG ENSG00000166888:ENST0000054387 GTACCCACCACACTCTCACTCCATCCCCCCGTATCAAGGCCTCTCCCCAG ENSG00000166888:ENST0000055615 GTACCCACCACACTCTCACTCCATCCCCCCGTATCAAGGCCTCTCCCCAG ENSG00000166888:ENST0000045407 GTACCCACCACACTCTCACTCCATCCCCCCGTATCAAGGCCTCTCCCCAG ENSG00000166888:ENST0000053891 GTACCCACCACACTCTCACTCCATCCCCCCGTATCAAGGCCTCTCCCCAG ENSG00000166888:ENST0000053721 GTACCCACCACACTCTCACTCCATCCCCCCGTATCAAGGCCTCTCCCCAG ENSG00000166888:ENST0000053520 GTACCCACCACACTCTCACTCCATCCCCCCGTATCAAGGCCTCTCCCCAG isotig46679 ATACGCTGTGCTGAGAGAAAACCTGAGCCCT------------------- isotig12565 GTTCATCTGTGTGACACCAACGACCTGCAGC------------------- isotig12566 -------------------------------------------------- ENSG00000166888:ENST0000030013 AAGAATCAGTCAACGTGTTGTCAGCCTTCCAGGAGCCTCACCTGCAGATG ENSG00000166888:ENST0000054387 AAGAATCAGTCAACGTGTTGTCAGCCTTCCAGGAGCCTCACCTGCAGATG ENSG00000166888:ENST0000055615 AAGAATCAGTCAACGTGTTGTCAGCCTTCCAGGAGCCTCACCTGCAGATG ENSG00000166888:ENST0000045407 AAGAATCAGTCAACGTGTTGTCAGCCTTCCAGGAGCCTCACCTGCAGATG ENSG00000166888:ENST0000053891 AAGAATCAGTCAACGTGTTGTCAGCCTTCCAGGAGCCTCACCTGCAGATG ENSG00000166888:ENST0000053721 AAGAATCAGTCAACGTGTTGTCAGCCTTCCAGGAGCCTCACCTGCAGATG ENSG00000166888:ENST0000053520 AAGAATCAGTCAACGTGTTGTCAGCCTTCCAGGAGCCTCACCTGCAGATG isotig46679 -------------------------------------------------- isotig12565 -------------------------------------------------- isotig12566 -------------------------------------------------- ENSG00000166888:ENST0000030013 CCCCCCAGCCTGGGCCAGATGAGCCTGCCCTTTGACCAGCCTCACCCCCA ENSG00000166888:ENST0000054387 CCCCCCAGCCTGGGCCAGATGAGCCTGCCCTTTGACCAGCCTCACCCCCA ENSG00000166888:ENST0000055615 CCCCCCAGCCTGGGCCAGATGAGCCTGCCCTTTGACCAGCCTCACCCCCA ENSG00000166888:ENST0000045407 CCCCCCAGCCTGGGCCAGATGAGCCTGCCCTTTGACCAGCCTCACCCCCA ENSG00000166888:ENST0000053891 CCCCCCAGCCTGGGCCAGATGAGCCTGCCCTTTGACCAGCCTCACCCCCA ENSG00000166888:ENST0000053721 CCCCCCAGCCTGGGCCAGATGAGCCTGCCCTTTGACCAGCCTCACCCCCA ENSG00000166888:ENST0000053520 CCCCCCAGCCTGGGCCAGATGAGCCTGCCCTTTGACCAGCCTCACCCCCA isotig46679 ------------ACCACAATTGAAACAGCAATGAAGTCTCCATATTCTGA isotig12565 ------------AATACCATTGACCTGCCGATGTCCCCCCCGCAC----- isotig12566 ------------GTTCTGGTTTCGCTGTTAGGGAAAGGGGGACAGTGCAG ENSG00000166888:ENST0000030013 GGGCCTGCTGCCGTGCCAGCCTCAGGAGCATGCTGTGTCCAGCCCTGACC ENSG00000166888:ENST0000054387 GGGCCTGCTGCCGTGCCAGCCTCAGGAGCATGCTGTGTCCAGCCCTGACC ENSG00000166888:ENST0000055615 GGGCCTGCTGCCGTGCCAGCCTCAGGAGCATGCTGTGTCCAGCCCTGACC ENSG00000166888:ENST0000045407 GGGCCTGCTGCCGTGCCAGCCTCAGGAGCATGCTGTGTCCAGCCCTGACC ENSG00000166888:ENST0000053891 GGGCCTGCTGCCGTGCCAGCCTCAGGAGCATGCTGTGTCCAGCCCTGACC ENSG00000166888:ENST0000053721 GGGCCTGCTGCCGTGCCAGCCTCAGGAGCATGCTGTGTCCAGCCCTGACC ENSG00000166888:ENST0000053520 GGGCCTGCTGCCGTGCCAGCCTCAGGAGCATGCTGTGTCCAGCCCTGACC isotig46679 GCGGTAC---------------------AAAGCGACTCTTCAAGGAAGAG isotig12565 -------------------------------------------------- isotig12566 GTCCTTG---------------------------------------GAGG ENSG00000166888:ENST0000030013 CCCTGCTCTGCTCAGATGTGACCATGGTGGAAGACAGCTGCCTGAGCCAG ENSG00000166888:ENST0000054387 CCCTGCTCTGCTCAGATGTGACCATGGTGGAAGACAGCTGCCTGAGCCAG ENSG00000166888:ENST0000055615 CCCTGCTCTGCTCAGATGTGACCATGGTGGAAGACAGCTGCCTGAGCCAG ENSG00000166888:ENST0000045407 CCCTGCTCTGCTCAGATGTGACCATGGTGGAAGACAGCTGCCTGAGCCAG ENSG00000166888:ENST0000053891 CCCTGCTCTGCTCAGATGTGACCATGGTGGAAGACAGCTGCCTGAGCCAG ENSG00000166888:ENST0000053721 CCCTGCTCTGCTCAGATGTGACCATGGTGGAAGACAGCTGCCTGAGCCAG ENSG00000166888:ENST0000053520 CCCTGCTCTGCTCAGATGTGACCATGGTGGAAGACAGCTGCCTGAGCCAG isotig46679 AGCAGATGAAAACGGAGACTGCTCTTTGCCAAAGTCCACAATTCATTTCT isotig12565 -------------------------------------------------- isotig12566 AGAGACAAGGACATGACCGGGTGTCTGGTGGTGAGTCCTGCTATGGAAGA ENSG00000166888:ENST0000030013 CCAGTGACAGCGTTTCCTCAGGGCACTTGGATTGGTGAAGACATATTCCC ENSG00000166888:ENST0000054387 CCAGTGACAGCGTTTCCTCAGGGCACTTGGATTGGTGAAGACATATTCCC ENSG00000166888:ENST0000055615 CCAGTGACAGCGTTTCCTCAGGGCACTTGGATTGGTGAAGACATATTCCC ENSG00000166888:ENST0000045407 CCAGTGACAGCGTTTCCTCAGGGCACTTGGATTGGTGAAGACATATTCCC ENSG00000166888:ENST0000053891 CCAGTGACAGCGTTTCCTCAGGGCACTTGGATTGGTGAAGACATATTCCC ENSG00000166888:ENST0000053721 CCAGTGACAGCGTTTCCTCAGGGCACTTGGATTGGTGAAGACATATTCCC ENSG00000166888:ENST0000053520 CCAGTGACAGCGTTTCCTCAGGGCACTTGGATTGGTGAAGACATATTCCC isotig46679 TCAGCTTTGATACTGGTTTCTAGAAAATGGCACAAATCCGAAGCTTTCCT isotig12565 ------TTTAGATTCATTGATGCAGTTTGGAAACGGAGGTGCGCCCTC-- isotig12566 GCTGTTTAT------------------TGGGTACTTCAG----------- ENSG00000166888:ENST0000030013 TCCTCTGCTGCCTCCCACTGAACAGGACCTCACTAAGCTTCTCCTGGAGG ENSG00000166888:ENST0000054387 TCCTCTGCTGCCTCCCACTGAACAGGACCTCACTAAGCTTCTCCTGGAGG ENSG00000166888:ENST0000055615 TCCTCTGCTGCCTCCCACTGAACAGGACCTCACTAAGCTTCTCCTGGAGG ENSG00000166888:ENST0000045407 TCCTCTGCTGCCTCCCACTGAACAGGACCTCACTAAGCTTCTCCTGGAGG ENSG00000166888:ENST0000053891 TCCTCTGCTGCCTCCCACTGAACAGGACCTCACTAAGCTTCTCCTGGAGG ENSG00000166888:ENST0000053721 TCCTCTGCTGCCTCCCACTGAACAGGACCTCACTAAGCTTCTCCTGGAGG ENSG00000166888:ENST0000053520 TCCTCTGCTGCCTCCCACTGAACAGGACCTCACTAAGCTTCTCCTGGAGG isotig46679 CTCACTA------------------------------------------G isotig12565 -------------------------------------------------G isotig12566 -------------------------------------------------G ENSG00000166888:ENST0000030013 GGCAAGGGGAGTCGGGGGGAGGGTCCTTGGGGGCACAGCCCCTCCTGCAG ENSG00000166888:ENST0000054387 GGCAAGGGGAGTCGGGGGGAGGGTCCTTGGGGGCACAGCCCCTCCTGCAG ENSG00000166888:ENST0000055615 GGCAAGGGGAGTCGGGGGGAGGGTCCTTGGGGGCACAGCCCCTCCTGCAG ENSG00000166888:ENST0000045407 GGCAAGGGGAGTCGGGGGGAGGGTCCTTGGGGGCACAGCCCCTCCTGCAG ENSG00000166888:ENST0000053891 GGCAAGGGGAGTCGGGGGGAGGGTCCTTGGGGGCACAGCCCCTCCTGCAG ENSG00000166888:ENST0000053721 GGCAAGGGGAGTCGGGGGGAGGGTCCTTGGGGGCACAGCCCCTCCTGCAG ENSG00000166888:ENST0000053520 GGCAAGGGGAGTCGGGGGGAGGGTCCTTGGGGGCACAGCCCCTCCTGCAG isotig46679 GTGACATTCCCCAACTGGGAGTGCTGCTGAAATGCAAACCAAAGCTTCAG isotig12565 GCAGGAGGGCAGTTGTCACTCACGTTCATGGATCTGAC------------ isotig12566 GTGACCGGGATTCAAGAGAAGACCAGAATCAGGCCTCA------------ ENSG00000166888:ENST0000030013 CCCTCCCACTATGGGCAATCTGGGATCTCAATGTCCCACATGGACCTAAG ENSG00000166888:ENST0000054387 CCCTCCCACTATGGGCAATCTGGGATCTCAATGTCCCACATGGACCTAAG ENSG00000166888:ENST0000055615 CCCTCCCACTATGGGCAATCTGGGATCTCAATGTCCCACATGGACCTAAG ENSG00000166888:ENST0000045407 CCCTCCCACTATGGGCAATCTGGGATCTCAATGTCCCACATGGACCTAAG ENSG00000166888:ENST0000053891 CCCTCCCACTATGGGCAATCTGGGATCTCAATGTCCCACATGGACCTAAG ENSG00000166888:ENST0000053721 CCCTCCCACTATGGGCAATCTGGGATCTCAATGTCCCACATGGACCTAAG ENSG00000166888:ENST0000053520 CCCTCCCACTATGGGCAATCTGGGATCTCAATGTCCCACATGGACCTAAG isotig46679 ATAAACACGCAGGAAAAGACAGCTTCGAGAAACCTATGTTCGCAATATAA isotig12565 ---------TTCGGAGTGCGCTACCTCCCCCATGTGAGGAGC-------- isotig12566 -------------------------------------------------- ENSG00000166888:ENST0000030013 GGCCAACCCCAGTTGG ENSG00000166888:ENST0000054387 GGCCAACCCCAGTTGG ENSG00000166888:ENST0000055615 GGCCAACCCCAGTTGG ENSG00000166888:ENST0000045407 GGCCAACCCCAGTTGG ENSG00000166888:ENST0000053891 GGCCAACCCCAGTTGG ENSG00000166888:ENST0000053721 GGCCAACCCCAGTTGG ENSG00000166888:ENST0000053520 GGCCAACCCCAGTTGG isotig46679 CAGAAGGCTGCTTTGC isotig12565 ---------------- isotig12566 ---------------- """, ) def test5(self): aligner = CodonAligner() # aligner.frameshift_score = -10.0 nucleotide_records = SeqIO.parse("codonalign/nucl5.fa", "fasta") protein_alignment = Align.read("codonalign/pro5.aln", "clustal") self.assertEqual(len(protein_alignment.sequences), 3) codon_alignments = [] nucleotide_record = next(nucleotide_records) protein_record = protein_alignment.sequences[0] self.assertEqual(nucleotide_record.id, protein_record.id) alignments = aligner.align(protein_record, nucleotide_record) self.assertEqual(len(alignments), 1) alignment = next(alignments) codon_alignments.append(alignment) self.assertTrue( np.array_equal(alignment.coordinates, np.array([[0, 183], [0, 549]])) ) self.assertEqual( str(alignment), """\ isotig697 0 R G D Q R S N F Q L S P S T M Q I S T G isotig697 0 TGAGGCGATCAACGCAGCAACTTCCAGCTGTCTCCCTCCACCATGCAGATCTCCACAGGG isotig697 20 L L C L L L V A T G F T S Q V L A H P G isotig697 60 CTTCTGTGCcTGCTGCTTGTGGCCACTGGCTTCACTTCCCAGGTGCTGGCTCACCCAGGC isotig697 40 S I P S T Y C F V M T S K K I P K S L L isotig697 120 TCTATCCCATCTACCTaCTGCTTTGTTATGACCAGTAAGAaGATCCCCAAATCACTACTG isotig697 60 K S Y K R I S N S R C T L K A I L F K T isotig697 180 AaGAGCTACAAAaGAATCTCCAACAGCAGATGCACCcTGAAAGCCATACTCTTCAAGACC isotig697 80 K S G K E I C A D P K K K W V Q D A T K isotig697 240 AAGTCGGGCAAAGAGATCTGTGCTGACCCCAAGAAGAAGTGGGTCcAGGATGCCACAAAG isotig697 100 H L D Q I L Q T P K P T I P S F E T H P isotig697 300 CACCTGGACCAAATCCTTCAAACTCCAAAACCGACAATCCCCTCTTTTGAGACTCACCCA isotig697 120 E T K K C F I H S P F L R R A P R S T Q isotig697 360 GAGACTAAGAAATGCTTCATTCATTCTCCATTCCTAAGACGTGCTCCAAGGTCAACTCAG isotig697 140 H H S P R T W L H L V M D R T E S H Y V isotig697 420 CACCATTCCCCAAGGACTTGGCTTCATTTAGTTATGGATAGAACTGAAAGTCATTATGTT isotig697 160 Q N K P D L K R L C N F L N M Q N L K R isotig697 480 CAGAATAAGCCAGACTTGAAGAGGTTGTGTAATTTCTTGAATATGCAAAATCTTAAAAGG isotig697 180 G A C 183 isotig697 540 GGGGCATGC 549 """, ) nucleotide_record = next(nucleotide_records) protein_record = protein_alignment.sequences[1] self.assertEqual(nucleotide_record.id, protein_record.id) alignments = aligner.align(protein_record, nucleotide_record) self.assertEqual(len(alignments), 1) alignment = next(alignments) codon_alignments.append(alignment) self.assertTrue( np.array_equal(alignment.coordinates, np.array([[0, 65], [0, 195]])) ) self.assertEqual( str(alignment), """\ ENSG00000 0 M K V S A A L L C L L L I A A T F I P Q ENSG00000 0 ATGAAAGTCTCTGCCGCCCTTCTGTGCCTGCTGCTCATAGCAGCCACCTTCATTCCCCAA ENSG00000 20 G L A Q P D A I N A P V T C C Y N F T N ENSG00000 60 GGGCTCGCTCAGCCAGATGCAATCAATGCCCCAGTCACCTGCTGTTATAACTTCACCAAT ENSG00000 40 R K I S V Q R L A S Y R R I T S S K C P ENSG00000 120 AGGAAGATCTCAGTGCAGAGGCTCGCGAGCTATAGAAGAATCACCAGCAGCAAGTGTCCC ENSG00000 60 K E A V M 65 ENSG00000 180 AAAGAAGCTGTGATG 195 """, ) nucleotide_record = next(nucleotide_records) protein_record = protein_alignment.sequences[2] self.assertEqual(nucleotide_record.id, protein_record.id) alignments = aligner.align(protein_record, nucleotide_record) self.assertEqual(len(alignments), 1) alignment = next(alignments) codon_alignments.append(alignment) self.assertTrue( np.array_equal(alignment.coordinates, np.array([[0, 99], [9, 306]])) ) self.assertEqual( str(alignment), """\ ENSG00000 0 M K V S A A L L C L L L I A A T F I P Q ENSG00000 9 ATGAAAGTCTCTGCCGCCCTTCTGTGCCTGCTGCTCATAGCAGCCACCTTCATTCCCCAA ENSG00000 20 G L A Q P D A I N A P V T C C Y N F T N ENSG00000 69 GGGCTCGCTCAGCCAGATGCAATCAATGCCCCAGTCACCTGCTGTTATAACTTCACCAAT ENSG00000 40 R K I S V Q R L A S Y R R I T S S K C P ENSG00000 129 AGGAAGATCTCAGTGCAGAGGCTCGCGAGCTATAGAAGAATCACCAGCAGCAAGTGTCCC ENSG00000 60 K E A V I F K T I V A K E I C A D P K Q ENSG00000 189 AAAGAAGCTGTGATCTTCAAGACCATTGTGGCCAAGGAGATCTGTGCTGACCCCAAGCAG ENSG00000 80 K W V Q D S M D H L D K Q T Q T P K T ENSG00000 249 AAGTGGGTTCAGGATTCCATGGACCACCTGGACAAGCAAACCCAAACTCCGAAGACT ENSG00000 99 ENSG00000 306 """, ) alignment = protein_alignment.mapall(codon_alignments) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[0, 42, 126, 126, 231, 333, 549], [0, 0, 84, 90, 195, 195, 195], [9, 9, 93, 99, 204, 306, 306]]) # fmt: on ) ) self.assertEqual( format(alignment, "clustal"), """\ isotig69710 TGAGGCGATCAACGCAGCAACTTCCAGCTGTCTCCCTCCACCATGCAGAT ENSG00000108691:ENST0000058090 ------------------------------------------ATGAAAGT ENSG00000108691:ENST0000022583 ------------------------------------------ATGAAAGT isotig69710 CTCCACAGGGCTTCTGTGCcTGCTGCTTGTGGCCACTGGCTTCACTTCCC ENSG00000108691:ENST0000058090 CTCTGCCGCCCTTCTGTGCCTGCTGCTCATAGCAGCCACCTTCATTCCCC ENSG00000108691:ENST0000022583 CTCTGCCGCCCTTCTGTGCCTGCTGCTCATAGCAGCCACCTTCATTCCCC isotig69710 AGGTGCTGGCTCACCCAGGCTCTATC------CCATCTACCTaCTGCTTT ENSG00000108691:ENST0000058090 AAGGGCTCGCTCAGCCAGATGCAATCAATGCCCCAGTCACCTGCTGTTAT ENSG00000108691:ENST0000022583 AAGGGCTCGCTCAGCCAGATGCAATCAATGCCCCAGTCACCTGCTGTTAT isotig69710 GTTATGACCAGTAAGAaGATCCCCAAATCACTACTGAaGAGCTACAAAaG ENSG00000108691:ENST0000058090 AACTTCACCAATAGGAAGATCTCAGTGCAGAGGCTCGCGAGCTATAGAAG ENSG00000108691:ENST0000022583 AACTTCACCAATAGGAAGATCTCAGTGCAGAGGCTCGCGAGCTATAGAAG isotig69710 AATCTCCAACAGCAGATGCACCcTGAAAGCCATACTCTTCAAGACCAAGT ENSG00000108691:ENST0000058090 AATCACCAGCAGCAAGTGTCCCAAAGAAGCTGTGATG------------- ENSG00000108691:ENST0000022583 AATCACCAGCAGCAAGTGTCCCAAAGAAGCTGTGATCTTCAAGACCATTG isotig69710 CGGGCAAAGAGATCTGTGCTGACCCCAAGAAGAAGTGGGTCcAGGATGCC ENSG00000108691:ENST0000058090 -------------------------------------------------- ENSG00000108691:ENST0000022583 TGGCCAAGGAGATCTGTGCTGACCCCAAGCAGAAGTGGGTTCAGGATTCC isotig69710 ACAAAGCACCTGGACCAAATCCTTCAAACTCCAAAACCGACAATCCCCTC ENSG00000108691:ENST0000058090 -------------------------------------------------- ENSG00000108691:ENST0000022583 ATGGACCACCTGGACAAGCAAACCCAAACTCCGAAGACT----------- isotig69710 TTTTGAGACTCACCCAGAGACTAAGAAATGCTTCATTCATTCTCCATTCC ENSG00000108691:ENST0000058090 -------------------------------------------------- ENSG00000108691:ENST0000022583 -------------------------------------------------- isotig69710 TAAGACGTGCTCCAAGGTCAACTCAGCACCATTCCCCAAGGACTTGGCTT ENSG00000108691:ENST0000058090 -------------------------------------------------- ENSG00000108691:ENST0000022583 -------------------------------------------------- isotig69710 CATTTAGTTATGGATAGAACTGAAAGTCATTATGTTCAGAATAAGCCAGA ENSG00000108691:ENST0000058090 -------------------------------------------------- ENSG00000108691:ENST0000022583 -------------------------------------------------- isotig69710 CTTGAAGAGGTTGTGTAATTTCTTGAATATGCAAAATCTTAAAAGGGGGG ENSG00000108691:ENST0000058090 -------------------------------------------------- ENSG00000108691:ENST0000022583 -------------------------------------------------- isotig69710 CATGC ENSG00000108691:ENST0000058090 ----- ENSG00000108691:ENST0000022583 ----- """, ) class Test_build(unittest.TestCase): def test_build1(self): aligner = CodonAligner() codon_alignments = [] seq1 = SeqRecord( Seq( "TCAGGGACTGCGAGAACCAAGCTACTGCTGCTGCTGGCTGCGCTCTGCGCCGCAGGTGGGGCGCTGGAG" ), id="pro1", ) seq2 = SeqRecord( Seq("TCAGGGACTTCGAGAACCAAGCGCTCCTGCTGCTGGCTGCGCTCGGCGCCGCAGGTGGAGCACTGGAG"), id="pro2", ) pro1 = SeqRecord(Seq("SGTARTKLLLLLAALCAAGGALE"), id="pro1") pro2 = SeqRecord(Seq("SGTSRTKRLLLLAALGAAGGALE"), id="pro2") alignments = aligner.align(pro1, seq1) self.assertEqual(len(alignments), 1) alignment = next(alignments) codon_alignments.append(alignment) self.assertTrue( np.array_equal(alignment.coordinates, np.array([[0, 23], [0, 69]])) ) self.assertEqual( str(alignment), """\ pro1 0 S G T A R T K L L L L L A A L C A A G G pro1 0 TCAGGGACTGCGAGAACCAAGCTACTGCTGCTGCTGGCTGCGCTCTGCGCCGCAGGTGGG pro1 20 A L E 23 pro1 60 GCGCTGGAG 69 """, ) alignments = aligner.align(pro2, seq2) self.assertEqual(len(alignments), 1) alignment = next(alignments) codon_alignments.append(alignment) self.assertTrue( np.array_equal( alignment.coordinates, np.array([[0, 8, 8, 23], [0, 24, 23, 68]]) ) ) self.assertEqual( str(alignment), """\ pro2 0 S G T S R T K R 8 pro2 0 TCAGGGACTTCGAGAACCAAGCGC 24 pro2 8 L L L L A A L G A A G G A L E 23 pro2 23 CTCCTGCTGCTGGCTGCGCTCGGCGCCGCAGGTGGAGCACTGGAG 68 """, ) alignment = Alignment([pro1, pro2]) alignment = alignment.mapall(codon_alignments) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[0, 24, 24, 69], [0, 24, 23, 68]]) # fmt: on ) ) self.assertEqual( str(alignment), """\ pro1 0 TCAGGGACTGCGAGAACCAAGCTA 24 0 |||||||||.||||||||||||.. pro2 0 TCAGGGACTTCGAGAACCAAGCGC 24 pro1 24 CTGCTGCTGCTGGCTGCGCTCTGCGCCGCAGGTGGGGCGCTGGAG 69 24 ||.||||||||||||||||||.|||||||||||||.||.|||||| 69 pro2 23 CTCCTGCTGCTGGCTGCGCTCGGCGCCGCAGGTGGAGCACTGGAG 68 """, ) def test_build2(self): aligner = CodonAligner() codon_alignments = [] seq1 = SeqRecord( Seq( "ATGAAAAAGCACGAGTTACTTTGCCAAGGGACAAGTAACAAGCTCACCCAGTTGGGCACTTTTGAAGACCACTTTCTGAGCCTACAGAGGATGTTCAACAACTGTGAGGTGGTCCTTGGGAATTTGGAAATTACCTACATGCAGAGTAGTTACAACCTTTCTTTTCTCAAGACCATCCAGGAGGTTGCCGGCTATGTACTCATTGCCCTC" ), id="pro1", ) seq2 = SeqRecord( Seq( "ATGAAAAAGCACGAGTTCTTTGCCAAGGGACAAGTAACAAGCTCACCCAGTTGGGCACTTTTGAAGACCACTTTCTGAGCCTACAGAGGATGTTCAACAATGTGAGGTGGTCCTTGGGAATTTGGAAATTACCTACATGCAGAGTAGTTACAACCTTTCTTTTCTCAAGACCATCCAGGAGGTTGCCGGCTATGTACTCATTGCCCTC" ), id="pro2", ) seq3 = SeqRecord( Seq( "ATGAAAAAGCACGAGTTACTTTGCCAAGGGACAAGTAACAAGCTCACCCTTGGGCACTTTTGAAGACCACTTTCTGAGCCTACAGAGGATGTTCAACAACTGTGAGGTGGTCCTTGGGAATTTGGAAATTACCTACATGCAGAGTAGTTACAACCTTTCTTTTCTCAAGACCATCCAGGAGGTTGCCGGCTATGTACTCATTGCCCTC" ), id="pro3", ) pro1 = SeqRecord( Seq( "MKKHELLCQGTSNKLTQLGTFEDHFLSLQRMFNNCEVVLGNLEITYMQSSYNLSFLKTIQEVAGYVLIAL" ), id="pro1", ) pro2 = SeqRecord( Seq( "MKKHEFLCQGTSNKLTQLGTFEDHFLSLQRMFNNCEVVLGNLEITYMQSSYNLSFLKTIQEVAGYVLIAL" ), id="pro2", ) pro3 = SeqRecord( Seq( "MKKHELLCQGTSNKLTLLGTFEDHFLSLQRMFNNCEVVLGNLEITYMQSSYNLSFLKTIQEVAGYVLIAL" ), id="pro3", ) alignments = aligner.align(pro1, seq1) self.assertEqual(len(alignments), 1) alignment = next(alignments) codon_alignments.append(alignment) self.assertTrue( np.array_equal(alignment.coordinates, np.array([[0, 70], [0, 210]])) ) self.assertEqual( str(alignment), """\ pro1 0 M K K H E L L C Q G T S N K L T Q L G T pro1 0 ATGAAAAAGCACGAGTTACTTTGCCAAGGGACAAGTAACAAGCTCACCCAGTTGGGCACT pro1 20 F E D H F L S L Q R M F N N C E V V L G pro1 60 TTTGAAGACCACTTTCTGAGCCTACAGAGGATGTTCAACAACTGTGAGGTGGTCCTTGGG pro1 40 N L E I T Y M Q S S Y N L S F L K T I Q pro1 120 AATTTGGAAATTACCTACATGCAGAGTAGTTACAACCTTTCTTTTCTCAAGACCATCCAG pro1 60 E V A G Y V L I A L 70 pro1 180 GAGGTTGCCGGCTATGTACTCATTGCCCTC 210 """, ) alignments = aligner.align(pro2, seq2) self.assertEqual(len(alignments), 1) alignment = next(alignments) codon_alignments.append(alignment) self.assertTrue( np.array_equal( alignment.coordinates, np.array([[0, 6, 6, 34, 34, 70], [0, 18, 17, 101, 100, 208]]), ) ) self.assertEqual( str(alignment), """\ pro2 0 M K K H E F 6 pro2 0 ATGAAAAAGCACGAGTTC 18 pro2 6 L C Q G T S N K L T Q L G T F E D H F L pro2 17 CTTTGCCAAGGGACAAGTAACAAGCTCACCCAGTTGGGCACTTTTGAAGACCACTTTCTG pro2 26 S L Q R M F N N 34 pro2 77 AGCCTACAGAGGATGTTCAACAAT 101 pro2 34 C E V V L G N L E I T Y M Q S S Y N L S pro2 100 TGTGAGGTGGTCCTTGGGAATTTGGAAATTACCTACATGCAGAGTAGTTACAACCTTTCT pro2 54 F L K T I Q E V A G Y V L I A L 70 pro2 160 TTTCTCAAGACCATCCAGGAGGTTGCCGGCTATGTACTCATTGCCCTC 208 """, ) alignments = aligner.align(pro3, seq3) self.assertEqual(len(alignments), 1) alignment = next(alignments) codon_alignments.append(alignment) self.assertTrue( np.array_equal( alignment.coordinates, np.array([[0, 17, 17, 70], [0, 51, 49, 208]]) ) ) self.assertEqual( str(alignment), """\ pro3 0 M K K H E L L C Q G T S N K L T L 17 pro3 0 ATGAAAAAGCACGAGTTACTTTGCCAAGGGACAAGTAACAAGCTCACCCTT 51 pro3 17 L G T F E D H F L S L Q R M F N N C E V pro3 49 TTGGGCACTTTTGAAGACCACTTTCTGAGCCTACAGAGGATGTTCAACAACTGTGAGGTG pro3 37 V L G N L E I T Y M Q S S Y N L S F L K pro3 109 GTCCTTGGGAATTTGGAAATTACCTACATGCAGAGTAGTTACAACCTTTCTTTTCTCAAG pro3 57 T I Q E V A G Y V L I A L 70 pro3 169 ACCATCCAGGAGGTTGCCGGCTATGTACTCATTGCCCTC 208 """, ) alignment = Alignment([pro1, pro2, pro3]) alignment = alignment.mapall(codon_alignments) self.assertEqual( str(alignment), """\ pro1 0 ATGAAAAAGCACGAGTTA 18 pro2 0 ATGAAAAAGCACGAGTTC 18 pro3 0 ATGAAAAAGCACGAGTTA 18 pro1 18 CTTTGCCAAGGGACAAGTAACAAGCTCACCCAG 51 pro2 17 CTTTGCCAAGGGACAAGTAACAAGCTCACCCAG 50 pro3 18 CTTTGCCAAGGGACAAGTAACAAGCTCACCCTT 51 pro1 51 TTGGGCACTTTTGAAGACCACTTTCTGAGCCTACAGAGGATGTTCAACAAC 102 pro2 50 TTGGGCACTTTTGAAGACCACTTTCTGAGCCTACAGAGGATGTTCAACAAT 101 pro3 49 TTGGGCACTTTTGAAGACCACTTTCTGAGCCTACAGAGGATGTTCAACAAC 100 pro1 102 TGTGAGGTGGTCCTTGGGAATTTGGAAATTACCTACATGCAGAGTAGTTACAACCTTTCT pro2 100 TGTGAGGTGGTCCTTGGGAATTTGGAAATTACCTACATGCAGAGTAGTTACAACCTTTCT pro3 100 TGTGAGGTGGTCCTTGGGAATTTGGAAATTACCTACATGCAGAGTAGTTACAACCTTTCT pro1 162 TTTCTCAAGACCATCCAGGAGGTTGCCGGCTATGTACTCATTGCCCTC 210 pro2 160 TTTCTCAAGACCATCCAGGAGGTTGCCGGCTATGTACTCATTGCCCTC 208 pro3 160 TTTCTCAAGACCATCCAGGAGGTTGCCGGCTATGTACTCATTGCCCTC 208 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[0, 18, 18, 51, 51, 102, 102, 210], [0, 18, 17, 50, 50, 101, 100, 208], [0, 18, 18, 51, 49, 100, 100, 208]]) # fmt: on ) ) def test_build3(self): # use Yeast mitochondrial codon table codon_table = CodonTable.unambiguous_dna_by_id[3] aligner = CodonAligner(codon_table=codon_table) codon_alignments = [] seq1 = SeqRecord( Seq( "ATGGCAAGGGACCACCCAGTTGGGCACTGATATGATCGGGTGTATTTGCAGAGTAGTAACCTTTCTTTTCTCAAGACCATCCAG" ), id="pro1", ) seq2 = SeqRecord( Seq( "ATGGCAAGGCACCATCCAGTTGAGCACTGATATGATCGGGTGTATTTGCAGAGTAGTAACGTGTCTCTGCTCAAGACCATCCAG" ), id="pro2", ) seq3 = SeqRecord( Seq( "ATGGCAGGGGACCACCCAGTTGGGCACTGATATGATCGTGTGTATCTGCAGAGTAGTAACCACTCTTTTCTCATGACCATCCAG" ), id="pro3", ) pro1 = SeqRecord(Seq("MARDHPVGHWYDRVYLQSSNTSFTKTIQ"), id="pro1") pro2 = SeqRecord(Seq("MARHHPVEHWYDRVYLQSSNVSTTKTIQ"), id="pro2") pro3 = SeqRecord(Seq("MAGDHPVGHWYDRVYTQSSNHSFTMTIQ"), id="pro3") alignments = aligner.align(pro1, seq1) self.assertEqual(len(alignments), 1) alignment = next(alignments) codon_alignments.append(alignment) self.assertTrue( np.array_equal(alignment.coordinates, np.array([[0, 28], [0, 84]])) ) self.assertEqual( str(alignment), """\ pro1 0 M A R D H P V G H W Y D R V Y L Q S S N pro1 0 ATGGCAAGGGACCACCCAGTTGGGCACTGATATGATCGGGTGTATTTGCAGAGTAGTAAC pro1 20 T S F T K T I Q 28 pro1 60 CTTTCTTTTCTCAAGACCATCCAG 84 """, ) alignments = aligner.align(pro2, seq2) self.assertEqual(len(alignments), 1) alignment = next(alignments) codon_alignments.append(alignment) self.assertTrue( np.array_equal(alignment.coordinates, np.array([[0, 28], [0, 84]])) ) self.assertEqual( str(alignment), """\ pro2 0 M A R H H P V E H W Y D R V Y L Q S S N pro2 0 ATGGCAAGGCACCATCCAGTTGAGCACTGATATGATCGGGTGTATTTGCAGAGTAGTAAC pro2 20 V S T T K T I Q 28 pro2 60 GTGTCTCTGCTCAAGACCATCCAG 84 """, ) alignments = aligner.align(pro3, seq3) self.assertEqual(len(alignments), 1) alignment = next(alignments) codon_alignments.append(alignment) self.assertTrue( np.array_equal(alignment.coordinates, np.array([[0, 28], [0, 84]])) ) self.assertEqual( str(alignment), """\ pro3 0 M A G D H P V G H W Y D R V Y T Q S S N pro3 0 ATGGCAGGGGACCACCCAGTTGGGCACTGATATGATCGTGTGTATCTGCAGAGTAGTAAC pro3 20 H S F T M T I Q 28 pro3 60 CACTCTTTTCTCATGACCATCCAG 84 """, ) alignment = Alignment([pro1, pro2, pro3]) alignment = alignment.mapall(codon_alignments) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[0, 84], [0, 84], [0, 84]]) # fmt: on ) ) self.assertEqual( str(alignment), """\ pro1 0 ATGGCAAGGGACCACCCAGTTGGGCACTGATATGATCGGGTGTATTTGCAGAGTAGTAAC pro2 0 ATGGCAAGGCACCATCCAGTTGAGCACTGATATGATCGGGTGTATTTGCAGAGTAGTAAC pro3 0 ATGGCAGGGGACCACCCAGTTGGGCACTGATATGATCGTGTGTATCTGCAGAGTAGTAAC pro1 60 CTTTCTTTTCTCAAGACCATCCAG 84 pro2 60 GTGTCTCTGCTCAAGACCATCCAG 84 pro3 60 CACTCTTTTCTCATGACCATCCAG 84 """, ) class Test_dn_ds(unittest.TestCase): def test_dn_ds(self): aligner = CodonAligner() nucleotide_records = SeqIO.index("codonalign/egfr_nucl.fa", "fasta") protein_alignment = Align.read("codonalign/egfr_pro.aln", "clustal") self.assertEqual(len(protein_alignment.sequences), 6) codon_alignments = [] protein_record = protein_alignment.sequences[0] self.assertEqual(protein_record.id, "gi|17136534|ref|NP_476758.1|") nucleotide_record = nucleotide_records["gi|24657088|ref|NM_057410.3|"] alignments = aligner.align(protein_record, nucleotide_record) self.assertEqual(len(alignments), 1) alignment = next(alignments) codon_alignments.append(alignment) self.assertTrue( np.array_equal(alignment.coordinates, np.array([[0, 1377], [84, 4215]])) ) self.assertEqual( str(alignment), """\ gi|171365 0 M M I I S M W M S I S R G L W D S S S I gi|246570 84 ATGATGATTATCAGCATGTGGATGAGCATATCGCGAGGATTGTGGGACAGCAGCTCCATC gi|171365 20 W S V L L I L A C M A S I T T S S S V S gi|246570 144 TGGTCGGTGCTGCTGATCCTCGCCTGCATGGCATCCATCACCACAAGCTCATCGGTCAGC gi|171365 40 N A G Y V D N G N M K V C I G T K S R L gi|246570 204 AATGCCGGCTATGTGGATAATGGCAATATGAAAGTCTGCATCGGCACTAAATCTCGGCTC gi|171365 60 S V P S N K E H H Y R N L R D R Y T N C gi|246570 264 TCCGTGCCCTCCAACAAGGAACATCATTACCGGAACCTCAGAGATCGGTACACGAACTGT gi|171365 80 T Y V D G N L E L T W L P N E N L D L S gi|246570 324 ACGTATGTGGATGGCAACCTGGAGCTGACCTGGCTGCCCAACGAGAATTTGGACCTCAGC gi|171365 100 F L D N I R E V T G Y I L I S H V D V K gi|246570 384 TTCCTGGACAACATACGGGAGGTCACCGGCTATATTCTGATCAGTCATGTGGACGTTAAG gi|171365 120 K V V F P K L Q I I R G R T L F S L S V gi|246570 444 AAAGTGGTATTTCCCAAACTACAAATCATTCGCGGACGCACGCTGTTCAGCTTATCCGTG gi|171365 140 E E E K Y A L F V T Y S K M Y T L E I P gi|246570 504 GAGGAGGAGAAGTATGCCTTGTTCGTCACTTATTCCAAAATGTACACGCTGGAGATTCCC gi|171365 160 D L R D V L N G Q V G F H N N Y N L C H gi|246570 564 GATCTACGCGATGTCTTAAATGGCCAAGTGGGCTTCCACAACAACTACAATCTCTGCCAC gi|171365 180 M R T I Q W S E I V S N G T D A Y Y N Y gi|246570 624 ATGCGAACGATCCAGTGGTCGGAGATTGTATCCAACGGCACGGATGCATACTACAACTAC gi|171365 200 D F T A P E R E C P K C H E S C T H G C gi|246570 684 GACTTTACTGCTCCGGAGCGCGAGTGTCCCAAGTGCCACGAGAGCTGCACGCACGGATGT gi|171365 220 W G E G P K N C Q K F S K L T C S P Q C gi|246570 744 TGGGGCGAGGGTCCCAAGAATTGCCAGAAGTTCAGCAAGCTCACCTGCTCGCCACAGTGT gi|171365 240 A G G R C Y G P K P R E C C H L F C A G gi|246570 804 GCCGGAGGTCGTTGCTATGGACCAAAGCCGCGGGAGTGTTGTCACCTCTTCTGCGCCGGA gi|171365 260 G C T G P T Q K D C I A C K N F F D E G gi|246570 864 GGATGCACTGGTCCCACGCAAAAGGATTGCATCGCCTGCAAGAACTTCTTCGACGAGGGC gi|171365 280 V C K E E C P P M R K Y N P T T Y V L E gi|246570 924 GTATGCAAGGAGGAATGCCCGCCCATGCGCAAGTACAATCCCACCACCTATGTTCTTGAA gi|171365 300 T N P E G K Y A Y G A T C V K E C P G H gi|246570 984 ACGAATCCTGAGGGAAAGTATGCCTATGGTGCCACCTGCGTCAAGGAGTGTCCCGGTCAT gi|171365 320 L L R D N G A C V R S C P Q D K M D K G gi|246570 1044 CTGTTGCGTGATAATGGCGCCTGCGTGCGCAGCTGTCCCCAGGACAAGATGGACAAGGGG gi|171365 340 G E C V P C N G P C P K T C P G V T V L gi|246570 1104 GGCGAGTGTGTGCCCTGCAATGGACCGTGCCCCAAAACCTGCCCGGGCGTTACTGTCCTG gi|171365 360 H A G N I D S F R N C T V I D G N I R I gi|246570 1164 CATGCCGGCAACATTGACTCGTTCCGGAATTGTACGGTGATCGATGGCAACATTCGCATT gi|171365 380 L D Q T F S G F Q D V Y A N Y T M G P R gi|246570 1224 TTGGATCAGACCTTCTCGGGCTTCCAGGATGTCTATGCCAACTACACGATGGGACCACGA gi|171365 400 Y I P L D P E R L E V F S T V K E I T G gi|246570 1284 TACATACCGCTGGATCCCGAGCGACTGGAGGTGTTCTCCACGGTGAAGGAGATCACCGGG gi|171365 420 Y L N I E G T H P Q F R N L S Y F R N L gi|246570 1344 TATCTGAATATCGAGGGAACCCACCCGCAGTTCCGGAATCTGTCGTACTTCCGCAATCTG gi|171365 440 E T I H G R Q L M E S M F A A L A I V K gi|246570 1404 GAAACAATTCATGGCCGCCAGCTGATGGAGAGCATGTTTGCCGCTTTGGCGATCGTTAAG gi|171365 460 S S L Y S L E M R N L K Q I S S G S V V gi|246570 1464 TCATCCCTGTACAGCCTGGAGATGCGCAATCTGAAGCAGATTAGTTCCGGCAGTGTGGTC gi|171365 480 I Q H N R D L C Y V S N I R W P A I Q K gi|246570 1524 ATCCAGCATAATAGAGACCTCTGCTACGTAAGCAATATCCGTTGGCCGGCCATTCAGAAG gi|171365 500 E P E Q K V W V N E N L R A D L C E K N gi|246570 1584 GAGCCCGAACAGAAGGTGTGGGTCAACGAGAATCTCAGGGCGGATCTATGCGAGAAAAAT gi|171365 520 G T I C S D Q C N E D G C W G A G T D Q gi|246570 1644 GGAACCATTTGCTCGGATCAGTGCAACGAGGACGGCTGCTGGGGAGCTGGCACGGATCAG gi|171365 540 C L T C K N F N F N G T C I A D C G Y I gi|246570 1704 TGCCTTACCTGCAAGAACTTCAATTTCAATGGCACCTGCATCGCCGACTGTGGTTATATA gi|171365 560 S N A Y K F D N R T C K I C H P E C R T gi|246570 1764 TCCAATGCCTACAAGTTTGACAATAGAACGTGCAAGATATGCCATCCAGAGTGCCGGACT gi|171365 580 C N G A G A D H C Q E C V H V R D G Q H gi|246570 1824 TGCAATGGAGCTGGAGCAGATCACTGCCAGGAGTGCGTCCATGTGAGGGACGGTCAGCAC gi|171365 600 C V S E C P K N K Y N D R G V C R E C H gi|246570 1884 TGTGTGTCCGAGTGCCCGAAGAACAAGTACAACGATCGTGGTGTCTGCCGAGAGTGCCAC gi|171365 620 A T C D G C T G P K D T I G I G A C T T gi|246570 1944 GCCACCTGCGATGGATGCACTGGGCCCAAGGACACCATCGGCATTGGAGCGTGTACAACG gi|171365 640 C N L A I I N N D A T V K R C L L K D D gi|246570 2004 TGCAATTTGGCCATTATCAACAATGACGCCACAGTAAAACGCTGCCTGCTGAAGGACGAC gi|171365 660 K C P D G Y F W E Y V H P Q E Q G S L K gi|246570 2064 AAGTGCCCCGATGGGTACTTCTGGGAGTATGTGCATCCACAAGAGCAGGGATCGCTAAAG gi|171365 680 P L A G R A V C R K C H P L C E L C T N gi|246570 2124 CCATTGGCCGGCAGAGCAGTTTGCCGAAAGTGCCATCCCCTTTGCGAGCTGTGCACCAAC gi|171365 700 Y G Y H E Q V C S K C T H Y K R R E Q C gi|246570 2184 TACGGATACCATGAACAGGTGTGCTCCAAGTGCACCCACTACAAGCGACGAGAGCAGTGC gi|171365 720 E T E C P A D H Y T D E E Q R E C F Q C gi|246570 2244 GAGACCGAGTGTCCGGCCGATCACTACACGGATGAGGAGCAGCGCGAGTGCTTCCAGTGC gi|171365 740 H P E C N G C T G P G A D D C K S C R N gi|246570 2304 CACCCAGAATGCAACGGTTGCACTGGTCCGGGTGCCGACGATTGCAAGTCTTGTCGCAAC gi|171365 760 F K L F D A N E T G P Y V N S T M F N C gi|246570 2364 TTCAAGTTGTTCGACGCGAATGAGACGGGTCCCTATGTGAACTCCACGATGTTCAATTGC gi|171365 780 T S K C P L E M R H V N Y Q Y T A I G P gi|246570 2424 ACCTCGAAGTGTCCCTTGGAGATGCGACATGTGAACTATCAGTACACGGCCATTGGACCC gi|171365 800 Y C A A S P P R S S K I T A N L D V N M gi|246570 2484 TACTGTGCAGCTAGTCCGCCGAGGAGCAGCAAGATAACTGCCAATCTGGATGTGAACATG gi|171365 820 I F I I T G A V L V P T I C I L C V V T gi|246570 2544 ATCTTCATTATCACTGGTGCTGTTCTGGTGCCGACGATCTGCATCCTCTGCGTGGTCACA gi|171365 840 Y I C R Q K Q K A K K E T V K M T M A L gi|246570 2604 TACATTTGTCGGCAAAAGCAAAAGGCCAAGAAAGAAACAGTGAAGATGACCATGGCTCTG gi|171365 860 S G C E D S E P L R P S N I G A N L C K gi|246570 2664 TCCGGCTGTGAGGATTCCGAGCCGCTGCGTCCCTCGAACATTGGAGCCAATCTATGCAAG gi|171365 880 L R I V K D A E L R K G G V L G M G A F gi|246570 2724 TTGCGCATTGTCAAGGACGCCGAGTTGCGCAAGGGCGGAGTCCTCGGAATGGGAGCCTTT gi|171365 900 G R V Y K G V W V P E G E N V K I P V A gi|246570 2784 GGACGAGTGTACAAGGGCGTTTGGGTGCCGGAGGGTGAGAACGTCAAGATTCCAGTGGCC gi|171365 920 I K E L L K S T G A E S S E E F L R E A gi|246570 2844 ATTAAGGAGCTGCTCAAGTCCACAGGCGCCGAGTCAAGCGAAGAGTTCCTCCGCGAAGCC gi|171365 940 Y I M A S V E H V N L L K L L A V C M S gi|246570 2904 TACATCATGGCCTCTGTGGAGCACGTTAATCTGCTGAAGCTCCTGGCCGTCTGCATGTCC gi|171365 960 S Q M M L I T Q L M P L G C L L D Y V R gi|246570 2964 TCACAAATGATGCTAATCACGCAACTGATGCCGCTTGGCTGCCTGTTGGACTATGTGCGA gi|171365 980 N N R D K I G S K A L L N W S T Q I A K gi|246570 3024 AATAACCGGGACAAGATCGGCTCTAAGGCTCTGCTCAACTGGAGCACGCAAATCGCCAAG gi|171365 1000 G M S Y L E E K R L V H R D L A A R N V gi|246570 3084 GGCATGTCGTATCTGGAGGAGAAGCGACTGGTCCACAGAGACTTGGCTGCCCGCAATGTC gi|171365 1020 L V Q T P S L V K I T D F G L A K L L S gi|246570 3144 CTGGTGCAGACTCCCTCGCTGGTGAAGATCACCGACTTTGGGCTGGCCAAGTTGCTGAGC gi|171365 1040 S D S N E Y K A A G G K M P I K W L A L gi|246570 3204 AGCGATTCCAATGAGTACAAGGCTGCTGGCGGCAAGATGCCCATCAAGTGGTTGGCACTG gi|171365 1060 E C I R N R V F T S K S D V W A F G V T gi|246570 3264 GAGTGCATTCGCAATCGTGTATTCACCAGCAAGTCCGATGTCTGGGCCTTTGGTGTGACA gi|171365 1080 I W E L L T F G Q R P H E N I P A K D I gi|246570 3324 ATTTGGGAACTGCTGACCTTTGGCCAGCGTCCACACGAGAACATCCCCGCTAAGGATATT gi|171365 1100 P D L I E V G L K L E Q P E I C S L D I gi|246570 3384 CCCGATCTTATTGAAGTCGGTCTGAAGCTGGAGCAGCCGGAGATTTGTTCGCTGGACATT gi|171365 1120 Y C T L L S C W H L D A A M R P T F K Q gi|246570 3444 TACTGCACACTTCTCTCGTGCTGGCACTTGGATGCCGCCATGCGTCCAACCTTCAAGCAG gi|171365 1140 L T T V F A E F A R D P G R Y L A I P G gi|246570 3504 CTGACTACGGTCTTTGCTGAGTTCGCCAGAGATCCGGGTCGCTATCTGGCCATTCCCGGG gi|171365 1160 D K F T R L P A Y T S Q D E K D L I R K gi|246570 3564 GATAAGTTCACCCGGCTGCCGGCCTACACGAGTCAGGATGAGAAGGATCTCATCCGAAAA gi|171365 1180 L A P T T D G S E A I A E P D D Y L Q P gi|246570 3624 TTGGCTCCCACCACCGATGGGTCCGAAGCCATTGCGGAACCCGATGACTACCTGCAACCC gi|171365 1200 K A A P G P S H R T D C T D E I P K L N gi|246570 3684 AAGGCAGCACCTGGTCCTAGTCACAGAACCGACTGCACGGATGAGATACCCAAGCTGAAC gi|171365 1220 R Y C K D P S N K N S S T G D D E T D S gi|246570 3744 CGCTACTGCAAGGATCCTAGCAACAAGAATTCGAGTACCGGAGACGATGAGACGGATTCG gi|171365 1240 S A R E V G V G N L R L D L P V D E D D gi|246570 3804 AGTGCCCGGGAAGTGGGCGTGGGTAATCTGCGCCTCGATCTACCAGTCGATGAGGATGAT gi|171365 1260 Y L M P T C Q P G P N N N N N I N N P N gi|246570 3864 TACCTGATGCCCACATGCCAACCGGGGCCCAACAACAACAACAACATAAATAATCCCAAT gi|171365 1280 Q N N M A A V G V A A G Y M D L I G V P gi|246570 3924 CAAAACAATATGGCAGCTGTGGGCGTGGCTGCCGGCTACATGGATCTCATCGGAGTGCCC gi|171365 1300 V S V D N P E Y L L N A Q T L G V G E S gi|246570 3984 GTTAGTGTGGACAATCCGGAGTATCTGCTAAACGCGCAGACACTGGGTGTTGGGGAGTCG gi|171365 1320 P I P T Q T I G I P V M G V P G T M E V gi|246570 4044 CCGATACCCACCCAGACCATCGGGATACCGGTGATGGGAGTCCCGGGCACCATGGAGGTC gi|171365 1340 K V P M P G S E P T S S D H E Y Y N D T gi|246570 4104 AAGGTGCCAATGCCAGGCAGTGAGCCAACGAGCTCCGATCACGAGTACTACAATGATACC gi|171365 1360 Q R E L Q P L H R N R N T E T R V 1377 gi|246570 4164 CAACGGGAGTTGCAGCCACTGCATCGAAACCGCAACACGGAGACGAGGGTG 4215 """, ) protein_record = protein_alignment.sequences[1] self.assertEqual(protein_record.id, "gi|17136536|ref|NP_476759.1|") nucleotide_record = nucleotide_records["gi|24657104|ref|NM_057411.3|"] alignments = aligner.align(protein_record, nucleotide_record) self.assertEqual(len(alignments), 1) alignment = next(alignments) codon_alignments.append(alignment) self.assertTrue( np.array_equal(alignment.coordinates, np.array([[0, 1426], [22, 4300]])) ) self.assertEqual( str(alignment), """\ gi|171365 0 M L L R R R N G P C P F P L L L L L L A gi|246571 22 ATGCTGCTGCGACGGCGCAACGGCCCCTGCCCCTTCCCCCTGCTGCTCCTGCTCCTGGCC gi|171365 20 H C I C I W P A S A A R D R Y A R Q N N gi|246571 82 CACTGCATTTGCATTTGGCCCGCGTCGGCGGCCCGCGATCGCTACGCCCGCCAGAACAAT gi|171365 40 R Q R H Q D I D R D R D R D R F L Y R S gi|246571 142 CGCCAGCGCCATCAGGATATAGATCGCGATCGGGATCGAGATCGATTCCTATACCGCAGC gi|171365 60 S S A Q N R Q R G G A N F A L G L G A N gi|246571 202 AGTTCGGCCCAAAATCGACAGAGGGGCGGGGCCAACTTCGCCCTGGGACTGGGAGCCAAC gi|171365 80 G V T I P T S L E D K N K N E F V K G K gi|246571 262 GGAGTCACCATTCCCACCAGTCTGGAGGATAAGAACAAGAACGAGTTCGTCAAGGGGAAA gi|171365 100 I C I G T K S R L S V P S N K E H H Y R gi|246571 322 ATCTGCATCGGCACTAAATCTCGGCTCTCCGTGCCCTCCAACAAGGAACATCATTACCGG gi|171365 120 N L R D R Y T N C T Y V D G N L E L T W gi|246571 382 AACCTCAGAGATCGGTACACGAACTGTACGTATGTGGATGGCAACCTGGAGCTGACCTGG gi|171365 140 L P N E N L D L S F L D N I R E V T G Y gi|246571 442 CTGCCCAACGAGAATTTGGACCTCAGCTTCCTGGACAACATACGGGAGGTCACCGGCTAT gi|171365 160 I L I S H V D V K K V V F P K L Q I I R gi|246571 502 ATTCTGATCAGTCATGTGGACGTTAAGAAAGTGGTATTTCCCAAACTACAAATCATTCGC gi|171365 180 G R T L F S L S V E E E K Y A L F V T Y gi|246571 562 GGACGCACGCTGTTCAGCTTATCCGTGGAGGAGGAGAAGTATGCCTTGTTCGTCACTTAT gi|171365 200 S K M Y T L E I P D L R D V L N G Q V G gi|246571 622 TCCAAAATGTACACGCTGGAGATTCCCGATCTACGCGATGTCTTAAATGGCCAAGTGGGC gi|171365 220 F H N N Y N L C H M R T I Q W S E I V S gi|246571 682 TTCCACAACAACTACAATCTCTGCCACATGCGAACGATCCAGTGGTCGGAGATTGTATCC gi|171365 240 N G T D A Y Y N Y D F T A P E R E C P K gi|246571 742 AACGGCACGGATGCATACTACAACTACGACTTTACTGCTCCGGAGCGCGAGTGTCCCAAG gi|171365 260 C H E S C T H G C W G E G P K N C Q K F gi|246571 802 TGCCACGAGAGCTGCACGCACGGATGTTGGGGCGAGGGTCCCAAGAATTGCCAGAAGTTC gi|171365 280 S K L T C S P Q C A G G R C Y G P K P R gi|246571 862 AGCAAGCTCACCTGCTCGCCACAGTGTGCCGGAGGTCGTTGCTATGGACCAAAGCCGCGG gi|171365 300 E C C H L F C A G G C T G P T Q K D C I gi|246571 922 GAGTGTTGTCACCTCTTCTGCGCCGGAGGATGCACTGGTCCCACGCAAAAGGATTGCATC gi|171365 320 A C K N F F D E G V C K E E C P P M R K gi|246571 982 GCCTGCAAGAACTTCTTCGACGAGGGCGTATGCAAGGAGGAATGCCCGCCCATGCGCAAG gi|171365 340 Y N P T T Y V L E T N P E G K Y A Y G A gi|246571 1042 TACAATCCCACCACCTATGTTCTTGAAACGAATCCTGAGGGAAAGTATGCCTATGGTGCC gi|171365 360 T C V K E C P G H L L R D N G A C V R S gi|246571 1102 ACCTGCGTCAAGGAGTGTCCCGGTCATCTGTTGCGTGATAATGGCGCCTGCGTGCGCAGC gi|171365 380 C P Q D K M D K G G E C V P C N G P C P gi|246571 1162 TGTCCCCAGGACAAGATGGACAAGGGGGGCGAGTGTGTGCCCTGCAATGGACCGTGCCCC gi|171365 400 K T C P G V T V L H A G N I D S F R N C gi|246571 1222 AAAACCTGCCCGGGCGTTACTGTCCTGCATGCCGGCAACATTGACTCGTTCCGGAATTGT gi|171365 420 T V I D G N I R I L D Q T F S G F Q D V gi|246571 1282 ACGGTGATCGATGGCAACATTCGCATTTTGGATCAGACCTTCTCGGGCTTCCAGGATGTC gi|171365 440 Y A N Y T M G P R Y I P L D P E R L E V gi|246571 1342 TATGCCAACTACACGATGGGACCACGATACATACCGCTGGATCCCGAGCGACTGGAGGTG gi|171365 460 F S T V K E I T G Y L N I E G T H P Q F gi|246571 1402 TTCTCCACGGTGAAGGAGATCACCGGGTATCTGAATATCGAGGGAACCCACCCGCAGTTC gi|171365 480 R N L S Y F R N L E T I H G R Q L M E S gi|246571 1462 CGGAATCTGTCGTACTTCCGCAATCTGGAAACAATTCATGGCCGCCAGCTGATGGAGAGC gi|171365 500 M F A A L A I V K S S L Y S L E M R N L gi|246571 1522 ATGTTTGCCGCTTTGGCGATCGTTAAGTCATCCCTGTACAGCCTGGAGATGCGCAATCTG gi|171365 520 K Q I S S G S V V I Q H N R D L C Y V S gi|246571 1582 AAGCAGATTAGTTCCGGCAGTGTGGTCATCCAGCATAATAGAGACCTCTGCTACGTAAGC gi|171365 540 N I R W P A I Q K E P E Q K V W V N E N gi|246571 1642 AATATCCGTTGGCCGGCCATTCAGAAGGAGCCCGAACAGAAGGTGTGGGTCAACGAGAAT gi|171365 560 L R A D L C E K N G T I C S D Q C N E D gi|246571 1702 CTCAGGGCGGATCTATGCGAGAAAAATGGAACCATTTGCTCGGATCAGTGCAACGAGGAC gi|171365 580 G C W G A G T D Q C L T C K N F N F N G gi|246571 1762 GGCTGCTGGGGAGCTGGCACGGATCAGTGCCTTACCTGCAAGAACTTCAATTTCAATGGC gi|171365 600 T C I A D C G Y I S N A Y K F D N R T C gi|246571 1822 ACCTGCATCGCCGACTGTGGTTATATATCCAATGCCTACAAGTTTGACAATAGAACGTGC gi|171365 620 K I C H P E C R T C N G A G A D H C Q E gi|246571 1882 AAGATATGCCATCCAGAGTGCCGGACTTGCAATGGAGCTGGAGCAGATCACTGCCAGGAG gi|171365 640 C V H V R D G Q H C V S E C P K N K Y N gi|246571 1942 TGCGTCCATGTGAGGGACGGTCAGCACTGTGTGTCCGAGTGCCCGAAGAACAAGTACAAC gi|171365 660 D R G V C R E C H A T C D G C T G P K D gi|246571 2002 GATCGTGGTGTCTGCCGAGAGTGCCACGCCACCTGCGATGGATGCACTGGGCCCAAGGAC gi|171365 680 T I G I G A C T T C N L A I I N N D A T gi|246571 2062 ACCATCGGCATTGGAGCGTGTACAACGTGCAATTTGGCCATTATCAACAATGACGCCACA gi|171365 700 V K R C L L K D D K C P D G Y F W E Y V gi|246571 2122 GTAAAACGCTGCCTGCTGAAGGACGACAAGTGCCCCGATGGGTACTTCTGGGAGTATGTG gi|171365 720 H P Q E Q G S L K P L A G R A V C R K C gi|246571 2182 CATCCACAAGAGCAGGGATCGCTAAAGCCATTGGCCGGCAGAGCAGTTTGCCGAAAGTGC gi|171365 740 H P L C E L C T N Y G Y H E Q V C S K C gi|246571 2242 CATCCCCTTTGCGAGCTGTGCACCAACTACGGATACCATGAACAGGTGTGCTCCAAGTGC gi|171365 760 T H Y K R R E Q C E T E C P A D H Y T D gi|246571 2302 ACCCACTACAAGCGACGAGAGCAGTGCGAGACCGAGTGTCCGGCCGATCACTACACGGAT gi|171365 780 E E Q R E C F Q C H P E C N G C T G P G gi|246571 2362 GAGGAGCAGCGCGAGTGCTTCCAGTGCCACCCAGAATGCAACGGTTGCACTGGTCCGGGT gi|171365 800 A D D C K S C R N F K L F D A N E T G P gi|246571 2422 GCCGACGATTGCAAGTCTTGTCGCAACTTCAAGTTGTTCGACGCGAATGAGACGGGTCCC gi|171365 820 Y V N S T M F N C T S K C P L E M R H V gi|246571 2482 TATGTGAACTCCACGATGTTCAATTGCACCTCGAAGTGTCCCTTGGAGATGCGACATGTG gi|171365 840 N Y Q Y T A I G P Y C A A S P P R S S K gi|246571 2542 AACTATCAGTACACGGCCATTGGACCCTACTGTGCAGCTAGTCCGCCGAGGAGCAGCAAG gi|171365 860 I T A N L D V N M I F I I T G A V L V P gi|246571 2602 ATAACTGCCAATCTGGATGTGAACATGATCTTCATTATCACTGGTGCTGTTCTGGTGCCG gi|171365 880 T I C I L C V V T Y I C R Q K Q K A K K gi|246571 2662 ACGATCTGCATCCTCTGCGTGGTCACATACATTTGTCGGCAAAAGCAAAAGGCCAAGAAA gi|171365 900 E T V K M T M A L S G C E D S E P L R P gi|246571 2722 GAAACAGTGAAGATGACCATGGCTCTGTCCGGCTGTGAGGATTCCGAGCCGCTGCGTCCC gi|171365 920 S N I G A N L C K L R I V K D A E L R K gi|246571 2782 TCGAACATTGGAGCCAATCTATGCAAGTTGCGCATTGTCAAGGACGCCGAGTTGCGCAAG gi|171365 940 G G V L G M G A F G R V Y K G V W V P E gi|246571 2842 GGCGGAGTCCTCGGAATGGGAGCCTTTGGACGAGTGTACAAGGGCGTTTGGGTGCCGGAG gi|171365 960 G E N V K I P V A I K E L L K S T G A E gi|246571 2902 GGTGAGAACGTCAAGATTCCAGTGGCCATTAAGGAGCTGCTCAAGTCCACAGGCGCCGAG gi|171365 980 S S E E F L R E A Y I M A S V E H V N L gi|246571 2962 TCAAGCGAAGAGTTCCTCCGCGAAGCCTACATCATGGCCTCTGTGGAGCACGTTAATCTG gi|171365 1000 L K L L A V C M S S Q M M L I T Q L M P gi|246571 3022 CTGAAGCTCCTGGCCGTCTGCATGTCCTCACAAATGATGCTAATCACGCAACTGATGCCG gi|171365 1020 L G C L L D Y V R N N R D K I G S K A L gi|246571 3082 CTTGGCTGCCTGTTGGACTATGTGCGAAATAACCGGGACAAGATCGGCTCTAAGGCTCTG gi|171365 1040 L N W S T Q I A K G M S Y L E E K R L V gi|246571 3142 CTCAACTGGAGCACGCAAATCGCCAAGGGCATGTCGTATCTGGAGGAGAAGCGACTGGTC gi|171365 1060 H R D L A A R N V L V Q T P S L V K I T gi|246571 3202 CACAGAGACTTGGCTGCCCGCAATGTCCTGGTGCAGACTCCCTCGCTGGTGAAGATCACC gi|171365 1080 D F G L A K L L S S D S N E Y K A A G G gi|246571 3262 GACTTTGGGCTGGCCAAGTTGCTGAGCAGCGATTCCAATGAGTACAAGGCTGCTGGCGGC gi|171365 1100 K M P I K W L A L E C I R N R V F T S K gi|246571 3322 AAGATGCCCATCAAGTGGTTGGCACTGGAGTGCATTCGCAATCGTGTATTCACCAGCAAG gi|171365 1120 S D V W A F G V T I W E L L T F G Q R P gi|246571 3382 TCCGATGTCTGGGCCTTTGGTGTGACAATTTGGGAACTGCTGACCTTTGGCCAGCGTCCA gi|171365 1140 H E N I P A K D I P D L I E V G L K L E gi|246571 3442 CACGAGAACATCCCCGCTAAGGATATTCCCGATCTTATTGAAGTCGGTCTGAAGCTGGAG gi|171365 1160 Q P E I C S L D I Y C T L L S C W H L D gi|246571 3502 CAGCCGGAGATTTGTTCGCTGGACATTTACTGCACACTTCTCTCGTGCTGGCACTTGGAT gi|171365 1180 A A M R P T F K Q L T T V F A E F A R D gi|246571 3562 GCCGCCATGCGTCCAACCTTCAAGCAGCTGACTACGGTCTTTGCTGAGTTCGCCAGAGAT gi|171365 1200 P G R Y L A I P G D K F T R L P A Y T S gi|246571 3622 CCGGGTCGCTATCTGGCCATTCCCGGGGATAAGTTCACCCGGCTGCCGGCCTACACGAGT gi|171365 1220 Q D E K D L I R K L A P T T D G S E A I gi|246571 3682 CAGGATGAGAAGGATCTCATCCGAAAATTGGCTCCCACCACCGATGGGTCCGAAGCCATT gi|171365 1240 A E P D D Y L Q P K A A P G P S H R T D gi|246571 3742 GCGGAACCCGATGACTACCTGCAACCCAAGGCAGCACCTGGTCCTAGTCACAGAACCGAC gi|171365 1260 C T D E I P K L N R Y C K D P S N K N S gi|246571 3802 TGCACGGATGAGATACCCAAGCTGAACCGCTACTGCAAGGATCCTAGCAACAAGAATTCG gi|171365 1280 S T G D D E T D S S A R E V G V G N L R gi|246571 3862 AGTACCGGAGACGATGAGACGGATTCGAGTGCCCGGGAAGTGGGCGTGGGTAATCTGCGC gi|171365 1300 L D L P V D E D D Y L M P T C Q P G P N gi|246571 3922 CTCGATCTACCAGTCGATGAGGATGATTACCTGATGCCCACATGCCAACCGGGGCCCAAC gi|171365 1320 N N N N I N N P N Q N N M A A V G V A A gi|246571 3982 AACAACAACAACATAAATAATCCCAATCAAAACAATATGGCAGCTGTGGGCGTGGCTGCC gi|171365 1340 G Y M D L I G V P V S V D N P E Y L L N gi|246571 4042 GGCTACATGGATCTCATCGGAGTGCCCGTTAGTGTGGACAATCCGGAGTATCTGCTAAAC gi|171365 1360 A Q T L G V G E S P I P T Q T I G I P V gi|246571 4102 GCGCAGACACTGGGTGTTGGGGAGTCGCCGATACCCACCCAGACCATCGGGATACCGGTG gi|171365 1380 M G V P G T M E V K V P M P G S E P T S gi|246571 4162 ATGGGAGTCCCGGGCACCATGGAGGTCAAGGTGCCAATGCCAGGCAGTGAGCCAACGAGC gi|171365 1400 S D H E Y Y N D T Q R E L Q P L H R N R gi|246571 4222 TCCGATCACGAGTACTACAATGATACCCAACGGGAGTTGCAGCCACTGCATCGAAACCGC gi|171365 1420 N T E T R V 1426 gi|246571 4282 AACACGGAGACGAGGGTG 4300 """, ) protein_record = protein_alignment.sequences[2] self.assertEqual(protein_record.id, "gi|302179501|gb|ADK98534.1|") nucleotide_record = nucleotide_records["gi|302179500|gb|HM749883.1|"] alignments = aligner.align(protein_record, nucleotide_record) self.assertEqual(len(alignments), 1) alignment = next(alignments) codon_alignments.append(alignment) self.assertTrue( np.array_equal(alignment.coordinates, np.array([[0, 1185], [0, 3555]])) ) self.assertEqual( str(alignment), """\ gi|302179 0 M K K H E L L C Q G T S N K L T Q L G T gi|302179 0 ATGAAAAAGCACGAGTTACTTTGCCAAGGGACAAGTAACAAGCTCACCCAGTTGGGCACT gi|302179 20 F E D H F L S L Q R M F N N C E V V L G gi|302179 60 TTTGAAGACCACTTTCTGAGCCTACAGAGGATGTTCAACAACTGTGAGGTGGTCCTTGGG gi|302179 40 N L E I T Y M Q S S Y N L S F L K T I Q gi|302179 120 AATTTGGAAATTACCTACATGCAGAGTAGTTACAACCTTTCTTTTCTCAAGACCATCCAG gi|302179 60 E V A G Y V L I A L N T V E K I P L E N gi|302179 180 GAGGTTGCCGGCTATGTACTCATTGCCCTCAACACAGTGGAGAAGATTCCGCTGGAAAAC gi|302179 80 L Q I I R G N V L Y E N T H A L A V L S gi|302179 240 CTGCAGATCATCCGAGGAAATGTGCTTTATGAAAACACCCATGCCTTAGCCGTCTTATCC gi|302179 100 N Y G A N K T G L R E L P L R N L Q E I gi|302179 300 AACTATGGAGCAAACAAAACCGGACTGAGGGAGCTGCCCTTGAGAAACTTACAGGAAATT gi|302179 120 L Q G A V R F S N N P V L C N V E T I Q gi|302179 360 CTGCAAGGTGCCGTGAGATTCAGCAACAACCCTGTCCTCTGCAACGTGGAGACCATCCAG gi|302179 140 W R D I V N P D F L S N M T G D F Q N Q gi|302179 420 TGGCGGGACATCGTCAACCCTGATTTTCTAAGCAACATGACAGGGGACTTTCAGAACCAG gi|302179 160 Q G N C P K C D P A C L N R S C W G A G gi|302179 480 CAGGGCAACTGCCCAAAGTGTGATCCAGCCTGTCTCAACAGAAGCTGCTGGGGTGCCGGG gi|302179 180 E E N C Q K L T K I I C A Q Q C S G R C gi|302179 540 GAGGAGAACTGTCAGAAATTGACCAAAATCATCTGTGCCCAGCAGTGTTCCGGGCGCTGC gi|302179 200 R G R S P S D C C H N Q C A A G C T G P gi|302179 600 CGTGGCAGGTCCCCCAGTGACTGCTGCCACAACCAGTGTGCCGCTGGCTGCACAGGGCCA gi|302179 220 R E S D C L V C R R F R D E A T C K D T gi|302179 660 CGGGAGAGCGACTGCCTGGTCTGCCGCAGGTTCCGTGATGAAGCCACCTGCAAGGACACG gi|302179 240 C P P L M L Y D P T T Y E M K V N P L G gi|302179 720 TGTCCGCCACTCATGCTCTATGACCCTACCACCTACGAAATGAAGGTCAACCCGCTGGGG gi|302179 260 K Y S F G A T C V K K C P R N Y V V T D gi|302179 780 AAGTACAGCTTTGGCGCCACCTGTGTCAAGAAGTGTCCCCGTAACTACGTGGTGACAGAC gi|302179 280 H G S C V R A C S S D S Q E V E E D G V gi|302179 840 CACGGCTCCTGCGTCCGCGCCTGCAGTTCTGACAGCCAGGAGGTAGAGGAAGACGGTGTC gi|302179 300 R K C K K C D G P C G K V C N G I G I G gi|302179 900 CGCAAGTGTAAAAAGTGTGACGGGCCTTGTGGCAAAGTTTGTAACGGAATAGGAATCGGT gi|302179 320 E F K D T L S I N A T N I K H F R N C T gi|302179 960 GAGTTTAAAGACACACTTTCCATAAATGCTACAAACATTAAACACTTCAGAAACTGCACA gi|302179 340 S I S G D L H I L P V A F R G D S F T R gi|302179 1020 TCCATCAGTGGAGATCTTCATATCCTGCCAGTAGCATTTAGGGGTGACTCCTTCACACGT gi|302179 360 T A P L D P K E L D I L R T V K E I T G gi|302179 1080 ACTGCACCTCTGGACCCGAAAGAACTGGACATTCTAAGAACTGTAAAAGAAATAACAGGG gi|302179 380 F L L I Q A W P E N R T D L H A F E N L gi|302179 1140 TTTTTGCTGATTCAGGCCTGGCCCGAAAACAGGACTGACCTCCATGCTTTTGAGAACCTG gi|302179 400 E I I R G R T K Q H G Q F S L A V V G L gi|302179 1200 GAAATCATACGTGGCAGAACGAAGCAGCATGGCCAGTTTTCTCTTGCGGTTGTCGGCCTG gi|302179 420 D I T S L G L R S L K E I S D G D V I I gi|302179 1260 GATATAACATCTTTGGGATTACGCTCCCTCAAGGAGATAAGTGATGGTGATGTGATAATT gi|302179 440 S G N R N L C Y A D T I R W K K L F G T gi|302179 1320 TCAGGAAATCGAAACTTGTGCTATGCAGATACAATACGCTGGAAAAAACTTTTTGGGACC gi|302179 460 S T Q K T K I L N N R S E K Q C K A A G gi|302179 1380 TCAACTCAGAAAACCAAAATTTTAAACAACAGGAGTGAAAAACAGTGCAAGGCCGCAGGC gi|302179 480 H I C H P L C S S E G C W G P G P K Y C gi|302179 1440 CACATCTGTCACCCGCTGTGCTCATCAGAGGGCTGCTGGGGACCGGGACCCAAATACTGC gi|302179 500 M S C Q N F S R G K E C V G K C N I L E gi|302179 1500 ATGTCCTGCCAGAACTTCAGTCGTGGCAAGGAGTGTGTGGGAAAGTGCAACATTCTAGAG gi|302179 520 G E P R E F V E N S E C V Q C H P E C L gi|302179 1560 GGAGAGCCCAGAGAATTCGTGGAGAACTCCGAGTGTGTGCAGTGCCATCCAGAATGCCTG gi|302179 540 P Q A M N V T C T G R G P G N C V K C A gi|302179 1620 CCCCAGGCCATGAACGTGACCTGCACTGGACGCGGACCAGGCAACTGTGTAAAGTGCGCC gi|302179 560 H Y I D G P H C V K T C P A G V A G E N gi|302179 1680 CACTACATTGATGGCCCTCACTGCGTCAAGACCTGCCCTGCTGGAGTCGCGGGAGAGAAT gi|302179 580 G T L I W K F A D A N H V C L L C H P N gi|302179 1740 GGCACCCTGATCTGGAAGTTTGCAGATGCCAACCACGTGTGTCTCCTGTGCCACCCCAAC gi|302179 600 C T Y G C E G P G L E G C P Q K G P K I gi|302179 1800 TGCACCTATGGCTGTGAAGGGCCAGGTCTCGAAGGCTGTCCACAAAAAGGGCCCAAGATC gi|302179 620 P S I A T G I V G G L L L V V V L A L S gi|302179 1860 CCGTCCATTGCCACGGGCATCGTGGGCGGCCTGCTGCTGGTGGTGGTGCTGGCCCTGAGC gi|302179 640 V G L F M R R R H I V R K R T L R R L L gi|302179 1920 GTCGGCCTCTTCATGCGCAGGCGCCACATCGTGCGCAAGCGCACACTGCGCCGGCTGCTG gi|302179 660 Q E R E L V E P L T P S G E A P N Q A L gi|302179 1980 CAGGAGCGTGAGCTCGTGGAGCCTCTGACGCCCAGCGGAGAAGCTCCCAACCAAGCTCTC gi|302179 680 L R I L K E T E F K K V K V L G S G A F gi|302179 2040 TTGAGGATCCTAAAGGAAACAGAATTCAAGAAGGTCAAGGTGCTGGGCTCGGGAGCATTT gi|302179 700 G T V Y K G L W I P E G E K V K I P V A gi|302179 2100 GGCACCGTGTACAAGGGACTCTGGATCCCAGAAGGCGAGAAGGTTAAAATTCCTGTAGCT gi|302179 720 I K E L R E A T S P K A N K E I L D E A gi|302179 2160 ATCAAGGAATTAAGAGAAGCCACATCTCCAAAAGCCAACAAGGAAATTCTTGATGAGGCC gi|302179 740 Y V M A S V D N P H V C R L L G I C L T gi|302179 2220 TACGTGATGGCCAGTGTGGACAACCCCCATGTGTGCCGCCTCCTGGGCATCTGCCTGACC gi|302179 760 S T V Q L I T Q L M P F G C L L D Y V R gi|302179 2280 TCCACCGTGCAGCTCATCACACAGCTCATGCCCTTCGGCTGCCTGCTGGACTACGTCCGC gi|302179 780 E H K D N V G S Q Y L L N W C V Q I A K gi|302179 2340 GAGCACAAGGACAATGTCGGCTCCCAGTACCTGCTCAACTGGTGTGTGCAGATCGCAAAG gi|302179 800 G M N Y L E D R R L V H R D L A A R N V gi|302179 2400 GGCATGAATTACCTGGAAGACCGGCGCTTGGTGCATAGGGACCTGGCAGCCAGGAACGTG gi|302179 820 L V K T P Q H V K I T D F G L A K L L G gi|302179 2460 CTGGTGAAGACGCCGCAGCACGTGAAGATCACAGACTTCGGGCTGGCCAAGCTGCTGGGT gi|302179 840 A E E K E Y H A E G G K V P I K W M A L gi|302179 2520 GCCGAGGAGAAGGAGTATCATGCAGAAGGAGGCAAGGTCCCTATCAAATGGATGGCTTTG gi|302179 860 E S I L H R I Y T H Q S D V W S Y G V T gi|302179 2580 GAATCAATTTTACACCGAATTTATACCCATCAGAGTGATGTCTGGAGCTATGGAGTCACT gi|302179 880 V W E L M T F G S K P Y D G I P A S E I gi|302179 2640 GTTTGGGAGTTGATGACCTTTGGATCCAAGCCTTACGATGGAATCCCTGCGAGTGAGATC gi|302179 900 S T V L E K G E R L P Q P P I C T I D V gi|302179 2700 TCGACTGTCCTGGAGAAAGGAGAGCGCCTCCCACAGCCACCCATCTGCACCATCGACGTC gi|302179 920 Y M I M V K C W M I D A D S R P K F R E gi|302179 2760 TACATGATCATGGTCAAGTGCTGGATGATAGATGCAGACAGTCGCCCAAAGTTCCGTGAG gi|302179 940 L I L E F S K M A R D P Q R Y L V I Q G gi|302179 2820 TTGATCCTTGAATTCTCCAAGATGGCCCGAGACCCCCAGCGCTACCTTGTCATCCAGGGG gi|302179 960 D E R M H L P S P T D S N F Y R A L M D gi|302179 2880 GACGAGAGAATGCATTTGCCAAGCCCTACGGACTCCAACTTCTACCGCGCCCTGATGGAT gi|302179 980 E E D M E D V V D A D E Y L V P Q Q G F gi|302179 2940 GAGGAGGACATGGAGGATGTTGTGGATGCCGATGAGTACCTCGTCCCCCAGCAGGGCTTC gi|302179 1000 F H S P T T S R T P L L S S L S T S S N gi|302179 3000 TTCCACAGCCCCACCACCTCCCGGACACCCCTCCTCAGCTCGCTGAGCACCTCCAGCAAC gi|302179 1020 T P T V T C V D R N G S Y P L K E D S F gi|302179 3060 ACTCCCACTGTGACTTGCGTTGATAGAAATGGGAGCTACCCTCTCAAGGAAGACAGCTTC gi|302179 1040 L Q R Y S S D P T G A L I E D S M D D A gi|302179 3120 CTGCAGCGCTACAGCTCAGACCCCACTGGTGCCCTCATCGAGGACAGCATGGACGACGCT gi|302179 1060 F L P V P E Y V N Q S V P K R P A G S V gi|302179 3180 TTCCTCCCAGTACCCGAATATGTAAACCAATCTGTTCCCAAAAGACCCGCAGGCTCTGTC gi|302179 1080 Q N P V Y H N Q P L Y P A P G R D P Q Y gi|302179 3240 CAGAACCCTGTCTATCACAATCAGCCTCTATATCCAGCTCCTGGCAGAGACCCTCAGTAC gi|302179 1100 Q N S L S N A V D N P E Y L N T T H P A gi|302179 3300 CAAAATTCACTCAGCAACGCCGTGGACAACCCTGAGTATCTCAACACCACCCATCCTGCC gi|302179 1120 C I N G V L D G P A L W A Q K G S H Q F gi|302179 3360 TGTATCAATGGTGTGCTCGACGGCCCTGCCCTCTGGGCTCAGAAGGGCAGTCACCAATTT gi|302179 1140 S L D N P D Y Q Q A F F P K E A K S N G gi|302179 3420 AGCCTAGACAACCCTGACTACCAGCAGGCCTTCTTTCCCAAGGAAGCCAAGTCGAATGGC gi|302179 1160 I F K G P A A E N A E Y L R A A P A G S gi|302179 3480 ATCTTTAAGGGGCCTGCAGCTGAAAATGCAGAATACCTGCGGGCAGCACCAGCAGGCAGT gi|302179 1180 D F T G A 1185 gi|302179 3540 GACTTTACTGGGGCC 3555 """, ) protein_record = protein_alignment.sequences[3] self.assertEqual(protein_record.id, "gi|47522840|ref|NP_999172.1|") nucleotide_record = nucleotide_records["gi|47522839|ref|NM_214007.1|"] alignments = aligner.align(protein_record, nucleotide_record) self.assertEqual(len(alignments), 1) alignment = next(alignments) codon_alignments.append(alignment) self.assertTrue( np.array_equal(alignment.coordinates, np.array([[0, 1209], [126, 3753]])) ) self.assertEqual( str(alignment), """\ gi|475228 0 M R R S W A G G A A L L A L L A A H F Q gi|475228 126 ATGCGACGCTCCTGGGCGGGCGGCGCCGCGCTCCTGGCGCTGCTGGCCGCGCACTTCCAG gi|475228 20 A S P A L E E K K V C Q G T S N K L T Q gi|475228 186 GCGAGTCCGGCGCTGGAGGAGAAGAAAGTTTGCCAAGGTACAAGTAACAAGCTCACCCAG gi|475228 40 L G T F E D H F L S L Q R M F N N C E V gi|475228 246 CTGGGCACTTTCGAAGACCACTTTCTGAGCCTCCAGAGGATGTTCAATAACTGCGAGGTG gi|475228 60 V L G N L E I T Y M Q N S Y N L S F L K gi|475228 306 GTCCTTGGGAACTTGGAGATCACCTACATGCAGAACAGCTACAACCTGTCTTTCCTAAAG gi|475228 80 T I Q E V A G Y V L I A L N T V E K I P gi|475228 366 ACCATTCAGGAGGTCGCCGGCTACGTGCTCATCGCCCTCAACACCGTGGAGAAGATCCCT gi|475228 100 L E N L Q I I R G N V L Y E N T H A L A gi|475228 426 TTGGAAAACCTGCAGATCATCCGAGGAAATGTACTGTATGAAAACACCCATGCCTTAGCC gi|475228 120 V L S N Y G A N K T G L R E L P M R N L gi|475228 486 GTCTTATCCAACTACGGGGCCAATAAAACCGGCCTGAGGGAGCTGCCCATGAGGAACTTA gi|475228 140 Q E I L Q G A V R F S N N P A L C H A E gi|475228 546 CAAGAGATCCTGCAAGGCGCCGTGCGCTTCAGCAACAACCCTGCCCTCTGTCACGCGGAG gi|475228 160 S I Q W R D I V N S D F L S N M S M D F gi|475228 606 TCCATCCAGTGGAGGGACATTGTCAACAGCGACTTTCTAAGCAACATGTCCATGGACTTT gi|475228 180 Q S Q L G S C P K C D P G C L N G S C W gi|475228 666 CAGAGCCAGCTGGGCAGCTGCCCGAAGTGTGATCCAGGCTGTCTCAATGGGAGCTGCTGG gi|475228 200 G A G K E N C Q K L T K V I C A Q Q C S gi|475228 726 GGTGCTGGGAAGGAGAACTGCCAGAAATTGACCAAAGTCATCTGTGCCCAGCAGTGCTCC gi|475228 220 G R C R G R S P S D C C H N Q C A A G C gi|475228 786 GGGCGCTGCCGCGGCCGGTCGCCCAGTGACTGCTGCCACAACCAGTGCGCCGCTGGCTGC gi|475228 240 T G P R E S D C L V C R R F R D E A T C gi|475228 846 ACGGGGCCGCGGGAGAGCGACTGCCTGGTTTGCCGCAGATTCCGTGACGAGGCCACCTGC gi|475228 260 K D T C P P L M L Y N P T T Y Q M D V N gi|475228 906 AAGGACACATGCCCGCCGCTCATGCTCTACAACCCCACCACCTACCAGATGGACGTCAAC gi|475228 280 P L G K Y S F G A T C V K K C P R N Y V gi|475228 966 CCGCTGGGGAAGTACAGCTTTGGCGCCACCTGTGTCAAGAAGTGCCCTCGTAACTACGTG gi|475228 300 V T D H G S C V R A C S S D S Y E V E E gi|475228 1026 GTGACAGACCATGGCTCCTGTGTCCGTGCCTGCAGCTCCGACAGCTACGAGGTGGAGGAG gi|475228 320 D G V R K C K K C D G P C G K V C N G I gi|475228 1086 GACGGCGTCCGCAAGTGTAAAAAGTGTGACGGGCCCTGCGGCAAAGTTTGTAACGGGATA gi|475228 340 G I G E F K D T L S I N A T N I K H F R gi|475228 1146 GGGATTGGCGAGTTTAAAGACACACTTTCCATAAATGCTACGAATATCAAGCACTTCAGG gi|475228 360 N C T S I S G D L H I L P V A F R G D S gi|475228 1206 AACTGCACCTCGATCAGCGGAGATCTTCATATCCTGCCGGTAGCATTTAGGGGTGACTCC gi|475228 380 F T R T P P L D P K E L D I L K T V K E gi|475228 1266 TTCACACGCACGCCGCCTCTGGACCCCAAGGAACTGGACATCCTGAAAACCGTGAAGGAA gi|475228 400 I T G F L L I Q A W P E N R T G L H A F gi|475228 1326 ATAACAGGGTTTTTACTGATTCAGGCCTGGCCTGAAAACAGGACTGGCCTCCATGCTTTT gi|475228 420 E N L E I I R G R T K Q H G Q F S L A V gi|475228 1386 GAGAACCTGGAAATCATACGTGGCAGGACGAAGCAACATGGTCAGTTTTCCCTCGCGGTT gi|475228 440 V G L D I A S L G L R S L K E I S D G D gi|475228 1446 GTTGGCCTGGACATAGCGTCCTTGGGGATGCGCTCCCTCAAGGAGATCAGCGACGGAGAC gi|475228 460 V I V S G N R N L C Y A N T I S W K K L gi|475228 1506 GTGATCGTCTCAGGAAACCGAAACCTGTGCTATGCAAATACAATCAGCTGGAAAAAACTA gi|475228 480 F G T A S Q K T K I I N N R S E K E C K gi|475228 1566 TTTGGGACCGCAAGTCAGAAAACCAAAATTATAAACAACAGGAGCGAAAAAGAGTGCAAA gi|475228 500 A M G H I C N P L C S S E G C W G P E P gi|475228 1626 GCCATGGGCCACATCTGTAACCCGCTGTGCTCATCAGAGGGCTGCTGGGGCCCTGAACCC gi|475228 520 R D C M S C R N F S R G K E C V E K C N gi|475228 1686 AGAGACTGCATGTCCTGTCGAAACTTTAGCCGCGGCAAGGAATGTGTGGAGAAGTGCAAC gi|475228 540 V L E G E P R E F V E N A E C V Q C H P gi|475228 1746 GTTCTGGAGGGGGAGCCGAGAGAGTTCGTGGAGAATGCCGAGTGTGTGCAGTGCCACCCG gi|475228 560 E C L P Q A K N V T C M G R G P D S C V gi|475228 1806 GAGTGCCTGCCCCAGGCCAAGAACGTGACCTGCATGGGACGCGGACCGGACAGCTGTGTC gi|475228 580 R C A H Y I D G P H C V K T C P A G I A gi|475228 1866 CGGTGTGCTCACTACATCGACGGCCCTCACTGTGTCAAGACCTGCCCCGCGGGAATCGCA gi|475228 600 G E N S T L I W K F A D A N H V C H L C gi|475228 1926 GGAGAAAACAGCACCCTCATCTGGAAGTTTGCGGATGCCAACCACGTGTGTCACCTGTGC gi|475228 620 H P N C T Y G C V G P G L E G C A V D R gi|475228 1986 CACCCCAACTGCACCTACGGCTGTGTCGGACCAGGTCTCGAGGGCTGTGCGGTGGACAGG gi|475228 640 P K I P S I A T G I V G G L L L A V V L gi|475228 2046 CCCAAGATCCCGTCCATCGCCACCGGGATAGTGGGGGGCCTGCTTCTGGCCGTGGTGCTG gi|475228 660 A L G V G L F L R R R H I V R K R T L R gi|475228 2106 GCCCTGGGGGTCGGCCTCTTTCTGCGCAGGCGCCACATCGTCCGCAAGCGCACGCTGCGC gi|475228 680 R L L Q E R E L V E P L T P S G E A P N gi|475228 2166 CGGCTGCTGCAGGAGCGGGAGCTGGTTGAGCCTCTCACACCCAGTGGAGAAGCTCCCAAC gi|475228 700 Q A L L R I L K E T E F K K V K V L G S gi|475228 2226 CAAGCTCTCTTGAGGATCCTGAAGGAGACGGAATTCAAAAAGGTCAAGGTGCTGGGCTCC gi|475228 720 G A F G T V Y K G L W I P E G E K V K I gi|475228 2286 GGCGCGTTCGGCACGGTGTACAAGGGCCTCTGGATCCCAGAAGGTGAGAAGGTGAAAATT gi|475228 740 P V A I K E L R E A T S P K A N K E I L gi|475228 2346 CCTGTGGCTATCAAGGAATTAAGAGAAGCCACTTCTCCAAAAGCCAACAAGGAAATTCTT gi|475228 760 D E A Y V M A S V D N P H V C R L L G I gi|475228 2406 GACGAAGCCTACGTGATGGCCAGTGTGGACAATCCTCATGTGTGCCGCCTCCTGGGCATC gi|475228 780 C L T S T V Q L I T Q L M P F G C L L D gi|475228 2466 TGCCTGACCTCCACGGTGCAGCTCATCACGCAGCTCATGCCCTTCGGCTGCCTCCTGGAC gi|475228 800 Y V R E H K D N I G S Q H L L N W C V Q gi|475228 2526 TACGTCCGCGAGCACAAGGACAACATCGGCTCCCAGCACCTGCTCAACTGGTGTGTGCAG gi|475228 820 I A K G M N Y L E D R R L V H R D L A A gi|475228 2586 ATCGCAAAGGGCATGAACTATCTGGAAGACCGGCGCTTGGTGCACCGAGACCTGGCGGCC gi|475228 840 R N V L V K T P Q H V K I T D F G L A K gi|475228 2646 AGGAATGTGCTGGTGAAGACACCGCAGCATGTCAAGATCACTGACTTTGGGCTGGCCAAG gi|475228 860 L L G A E E K E Y H A E G G K V P I K W gi|475228 2706 CTGCTGGGCGCCGAGGAGAAAGAGTACCACGCGGAAGGAGGCAAAGTGCCCATCAAGTGG gi|475228 880 L A L E S I L H R V Y T H Q S D V W S Y gi|475228 2766 CTGGCTCTAGAGTCAATCCTGCACCGTGTATACACCCACCAGAGTGACGTCTGGAGCTAC gi|475228 900 G V T V W E L M T F G S K P Y D G I P A gi|475228 2826 GGAGTCACCGTTTGGGAGCTGATGACCTTTGGGTCCAAGCCTTATGACGGGATCCCCGCG gi|475228 920 S E I S T V L E K G E R L P Q P P I C T gi|475228 2886 AGTGAGATCTCGACCGTCCTGGAGAAGGGAGAGCGCCTCCCGCAGCCCCCCATCTGCACC gi|475228 940 I D V Y M I M V K C W M I D A D S R P K gi|475228 2946 ATTGATGTCTACATGATCATGGTCAAGTGCTGGATGATAGATGCTGATAGTCGCCCAAAG gi|475228 960 F R E L I I E F S K M A R D P Q R Y L V gi|475228 3006 TTCCGTGAGCTGATCATCGAATTCTCCAAAATGGCCCGAGACCCCCAGCGCTACCTTGTC gi|475228 980 I Q G D E R M H L P S P T D S N F Y R A gi|475228 3066 ATCCAGGGAGACGAGCGAATGCACTTGCCAAGCCCTACGGACTCCAACTTCTACCGCGCC gi|475228 1000 L M D E E D M E D V V D A D E Y L V P Q gi|475228 3126 CTGATGGACGAGGAGGACATGGAGGATGTGGTGGACGCCGACGAGTACCTCGTCCCCCAG gi|475228 1020 Q G F F H S P A T S R T P L L S S L S A gi|475228 3186 CAGGGCTTCTTCCACAGCCCCGCCACCTCCCGGACGCCGCTGCTCAGCTCTCTGAGCGCC gi|475228 1040 T S S T P A V A C V D R N G Q S Y P L K gi|475228 3246 ACCAGCAGCACCCCCGCTGTGGCTTGCGTTGACAGAAACGGGCAGAGTTATCCCCTCAAG gi|475228 1060 E D S F L Q R Y S S D P T G A L T E D S gi|475228 3306 GAAGACAGCTTCCTGCAGCGGTACAGCTCCGACCCCACTGGCGCCCTGACCGAGGACAGC gi|475228 1080 L D D T F L P A P E Y V N Q S V P K R P gi|475228 3366 CTAGACGACACTTTTCTCCCAGCACCCGAATATGTAAACCAGTCTGTTCCCAAGAGGCCC gi|475228 1100 A G S V Q N P V Y H N Q P L S A A P G R gi|475228 3426 GCGGGCTCCGTCCAGAACCCTGTCTACCACAATCAGCCTCTCAGTGCAGCTCCTGGCCGG gi|475228 1120 D P H Y Q N S H S N A V G N P E Y L N T gi|475228 3486 GACCCCCACTACCAGAACTCCCACAGCAATGCCGTGGGCAACCCTGAGTATCTCAACACC gi|475228 1140 P R P A C I N G G L D G P A F W A Q T G gi|475228 3546 CCCCGCCCCGCCTGCATCAACGGAGGACTGGACGGCCCTGCCTTCTGGGCACAGACAGGC gi|475228 1160 S H Q I N L D N P D Y Q Q A F F P K E A gi|475228 3606 AGCCACCAGATTAATCTGGACAACCCAGACTACCAGCAGGCCTTCTTCCCCAAGGAAGCC gi|475228 1180 K S N G I C K G P A A E N A E Y L R A A gi|475228 3666 AAGTCAAACGGCATCTGTAAGGGTCCCGCCGCCGAAAACGCAGAGTACCTAAGGGCGGCA gi|475228 1200 P A S S D L T G A 1209 gi|475228 3726 CCAGCCAGCAGTGACCTTACTGGGGCA 3753 """, ) protein_record = protein_alignment.sequences[4] self.assertEqual(protein_record.id, "gi|29725609|ref|NP_005219.2|") nucleotide_record = nucleotide_records["gi|41327737|ref|NM_005228.3|"] alignments = aligner.align(protein_record, nucleotide_record) self.assertEqual(len(alignments), 1) alignment = next(alignments) codon_alignments.append(alignment) self.assertTrue( np.array_equal(alignment.coordinates, np.array([[0, 1210], [246, 3876]])) ) self.assertEqual( str(alignment), """\ gi|297256 0 M R P S G T A G A A L L A L L A A L C P gi|413277 246 ATGCGACCCTCCGGGACGGCCGGGGCAGCGCTCCTGGCGCTGCTGGCTGCGCTCTGCCCG gi|297256 20 A S R A L E E K K V C Q G T S N K L T Q gi|413277 306 GCGAGTCGGGCTCTGGAGGAAAAGAAAGTTTGCCAAGGCACGAGTAACAAGCTCACGCAG gi|297256 40 L G T F E D H F L S L Q R M F N N C E V gi|413277 366 TTGGGCACTTTTGAAGATCATTTTCTCAGCCTCCAGAGGATGTTCAATAACTGTGAGGTG gi|297256 60 V L G N L E I T Y V Q R N Y D L S F L K gi|413277 426 GTCCTTGGGAATTTGGAAATTACCTATGTGCAGAGGAATTATGATCTTTCCTTCTTAAAG gi|297256 80 T I Q E V A G Y V L I A L N T V E R I P gi|413277 486 ACCATCCAGGAGGTGGCTGGTTATGTCCTCATTGCCCTCAACACAGTGGAGCGAATTCCT gi|297256 100 L E N L Q I I R G N M Y Y E N S Y A L A gi|413277 546 TTGGAAAACCTGCAGATCATCAGAGGAAATATGTACTACGAAAATTCCTATGCCTTAGCA gi|297256 120 V L S N Y D A N K T G L K E L P M R N L gi|413277 606 GTCTTATCTAACTATGATGCAAATAAAACCGGACTGAAGGAGCTGCCCATGAGAAATTTA gi|297256 140 Q E I L H G A V R F S N N P A L C N V E gi|413277 666 CAGGAAATCCTGCATGGCGCCGTGCGGTTCAGCAACAACCCTGCCCTGTGCAACGTGGAG gi|297256 160 S I Q W R D I V S S D F L S N M S M D F gi|413277 726 AGCATCCAGTGGCGGGACATAGTCAGCAGTGACTTTCTCAGCAACATGTCGATGGACTTC gi|297256 180 Q N H L G S C Q K C D P S C P N G S C W gi|413277 786 CAGAACCACCTGGGCAGCTGCCAAAAGTGTGATCCAAGCTGTCCCAATGGGAGCTGCTGG gi|297256 200 G A G E E N C Q K L T K I I C A Q Q C S gi|413277 846 GGTGCAGGAGAGGAGAACTGCCAGAAACTGACCAAAATCATCTGTGCCCAGCAGTGCTCC gi|297256 220 G R C R G K S P S D C C H N Q C A A G C gi|413277 906 GGGCGCTGCCGTGGCAAGTCCCCCAGTGACTGCTGCCACAACCAGTGTGCTGCAGGCTGC gi|297256 240 T G P R E S D C L V C R K F R D E A T C gi|413277 966 ACAGGCCCCCGGGAGAGCGACTGCCTGGTCTGCCGCAAATTCCGAGACGAAGCCACGTGC gi|297256 260 K D T C P P L M L Y N P T T Y Q M D V N gi|413277 1026 AAGGACACCTGCCCCCCACTCATGCTCTACAACCCCACCACGTACCAGATGGATGTGAAC gi|297256 280 P E G K Y S F G A T C V K K C P R N Y V gi|413277 1086 CCCGAGGGCAAATACAGCTTTGGTGCCACCTGCGTGAAGAAGTGTCCCCGTAATTATGTG gi|297256 300 V T D H G S C V R A C G A D S Y E M E E gi|413277 1146 GTGACAGATCACGGCTCGTGCGTCCGAGCCTGTGGGGCCGACAGCTATGAGATGGAGGAA gi|297256 320 D G V R K C K K C E G P C R K V C N G I gi|413277 1206 GACGGCGTCCGCAAGTGTAAGAAGTGCGAAGGGCCTTGCCGCAAAGTGTGTAACGGAATA gi|297256 340 G I G E F K D S L S I N A T N I K H F K gi|413277 1266 GGTATTGGTGAATTTAAAGACTCACTCTCCATAAATGCTACGAATATTAAACACTTCAAA gi|297256 360 N C T S I S G D L H I L P V A F R G D S gi|413277 1326 AACTGCACCTCCATCAGTGGCGATCTCCACATCCTGCCGGTGGCATTTAGGGGTGACTCC gi|297256 380 F T H T P P L D P Q E L D I L K T V K E gi|413277 1386 TTCACACATACTCCTCCTCTGGATCCACAGGAACTGGATATTCTGAAAACCGTAAAGGAA gi|297256 400 I T G F L L I Q A W P E N R T D L H A F gi|413277 1446 ATCACAGGGTTTTTGCTGATTCAGGCTTGGCCTGAAAACAGGACGGACCTCCATGCCTTT gi|297256 420 E N L E I I R G R T K Q H G Q F S L A V gi|413277 1506 GAGAACCTAGAAATCATACGCGGCAGGACCAAGCAACATGGTCAGTTTTCTCTTGCAGTC gi|297256 440 V S L N I T S L G L R S L K E I S D G D gi|413277 1566 GTCAGCCTGAACATAACATCCTTGGGATTACGCTCCCTCAAGGAGATAAGTGATGGAGAT gi|297256 460 V I I S G N K N L C Y A N T I N W K K L gi|413277 1626 GTGATAATTTCAGGAAACAAAAATTTGTGCTATGCAAATACAATAAACTGGAAAAAACTG gi|297256 480 F G T S G Q K T K I I S N R G E N S C K gi|413277 1686 TTTGGGACCTCCGGTCAGAAAACCAAAATTATAAGCAACAGAGGTGAAAACAGCTGCAAG gi|297256 500 A T G Q V C H A L C S P E G C W G P E P gi|413277 1746 GCCACAGGCCAGGTCTGCCATGCCTTGTGCTCCCCCGAGGGCTGCTGGGGCCCGGAGCCC gi|297256 520 R D C V S C R N V S R G R E C V D K C N gi|413277 1806 AGGGACTGCGTCTCTTGCCGGAATGTCAGCCGAGGCAGGGAATGCGTGGACAAGTGCAAC gi|297256 540 L L E G E P R E F V E N S E C I Q C H P gi|413277 1866 CTTCTGGAGGGTGAGCCAAGGGAGTTTGTGGAGAACTCTGAGTGCATACAGTGCCACCCA gi|297256 560 E C L P Q A M N I T C T G R G P D N C I gi|413277 1926 GAGTGCCTGCCTCAGGCCATGAACATCACCTGCACAGGACGGGGACCAGACAACTGTATC gi|297256 580 Q C A H Y I D G P H C V K T C P A G V M gi|413277 1986 CAGTGTGCCCACTACATTGACGGCCCCCACTGCGTCAAGACCTGCCCGGCAGGAGTCATG gi|297256 600 G E N N T L V W K Y A D A G H V C H L C gi|413277 2046 GGAGAAAACAACACCCTGGTCTGGAAGTACGCAGACGCCGGCCATGTGTGCCACCTGTGC gi|297256 620 H P N C T Y G C T G P G L E G C P T N G gi|413277 2106 CATCCAAACTGCACCTACGGATGCACTGGGCCAGGTCTTGAAGGCTGTCCAACGAATGGG gi|297256 640 P K I P S I A T G M V G A L L L L L V V gi|413277 2166 CCTAAGATCCCGTCCATCGCCACTGGGATGGTGGGGGCCCTCCTCTTGCTGCTGGTGGTG gi|297256 660 A L G I G L F M R R R H I V R K R T L R gi|413277 2226 GCCCTGGGGATCGGCCTCTTCATGCGAAGGCGCCACATCGTTCGGAAGCGCACGCTGCGG gi|297256 680 R L L Q E R E L V E P L T P S G E A P N gi|413277 2286 AGGCTGCTGCAGGAGAGGGAGCTTGTGGAGCCTCTTACACCCAGTGGAGAAGCTCCCAAC gi|297256 700 Q A L L R I L K E T E F K K I K V L G S gi|413277 2346 CAAGCTCTCTTGAGGATCTTGAAGGAAACTGAATTCAAAAAGATCAAAGTGCTGGGCTCC gi|297256 720 G A F G T V Y K G L W I P E G E K V K I gi|413277 2406 GGTGCGTTCGGCACGGTGTATAAGGGACTCTGGATCCCAGAAGGTGAGAAAGTTAAAATT gi|297256 740 P V A I K E L R E A T S P K A N K E I L gi|413277 2466 CCCGTCGCTATCAAGGAATTAAGAGAAGCAACATCTCCGAAAGCCAACAAGGAAATCCTC gi|297256 760 D E A Y V M A S V D N P H V C R L L G I gi|413277 2526 GATGAAGCCTACGTGATGGCCAGCGTGGACAACCCCCACGTGTGCCGCCTGCTGGGCATC gi|297256 780 C L T S T V Q L I T Q L M P F G C L L D gi|413277 2586 TGCCTCACCTCCACCGTGCAGCTCATCACGCAGCTCATGCCCTTCGGCTGCCTCCTGGAC gi|297256 800 Y V R E H K D N I G S Q Y L L N W C V Q gi|413277 2646 TATGTCCGGGAACACAAAGACAATATTGGCTCCCAGTACCTGCTCAACTGGTGTGTGCAG gi|297256 820 I A K G M N Y L E D R R L V H R D L A A gi|413277 2706 ATCGCAAAGGGCATGAACTACTTGGAGGACCGTCGCTTGGTGCACCGCGACCTGGCAGCC gi|297256 840 R N V L V K T P Q H V K I T D F G L A K gi|413277 2766 AGGAACGTACTGGTGAAAACACCGCAGCATGTCAAGATCACAGATTTTGGGCTGGCCAAA gi|297256 860 L L G A E E K E Y H A E G G K V P I K W gi|413277 2826 CTGCTGGGTGCGGAAGAGAAAGAATACCATGCAGAAGGAGGCAAAGTGCCTATCAAGTGG gi|297256 880 M A L E S I L H R I Y T H Q S D V W S Y gi|413277 2886 ATGGCATTGGAATCAATTTTACACAGAATCTATACCCACCAGAGTGATGTCTGGAGCTAC gi|297256 900 G V T V W E L M T F G S K P Y D G I P A gi|413277 2946 GGGGTGACCGTTTGGGAGTTGATGACCTTTGGATCCAAGCCATATGACGGAATCCCTGCC gi|297256 920 S E I S S I L E K G E R L P Q P P I C T gi|413277 3006 AGCGAGATCTCCTCCATCCTGGAGAAAGGAGAACGCCTCCCTCAGCCACCCATATGTACC gi|297256 940 I D V Y M I M V K C W M I D A D S R P K gi|413277 3066 ATCGATGTCTACATGATCATGGTCAAGTGCTGGATGATAGACGCAGATAGTCGCCCAAAG gi|297256 960 F R E L I I E F S K M A R D P Q R Y L V gi|413277 3126 TTCCGTGAGTTGATCATCGAATTCTCCAAAATGGCCCGAGACCCCCAGCGCTACCTTGTC gi|297256 980 I Q G D E R M H L P S P T D S N F Y R A gi|413277 3186 ATTCAGGGGGATGAAAGAATGCATTTGCCAAGTCCTACAGACTCCAACTTCTACCGTGCC gi|297256 1000 L M D E E D M D D V V D A D E Y L I P Q gi|413277 3246 CTGATGGATGAAGAAGACATGGACGACGTGGTGGATGCCGACGAGTACCTCATCCCACAG gi|297256 1020 Q G F F S S P S T S R T P L L S S L S A gi|413277 3306 CAGGGCTTCTTCAGCAGCCCCTCCACGTCACGGACTCCCCTCCTGAGCTCTCTGAGTGCA gi|297256 1040 T S N N S T V A C I D R N G L Q S C P I gi|413277 3366 ACCAGCAACAATTCCACCGTGGCTTGCATTGATAGAAATGGGCTGCAAAGCTGTCCCATC gi|297256 1060 K E D S F L Q R Y S S D P T G A L T E D gi|413277 3426 AAGGAAGACAGCTTCTTGCAGCGATACAGCTCAGACCCCACAGGCGCCTTGACTGAGGAC gi|297256 1080 S I D D T F L P V P E Y I N Q S V P K R gi|413277 3486 AGCATAGACGACACCTTCCTCCCAGTGCCTGAATACATAAACCAGTCCGTTCCCAAAAGG gi|297256 1100 P A G S V Q N P V Y H N Q P L N P A P S gi|413277 3546 CCCGCTGGCTCTGTGCAGAATCCTGTCTATCACAATCAGCCTCTGAACCCCGCGCCCAGC gi|297256 1120 R D P H Y Q D P H S T A V G N P E Y L N gi|413277 3606 AGAGACCCACACTACCAGGACCCCCACAGCACTGCAGTGGGCAACCCCGAGTATCTCAAC gi|297256 1140 T V Q P T C V N S T F D S P A H W A Q K gi|413277 3666 ACTGTCCAGCCCACCTGTGTCAACAGCACATTCGACAGCCCTGCCCACTGGGCCCAGAAA gi|297256 1160 G S H Q I S L D N P D Y Q Q D F F P K E gi|413277 3726 GGCAGCCACCAAATTAGCCTGGACAACCCTGACTACCAGCAGGACTTCTTTCCCAAGGAA gi|297256 1180 A K P N G I F K G S T A E N A E Y L R V gi|413277 3786 GCCAAGCCAAATGGCATCTTTAAGGGCTCCACAGCTGAAAATGCAGAATACCTAAGGGTC gi|297256 1200 A P Q S S E F I G A 1210 gi|413277 3846 GCGCCACAAAGCAGTGAATTTATTGGAGCA 3876 """, ) protein_record = protein_alignment.sequences[5] self.assertEqual(protein_record.id, "gi|6478868|gb|AAF14008.1|") nucleotide_record = nucleotide_records["gi|6478867|gb|M37394.2|RATEGFR"] alignments = aligner.align(protein_record, nucleotide_record) self.assertEqual(len(alignments), 1) alignment = next(alignments) codon_alignments.append(alignment) self.assertTrue( np.array_equal(alignment.coordinates, np.array([[0, 1209], [153, 3780]])) ) self.assertEqual( str(alignment), """\ gi|647886 0 M R P S G T A R T K L L L L L A A L C A gi|647886 153 ATGCGACCCTCAGGGACTGCGAGAACCAAGCTACTGCTGCTGCTGGCTGCGCTCTGCGCC gi|647886 20 A G G A L E E K K V C Q G T S N R L T Q gi|647886 213 GCAGGTGGGGCGCTGGAGGAAAAGAAAGTTTGCCAAGGCACAAGTAACAGGCTCACCCAA gi|647886 40 L G T F E D H F L S L Q R M F N N C E V gi|647886 273 CTAGGCACCTTTGAAGACCACTTTCTGAGCCTCCAGAGGATGTTCAACAACTGTGAAGTG gi|647886 60 V L G N L E I T Y V Q R N Y D L S F L K gi|647886 333 GTCCTTGGAAACTTGGAAATCACCTATGTGCAAAGGAATTATGACCTTTCCTTCTTAAAG gi|647886 80 T I Q E V A G Y V L I A L N T V E R I P gi|647886 393 ACCATCCAGGAGGTGGCTGGCTATGTTCTCATTGCCCTGAACACCGTGGAGAGAATCCCT gi|647886 100 L E N L Q I I R G N A L Y E N T Y A L A gi|647886 453 TTGGAGAACCTGCAGATCATCAGGGGAAATGCTCTCTACGAAAACACCTACGCCTTAGCC gi|647886 120 V L S N Y G T N K T G L R E L P M R N L gi|647886 513 GTCCTGTCCAACTATGGAACCAACAAAACTGGGCTTAGGGAACTGCCCATGCGGAACTTA gi|647886 140 Q E I L I G A V R F S N N P I L C N M E gi|647886 573 CAGGAAATTCTGATCGGTGCTGTGCGATTTAGCAACAACCCCATCCTCTGCAATATGGAG gi|647886 160 T I Q W R D I V Q D V F L S N M S M D V gi|647886 633 ACCATCCAGTGGAGGGACATCGTCCAAGATGTCTTTCTGAGCAACATGTCAATGGACGTA gi|647886 180 Q R H L T G C P K C D P S C P N G S C W gi|647886 693 CAGCGCCACCTGACGGGCTGCCCGAAATGTGATCCGAGCTGTCCCAATGGAAGCTGCTGG gi|647886 200 G R G E E N C Q K L T K I I C A Q Q C S gi|647886 753 GGAAGAGGAGAGGAGAACTGCCAGAAATTGACCAAAATCATCTGCGCCCAGCAATGTTCC gi|647886 220 R R C R G R S P S D C C H N Q C A A G C gi|647886 813 CGGCGTTGTCGTGGCAGGTCCCCTAGCGACTGCTGCCACAACCAGTGTGCCGCAGGGTGT gi|647886 240 T G P R E S D C L V C H R F R D E A T C gi|647886 873 ACAGGGCCCAGAGAGAGTGACTGTCTGGTCTGCCACAGGTTCCGAGATGAAGCCACGTGC gi|647886 260 K D T C P P L M L Y N P T T Y Q M D V N gi|647886 933 AAAGACACCTGCCCACCACTCATGCTGTACAACCCCACCACGTACCAGATGGATGTCAAC gi|647886 280 P E G K Y S F G A T C V K K C P R N Y V gi|647886 993 CCTGAGGGGAAGTACAGCTTTGGTGCCACCTGTGTGAAGAAATGCCCCAGAAACTACGTG gi|647886 300 V T D H G S C V R A C G P D Y Y E V E E gi|647886 1053 GTGACAGATCACGGCTCGTGTGTCCGGGCCTGTGGGCCAGACTACTATGAAGTAGAAGAA gi|647886 320 D G V S K C K K C D G P C R K V C N G I gi|647886 1113 GATGGAGTCAGCAAGTGTAAAAAATGTGACGGGCCCTGCCGCAAAGTTTGCAATGGCATA gi|647886 340 G I G E F K D T L S I N A T N I K H F K gi|647886 1173 GGCATTGGTGAATTTAAAGACACACTCTCCATAAATGCTACAAACATCAAACACTTCAAG gi|647886 360 Y C T A I S G D L H I L P V A F K G D S gi|647886 1233 TACTGCACTGCCATCAGTGGGGACCTCCACATCCTGCCAGTGGCCTTTAAGGGGGATTCT gi|647886 380 F T R T P P L D P R E L E I L K T V K E gi|647886 1293 TTCACCCGCACTCCTCCTCTAGACCCACGGGAACTAGAAATTCTCAAAACTGTGAAGGAA gi|647886 400 I T G F L L I Q A W P E N W T D L H A F gi|647886 1353 ATAACAGGGTTTTTGCTGATTCAGGCTTGGCCTGAAAACTGGACTGACCTCCATGCTTTT gi|647886 420 E N L E I I R G R T K Q H G Q F S L A V gi|647886 1413 GAGAACCTAGAAATAATTCGTGGCAGAACAAAGCAACATGGTCAGTTTTCTCTGGCGGTT gi|647886 440 V G L N I T S L G L R S L K E I S D G D gi|647886 1473 GTCGGCCTGAACATAACATCGCTGGGGTTGCGTTCCCTCAAGGAGATCAGTGATGGGGAT gi|647886 460 V I I S G N R N L C Y A N T I N W K K L gi|647886 1533 GTGATTATTTCTGGGAACCGAAATTTGTGCTACGCAAACACTATAAACTGGAAAAAACTC gi|647886 480 F G T P N Q K T K I M N N R A E K D C K gi|647886 1593 TTCGGGACGCCCAATCAAAAGACCAAAATCATGAACAACAGAGCTGAAAAGGACTGCAAG gi|647886 500 A T N H V C N P L C S S E G C W G P E P gi|647886 1653 GCCACGAACCACGTCTGTAATCCTTTATGCTCCTCGGAAGGCTGCTGGGGCCCTGAGCCC gi|647886 520 T D C V S C Q N V S R G R E C V D K C N gi|647886 1713 ACGGACTGTGTCTCCTGCCAGAATGTGAGCAGAGGCAGGGAGTGCGTGGACAAGTGCAAC gi|647886 540 I L E G E P R E F V E N S E C I Q C H P gi|647886 1773 ATCCTGGAGGGGGAACCGAGGGAGTTTGTGGAAAATTCTGAATGCATCCAGTGCCATCCA gi|647886 560 E C L P Q T M N I T C T G R G P D N C I gi|647886 1833 GAATGTCTGCCCCAGACCATGAACATCACCTGTACAGGCCGGGGGCCAGACAACTGCATC gi|647886 580 K C A H Y V D G P H C V K T C P S G I M gi|647886 1893 AAGTGTGCCCACTATGTTGATGGTCCCCACTGTGTCAAGACCTGCCCTTCGGGCATCATG gi|647886 600 G E N N T L V W K F A D A N N V C H L C gi|647886 1953 GGGGAGAACAACACCCTGGTCTGGAAGTTTGCAGATGCCAATAACGTCTGCCACCTCTGC gi|647886 620 H A N C T Y G C A G P G L K G C Q Q P E gi|647886 2013 CATGCAAACTGTACCTATGGATGTGCTGGGCCAGGCCTTAAAGGATGTCAACAACCAGAA gi|647886 640 G P K I P S I A T G I V G G L L F I V V gi|647886 2073 GGGCCAAAGATCCCATCCATCGCCACTGGGATTGTGGGTGGCCTCCTCTTCATAGTAGTG gi|647886 660 V A L G I G L F M R R R Q L V R K R T L gi|647886 2133 GTGGCCCTTGGGATCGGCCTCTTCATGCGTCGACGTCAGCTTGTCCGAAAACGTACACTA gi|647886 680 R R L L Q E R E L V E P L T P S G E A P gi|647886 2193 CGCCGCCTGCTTCAAGAGAGAGAGCTCGTGGAACCTCTCACACCCAGCGGAGAAGCTCCG gi|647886 700 N Q A H L R I L K E T E F K K I K V L G gi|647886 2253 AACCAAGCCCACTTGAGGATATTAAAGGAAACAGAATTCAAAAAGATCAAAGTTCTGGGT gi|647886 720 S G A F G T V Y K G L W I P E G E K V K gi|647886 2313 TCAGGAGCATTTGGCACAGTGTATAAGGGTCTCTGGATCCCAGAAGGCGAGAAAGTGAAA gi|647886 740 I P V A I K E L R E A T S P K A N K E I gi|647886 2373 ATCCCTGTGGCCATCAAGGAGTTAAGAGAAGCCACATCTCCCAAAGCCAACAAGGAAATC gi|647886 760 L D E A Y V M A S V D N P H V C R L L G gi|647886 2433 CTTGATGAAGCCTACGTGATGGCCAGTGTGGACAACCCTCATGTATGCCGCCTCCTGGGC gi|647886 780 I C L T S T V Q L I T Q L M P Y G C L L gi|647886 2493 ATCTGTCTGACCTCCACTGTCCAGCTCATTACACAACTCATGCCCTATGGTTGCCTCCTG gi|647886 800 D Y V R E H K D N I G S Q Y L L N W C V gi|647886 2553 GACTATGTCCGAGAACATAAGGACAACATTGGCTCCCAGTACCTACTCAACTGGTGTGTG gi|647886 820 Q I A K G M N Y L E D R R L V H R D L A gi|647886 2613 CAGATTGCAAAGGGCATGAACTACCTGGAAGACCGGCGTTTGGTACACCGTGACTTGGCA gi|647886 840 A R N V L V K T P Q H V K I T D F G L A gi|647886 2673 GCCAGGAATGTACTGGTAAAGACACCACAGCATGTCAAGATCACAGATTTTGGACTGGCC gi|647886 860 K L L G A E E K E Y H A E G G K V P I K gi|647886 2733 AAACTGCTTGGTGCTGAGGAGAAAGAATACCATGCAGAGGGGGGCAAAGTGCCTATCAAG gi|647886 880 W M A L E S I L H R I Y T H Q S D V W S gi|647886 2793 TGGATGGCTTTGGAATCAATTTTACACCGAATTTATACACACCAAAGCGACGTCTGGAGC gi|647886 900 Y G V T V W E L M T F G S K P Y D G I P gi|647886 2853 TATGGAGTCACCGTGTGGGAACTGATGACCTTTGGGTCCAAGCCTTATGATGGGATCCCT gi|647886 920 A S E I S S I L E K G E R L P Q P P I C gi|647886 2913 GCAAGTGAGATCTCATCCATCCTAGAGAAAGGAGAGCGCCTTCCACAGCCACCTATCTGC gi|647886 940 T I D V Y M I M V K C W M I D A D S R P gi|647886 2973 ACCATCGACGTCTACATGATCATGGTCAAGTGCTGGATGATAGATGCTGATAGCCGCCCA gi|647886 960 K F R E L I L E F S K M A R D P Q R Y L gi|647886 3033 AAGTTCCGAGAGTTGATTCTCGAATTCTCCAAAATGGCCAGAGACCCACAGCGCTACCTT gi|647886 980 V I Q G D E R M H L P S P T D S N F Y R gi|647886 3093 GTTATCCAGGGGGATGAAAGGATGCATTTGCCGAGCCCTACAGACTCCAACTTTTACCGA gi|647886 1000 A L M E E E D M E D V V D A D E Y L I P gi|647886 3153 GCCCTGATGGAGGAGGAGGACATGGAAGACGTAGTTGATGCTGATGAATACCTCATCCCA gi|647886 1020 Q Q G F F N S P S T S R T P L L S S L S gi|647886 3213 CAGCAAGGCTTCTTCAACAGCCCATCCACGTCACGGACTCCACTCTTGAGCTCTCTGAGT gi|647886 1040 A N S N S S T V A C I N R N G S C R V K gi|647886 3273 GCAAATAGCAACAGTTCCACTGTGGCTTGCATTAATAGAAATGGGAGCTGCCGTGTCAAA gi|647886 1060 E D A F L Q R Y S S D P T S V L T E D N gi|647886 3333 GAAGACGCCTTCTTGCAACGGTATAGCTCCGATCCCACCAGCGTCCTGACAGAGGACAAC gi|647886 1080 I D D T F L P V P E Y I N Q S V P K R P gi|647886 3393 ATAGATGACACATTCCTTCCCGTGCCTGAATATATAAACCAATCTGTTCCCAAGAGGCCG gi|647886 1100 A G S V Q N P V Y H N Q P L H P A P G R gi|647886 3453 GCTGGCTCTGTGCAGAACCCAGTCTATCACAATCAGCCCCTGCATCCAGCTCCTGGAAGA gi|647886 1120 D L H Y Q N P H S N A V S N P E Y L N T gi|647886 3513 GACCTGCATTATCAAAATCCCCATAGCAATGCGGTGAGCAACCCTGAGTATCTCAACACT gi|647886 1140 A Q P T C L S S G F D S S A L W I Q K G gi|647886 3573 GCCCAGCCGACCTGCCTCAGTAGTGGGTTTGACAGCTCTGCCCTCTGGATCCAGAAAGGC gi|647886 1160 S H Q M S L D N P D Y Q Q D F F P K E A gi|647886 3633 AGCCACCAAATGAGCCTGGACAACCCTGACTACCAGCAGGACTTCTTTCCCAAAGAAGCC gi|647886 1180 K P N G I F K G P T A E N A E Y L R V A gi|647886 3693 AAGCCGAATGGCATCTTTAAGGGCCCCACAGCTGAAAATGCAGAGTACCTGCGGGTGGCA gi|647886 1200 P P S S E F S G A 1209 gi|647886 3753 CCGCCAAGCAGTGAGTTTAGTGGAGCA 3780 """, ) alignment = protein_alignment.mapall(codon_alignments) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 84, 105, 114, 129, 171, 183, 198, 198, 210, 234, 366, 369, 492, 507, 531, 531, 741, 741, 807, 810, 1038, 1038, 1089, 1089, 1107, 1107, 1161, 1161, 1245, 1260, 1281, 1290, 1443, 1446, 1779, 1779, 1821, 1821, 1902, 1953, 1986, 2085, 2097, 2151, 2175, 2301, 2319, 2319, 2355, 2358, 2373, 2394, 2418, 2559, 2610, 2613, 2655, 2661, 3585, 3594, 3642, 3645, 3765, 3765, 3777, 3777, 3777, 3777, 3843, 3843, 3858, 3864, 3894, 3900, 3921, 3921, 3969, 3975, 4038, 4038, 4215], [ 22, 22, 31, 46, 88, 100, 115, 283, 295, 319, 451, 454, 577, 592, 616, 616, 826, 826, 892, 895, 1123, 1123, 1174, 1174, 1192, 1192, 1246, 1246, 1330, 1345, 1366, 1375, 1528, 1531, 1864, 1864, 1906, 1906, 1987, 2038, 2071, 2170, 2182, 2236, 2260, 2386, 2404, 2404, 2440, 2443, 2458, 2479, 2503, 2644, 2695, 2698, 2740, 2746, 3670, 3679, 3727, 3730, 3850, 3850, 3862, 3862, 3862, 3862, 3928, 3928, 3943, 3949, 3979, 3985, 4006, 4006, 4054, 4060, 4123, 4123, 4300], [ 0, 0, 0, 15, 15, 15, 15, 15, 15, 15, 147, 147, 270, 270, 294, 312, 522, 525, 591, 591, 819, 822, 873, 879, 897, 903, 957, 981, 1065, 1065, 1086, 1086, 1239, 1239, 1572, 1578, 1620, 1638, 1719, 1719, 1752, 1752, 1764, 1764, 1788, 1788, 1806, 1809, 1845, 1845, 1860, 1860, 1884, 1884, 1935, 1935, 1977, 1977, 2901, 2901, 2949, 2949, 3069, 3081, 3093, 3093, 3093, 3099, 3165, 3183, 3198, 3198, 3228, 3228, 3249, 3258, 3306, 3306, 3369, 3378, 3555], [ 126, 126, 126, 141, 183, 183, 198, 198, 210, 210, 342, 342, 465, 465, 489, 507, 717, 720, 786, 786, 1014, 1017, 1068, 1074, 1092, 1098, 1152, 1176, 1260, 1260, 1281, 1281, 1434, 1434, 1767, 1773, 1815, 1833, 1914, 1914, 1947, 1947, 1959, 1959, 1983, 1983, 2001, 2004, 2040, 2040, 2055, 2055, 2079, 2079, 2130, 2130, 2172, 2172, 3096, 3096, 3144, 3144, 3264, 3276, 3288, 3288, 3291, 3297, 3363, 3381, 3396, 3396, 3426, 3426, 3447, 3456, 3504, 3504, 3567, 3576, 3753], [ 246, 246, 246, 261, 303, 303, 318, 318, 330, 330, 462, 462, 585, 585, 609, 627, 837, 840, 906, 906, 1134, 1137, 1188, 1194, 1212, 1218, 1272, 1296, 1380, 1380, 1401, 1401, 1554, 1554, 1887, 1893, 1935, 1953, 2034, 2034, 2067, 2067, 2079, 2079, 2103, 2103, 2121, 2124, 2160, 2160, 2175, 2175, 2199, 2199, 2250, 2250, 2292, 2292, 3216, 3216, 3264, 3264, 3384, 3396, 3408, 3411, 3414, 3420, 3486, 3504, 3519, 3519, 3549, 3549, 3570, 3579, 3627, 3627, 3690, 3699, 3876], [ 153, 153, 153, 168, 210, 210, 225, 225, 237, 237, 369, 369, 492, 492, 516, 534, 744, 747, 813, 813, 1041, 1044, 1095, 1101, 1119, 1125, 1179, 1203, 1287, 1287, 1308, 1308, 1461, 1461, 1794, 1800, 1842, 1860, 1941, 1941, 1974, 1974, 1986, 1986, 2010, 2010, 2028, 2031, 2067, 2070, 2085, 2085, 2109, 2109, 2160, 2160, 2202, 2202, 3126, 3126, 3174, 3174, 3294, 3306, 3318, 3318, 3318, 3324, 3390, 3408, 3423, 3423, 3453, 3453, 3474, 3483, 3531, 3531, 3594, 3603, 3780]]) # fmt: on ) ) self.assertEqual( format(alignment, "clustal"), """\ gi|24657088|ref|NM_057410.3| ATGATGATTATCAGCATGTGGATGAGCATATCGCGAGGATTGTGGGACAG gi|24657104|ref|NM_057411.3| ---------------------ATGCTGCTGCGACGGCGCAACGGCCCCTG gi|302179500|gb|HM749883.1| ------------------------------ATGAAAAAGCACGAG----- gi|47522839|ref|NM_214007.1| ------------------------------ATGCGACGCTCCTGGGCGGG gi|41327737|ref|NM_005228.3| ------------------------------ATGCGACCCTCCGGGACGGC gi|6478867|gb|M37394.2|RATEGFR ------------------------------ATGCGACCCTCAGGGACTGC gi|24657088|ref|NM_057410.3| CAGCTCCATCTGGTCGGTGCTGCTGATCCTCGCCTGCATGGCATCCATCA gi|24657104|ref|NM_057411.3| CCCCTTCCCCCTGCTGCTCCTGCTCCTGGCCCACTGCATTTGCATTTGGC gi|302179500|gb|HM749883.1| -------------------------------------------------- gi|47522839|ref|NM_214007.1| CGGCGCCGCGCTCCTGGCGCTGCTGGCCGCGCACTTC------------C gi|41327737|ref|NM_005228.3| CGGGGCAGCGCTCCTGGCGCTGCTGGCTGCGCTCTGC------------C gi|6478867|gb|M37394.2|RATEGFR GAGAACCAAGCTACTGCTGCTGCTGGCTGCGCTCTGC------------G gi|24657088|ref|NM_057410.3| CCACAAGCTCATCG------------------------------------ gi|24657104|ref|NM_057411.3| CCGCGTCGGCGGCCCGCGATCGCTACGCCCGCCAGAACAATCGCCAGCGC gi|302179500|gb|HM749883.1| -------------------------------------------------- gi|47522839|ref|NM_214007.1| AGGCGAGTCCGGCG------------------------------------ gi|41327737|ref|NM_005228.3| CGGCGAGTCGGGCT------------------------------------ gi|6478867|gb|M37394.2|RATEGFR CCGCAGGTGGGGCG------------------------------------ gi|24657088|ref|NM_057410.3| -------------------------------------------------- gi|24657104|ref|NM_057411.3| CATCAGGATATAGATCGCGATCGGGATCGAGATCGATTCCTATACCGCAG gi|302179500|gb|HM749883.1| -------------------------------------------------- gi|47522839|ref|NM_214007.1| -------------------------------------------------- gi|41327737|ref|NM_005228.3| -------------------------------------------------- gi|6478867|gb|M37394.2|RATEGFR -------------------------------------------------- gi|24657088|ref|NM_057410.3| -------------------------------------------------- gi|24657104|ref|NM_057411.3| CAGTTCGGCCCAAAATCGACAGAGGGGCGGGGCCAACTTCGCCCTGGGAC gi|302179500|gb|HM749883.1| -------------------------------------------------- gi|47522839|ref|NM_214007.1| -------------------------------------------------- gi|41327737|ref|NM_005228.3| -------------------------------------------------- gi|6478867|gb|M37394.2|RATEGFR -------------------------------------------------- gi|24657088|ref|NM_057410.3| --------------------------------GTCAGCAATGCCGGCTAT gi|24657104|ref|NM_057411.3| TGGGAGCCAACGGAGTCACCATTCCCACCAGTCTGGAGGATAAGAACAAG gi|302179500|gb|HM749883.1| -------------------------------------------------- gi|47522839|ref|NM_214007.1| --------------------------------CTGGAGGAGAAG------ gi|41327737|ref|NM_005228.3| --------------------------------CTGGAGGAAAAG------ gi|6478867|gb|M37394.2|RATEGFR --------------------------------CTGGAGGAAAAG------ gi|24657088|ref|NM_057410.3| GTGGATAATGGCAATATGAAAGTCTGCATCGGCACTAAATCTCGGCTCTC gi|24657104|ref|NM_057411.3| AACGAGTTCGTCAAGGGGAAAATCTGCATCGGCACTAAATCTCGGCTCTC gi|302179500|gb|HM749883.1| ------------------TTACTTTGCCAAGGGACAAGTAACAAGCTCAC gi|47522839|ref|NM_214007.1| ------------------AAAGTTTGCCAAGGTACAAGTAACAAGCTCAC gi|41327737|ref|NM_005228.3| ------------------AAAGTTTGCCAAGGCACGAGTAACAAGCTCAC gi|6478867|gb|M37394.2|RATEGFR ------------------AAAGTTTGCCAAGGCACAAGTAACAGGCTCAC gi|24657088|ref|NM_057410.3| CGTGCCCTCCAACAAGGAACATCATTACCGGAACCTCAGAGATCGGTACA gi|24657104|ref|NM_057411.3| CGTGCCCTCCAACAAGGAACATCATTACCGGAACCTCAGAGATCGGTACA gi|302179500|gb|HM749883.1| CCAGTTGGGCACTTTTGAAGACCACTTTCTGAGCCTACAGAGGATGTTCA gi|47522839|ref|NM_214007.1| CCAGCTGGGCACTTTCGAAGACCACTTTCTGAGCCTCCAGAGGATGTTCA gi|41327737|ref|NM_005228.3| GCAGTTGGGCACTTTTGAAGATCATTTTCTCAGCCTCCAGAGGATGTTCA gi|6478867|gb|M37394.2|RATEGFR CCAACTAGGCACCTTTGAAGACCACTTTCTGAGCCTCCAGAGGATGTTCA gi|24657088|ref|NM_057410.3| CGAACTGTACGTATGTGGATGGCAACCTGGAGCTGACCTGGCTGCCCAAC gi|24657104|ref|NM_057411.3| CGAACTGTACGTATGTGGATGGCAACCTGGAGCTGACCTGGCTGCCCAAC gi|302179500|gb|HM749883.1| ACAACTGTGAGGTGGTCCTTGGGAATTTGGAAATTACCTACATGCAGAGT gi|47522839|ref|NM_214007.1| ATAACTGCGAGGTGGTCCTTGGGAACTTGGAGATCACCTACATGCAGAAC gi|41327737|ref|NM_005228.3| ATAACTGTGAGGTGGTCCTTGGGAATTTGGAAATTACCTATGTGCAGAGG gi|6478867|gb|M37394.2|RATEGFR ACAACTGTGAAGTGGTCCTTGGAAACTTGGAAATCACCTATGTGCAAAGG gi|24657088|ref|NM_057410.3| GAGAATTTGGACCTCAGCTTCCTGGACAACATACGGGAGGTCACCGGCTA gi|24657104|ref|NM_057411.3| GAGAATTTGGACCTCAGCTTCCTGGACAACATACGGGAGGTCACCGGCTA gi|302179500|gb|HM749883.1| ---AGTTACAACCTTTCTTTTCTCAAGACCATCCAGGAGGTTGCCGGCTA gi|47522839|ref|NM_214007.1| ---AGCTACAACCTGTCTTTCCTAAAGACCATTCAGGAGGTCGCCGGCTA gi|41327737|ref|NM_005228.3| ---AATTATGATCTTTCCTTCTTAAAGACCATCCAGGAGGTGGCTGGTTA gi|6478867|gb|M37394.2|RATEGFR ---AATTATGACCTTTCCTTCTTAAAGACCATCCAGGAGGTGGCTGGCTA gi|24657088|ref|NM_057410.3| TATTCTGATCAGTCATGTGGACGTTAAGAAAGTGGTATTTCCCAAACTAC gi|24657104|ref|NM_057411.3| TATTCTGATCAGTCATGTGGACGTTAAGAAAGTGGTATTTCCCAAACTAC gi|302179500|gb|HM749883.1| TGTACTCATTGCCCTCAACACAGTGGAGAAGATTCCGCTGGAAAACCTGC gi|47522839|ref|NM_214007.1| CGTGCTCATCGCCCTCAACACCGTGGAGAAGATCCCTTTGGAAAACCTGC gi|41327737|ref|NM_005228.3| TGTCCTCATTGCCCTCAACACAGTGGAGCGAATTCCTTTGGAAAACCTGC gi|6478867|gb|M37394.2|RATEGFR TGTTCTCATTGCCCTGAACACCGTGGAGAGAATCCCTTTGGAGAACCTGC gi|24657088|ref|NM_057410.3| AAATCATTCGCGGACGCACGCTGTTCAGCTTATCCGTGGAGGAGGAGAAG gi|24657104|ref|NM_057411.3| AAATCATTCGCGGACGCACGCTGTTCAGCTTATCCGTGGAGGAGGAGAAG gi|302179500|gb|HM749883.1| AGATCATCCGAGGAAATGTGCTTTAT---------------GAAAACACC gi|47522839|ref|NM_214007.1| AGATCATCCGAGGAAATGTACTGTAT---------------GAAAACACC gi|41327737|ref|NM_005228.3| AGATCATCAGAGGAAATATGTACTAC---------------GAAAATTCC gi|6478867|gb|M37394.2|RATEGFR AGATCATCAGGGGAAATGCTCTCTAC---------------GAAAACACC gi|24657088|ref|NM_057410.3| TATGCCTTGTTCGTC------------------ACTTATTCCAAAATGTA gi|24657104|ref|NM_057411.3| TATGCCTTGTTCGTC------------------ACTTATTCCAAAATGTA gi|302179500|gb|HM749883.1| CATGCCTTAGCCGTCTTATCCAACTATGGAGCAAACAAAACCGGACTGAG gi|47522839|ref|NM_214007.1| CATGCCTTAGCCGTCTTATCCAACTACGGGGCCAATAAAACCGGCCTGAG gi|41327737|ref|NM_005228.3| TATGCCTTAGCAGTCTTATCTAACTATGATGCAAATAAAACCGGACTGAA gi|6478867|gb|M37394.2|RATEGFR TACGCCTTAGCCGTCCTGTCCAACTATGGAACCAACAAAACTGGGCTTAG gi|24657088|ref|NM_057410.3| CACGCTGGAGATTCCCGATCTACGCGATGTCTTAAATGGCCAAGTGGGCT gi|24657104|ref|NM_057411.3| CACGCTGGAGATTCCCGATCTACGCGATGTCTTAAATGGCCAAGTGGGCT gi|302179500|gb|HM749883.1| GGAGCTGCCCTTGAGAAACTTACAGGAAATTCTGCAAGGTGCCGTGAGAT gi|47522839|ref|NM_214007.1| GGAGCTGCCCATGAGGAACTTACAAGAGATCCTGCAAGGCGCCGTGCGCT gi|41327737|ref|NM_005228.3| GGAGCTGCCCATGAGAAATTTACAGGAAATCCTGCATGGCGCCGTGCGGT gi|6478867|gb|M37394.2|RATEGFR GGAACTGCCCATGCGGAACTTACAGGAAATTCTGATCGGTGCTGTGCGAT gi|24657088|ref|NM_057410.3| TCCACAACAACTACAATCTCTGCCACATGCGAACGATCCAGTGGTCGGAG gi|24657104|ref|NM_057411.3| TCCACAACAACTACAATCTCTGCCACATGCGAACGATCCAGTGGTCGGAG gi|302179500|gb|HM749883.1| TCAGCAACAACCCTGTCCTCTGCAACGTGGAGACCATCCAGTGGCGGGAC gi|47522839|ref|NM_214007.1| TCAGCAACAACCCTGCCCTCTGTCACGCGGAGTCCATCCAGTGGAGGGAC gi|41327737|ref|NM_005228.3| TCAGCAACAACCCTGCCCTGTGCAACGTGGAGAGCATCCAGTGGCGGGAC gi|6478867|gb|M37394.2|RATEGFR TTAGCAACAACCCCATCCTCTGCAATATGGAGACCATCCAGTGGAGGGAC gi|24657088|ref|NM_057410.3| ATTGTATCCAACGGCACGGATGCATACTACAACTACGACTTTACTGCTCC gi|24657104|ref|NM_057411.3| ATTGTATCCAACGGCACGGATGCATACTACAACTACGACTTTACTGCTCC gi|302179500|gb|HM749883.1| ATCGTCAACCCTGATTTTCTAAGCAACATGACAGGGGACTTTCAGAACCA gi|47522839|ref|NM_214007.1| ATTGTCAACAGCGACTTTCTAAGCAACATGTCCATGGACTTTCAGAGCCA gi|41327737|ref|NM_005228.3| ATAGTCAGCAGTGACTTTCTCAGCAACATGTCGATGGACTTCCAGAACCA gi|6478867|gb|M37394.2|RATEGFR ATCGTCCAAGATGTCTTTCTGAGCAACATGTCAATGGACGTACAGCGCCA gi|24657088|ref|NM_057410.3| GGAGCGCGAGTGTCCCAAGTGCCACGAGAGCTGCACGCACGGA---TGTT gi|24657104|ref|NM_057411.3| GGAGCGCGAGTGTCCCAAGTGCCACGAGAGCTGCACGCACGGA---TGTT gi|302179500|gb|HM749883.1| GCAGGGCAACTGCCCAAAGTGTGATCCAGCCTGTCTCAACAGAAGCTGCT gi|47522839|ref|NM_214007.1| GCTGGGCAGCTGCCCGAAGTGTGATCCAGGCTGTCTCAATGGGAGCTGCT gi|41327737|ref|NM_005228.3| CCTGGGCAGCTGCCAAAAGTGTGATCCAAGCTGTCCCAATGGGAGCTGCT gi|6478867|gb|M37394.2|RATEGFR CCTGACGGGCTGCCCGAAATGTGATCCGAGCTGTCCCAATGGAAGCTGCT gi|24657088|ref|NM_057410.3| GGGGCGAGGGTCCCAAGAATTGCCAGAAGTTCAGCAAGCTCACCTGCTCG gi|24657104|ref|NM_057411.3| GGGGCGAGGGTCCCAAGAATTGCCAGAAGTTCAGCAAGCTCACCTGCTCG gi|302179500|gb|HM749883.1| GGGGTGCCGGGGAGGAGAACTGTCAGAAATTGACCAAAATCATCTGTGCC gi|47522839|ref|NM_214007.1| GGGGTGCTGGGAAGGAGAACTGCCAGAAATTGACCAAAGTCATCTGTGCC gi|41327737|ref|NM_005228.3| GGGGTGCAGGAGAGGAGAACTGCCAGAAACTGACCAAAATCATCTGTGCC gi|6478867|gb|M37394.2|RATEGFR GGGGAAGAGGAGAGGAGAACTGCCAGAAATTGACCAAAATCATCTGCGCC gi|24657088|ref|NM_057410.3| CCACAGTGTGCCGGAGGTCGTTGCTATGGACCAAAGCCGCGGGAGTGTTG gi|24657104|ref|NM_057411.3| CCACAGTGTGCCGGAGGTCGTTGCTATGGACCAAAGCCGCGGGAGTGTTG gi|302179500|gb|HM749883.1| CAGCAGTGTTCC---GGGCGCTGCCGTGGCAGGTCCCCCAGTGACTGCTG gi|47522839|ref|NM_214007.1| CAGCAGTGCTCC---GGGCGCTGCCGCGGCCGGTCGCCCAGTGACTGCTG gi|41327737|ref|NM_005228.3| CAGCAGTGCTCC---GGGCGCTGCCGTGGCAAGTCCCCCAGTGACTGCTG gi|6478867|gb|M37394.2|RATEGFR CAGCAATGTTCC---CGGCGTTGTCGTGGCAGGTCCCCTAGCGACTGCTG gi|24657088|ref|NM_057410.3| TCACCTCTTCTGCGCCGGAGGATGCACTGGTCCCACGCAAAAGGATTGCA gi|24657104|ref|NM_057411.3| TCACCTCTTCTGCGCCGGAGGATGCACTGGTCCCACGCAAAAGGATTGCA gi|302179500|gb|HM749883.1| CCACAACCAGTGTGCCGCTGGCTGCACAGGGCCACGGGAGAGCGACTGCC gi|47522839|ref|NM_214007.1| CCACAACCAGTGCGCCGCTGGCTGCACGGGGCCGCGGGAGAGCGACTGCC gi|41327737|ref|NM_005228.3| CCACAACCAGTGTGCTGCAGGCTGCACAGGCCCCCGGGAGAGCGACTGCC gi|6478867|gb|M37394.2|RATEGFR CCACAACCAGTGTGCCGCAGGGTGTACAGGGCCCAGAGAGAGTGACTGTC gi|24657088|ref|NM_057410.3| TCGCCTGCAAGAACTTCTTCGACGAGGGCGTATGCAAGGAGGAATGCCCG gi|24657104|ref|NM_057411.3| TCGCCTGCAAGAACTTCTTCGACGAGGGCGTATGCAAGGAGGAATGCCCG gi|302179500|gb|HM749883.1| TGGTCTGCCGCAGGTTCCGTGATGAAGCCACCTGCAAGGACACGTGTCCG gi|47522839|ref|NM_214007.1| TGGTTTGCCGCAGATTCCGTGACGAGGCCACCTGCAAGGACACATGCCCG gi|41327737|ref|NM_005228.3| TGGTCTGCCGCAAATTCCGAGACGAAGCCACGTGCAAGGACACCTGCCCC gi|6478867|gb|M37394.2|RATEGFR TGGTCTGCCACAGGTTCCGAGATGAAGCCACGTGCAAAGACACCTGCCCA gi|24657088|ref|NM_057410.3| CCCATGCGCAAGTACAATCCCACCACCTATGTTCTTGAAACGAATCCTGA gi|24657104|ref|NM_057411.3| CCCATGCGCAAGTACAATCCCACCACCTATGTTCTTGAAACGAATCCTGA gi|302179500|gb|HM749883.1| CCACTCATGCTCTATGACCCTACCACCTACGAAATGAAGGTCAACCCGCT gi|47522839|ref|NM_214007.1| CCGCTCATGCTCTACAACCCCACCACCTACCAGATGGACGTCAACCCGCT gi|41327737|ref|NM_005228.3| CCACTCATGCTCTACAACCCCACCACGTACCAGATGGATGTGAACCCCGA gi|6478867|gb|M37394.2|RATEGFR CCACTCATGCTGTACAACCCCACCACGTACCAGATGGATGTCAACCCTGA gi|24657088|ref|NM_057410.3| GGGAAAGTATGCCTATGGTGCCACCTGCGTCAAGGAGTGTCCC---GGTC gi|24657104|ref|NM_057411.3| GGGAAAGTATGCCTATGGTGCCACCTGCGTCAAGGAGTGTCCC---GGTC gi|302179500|gb|HM749883.1| GGGGAAGTACAGCTTTGGCGCCACCTGTGTCAAGAAGTGTCCCCGTAACT gi|47522839|ref|NM_214007.1| GGGGAAGTACAGCTTTGGCGCCACCTGTGTCAAGAAGTGCCCTCGTAACT gi|41327737|ref|NM_005228.3| GGGCAAATACAGCTTTGGTGCCACCTGCGTGAAGAAGTGTCCCCGTAATT gi|6478867|gb|M37394.2|RATEGFR GGGGAAGTACAGCTTTGGTGCCACCTGTGTGAAGAAATGCCCCAGAAACT gi|24657088|ref|NM_057410.3| ATCTGTTGCGTGATAATGGCGCCTGCGTGCGCAGCTGTCCCCAGGAC--- gi|24657104|ref|NM_057411.3| ATCTGTTGCGTGATAATGGCGCCTGCGTGCGCAGCTGTCCCCAGGAC--- gi|302179500|gb|HM749883.1| ACGTGGTGACAGACCACGGCTCCTGCGTCCGCGCCTGCAGTTCTGACAGC gi|47522839|ref|NM_214007.1| ACGTGGTGACAGACCATGGCTCCTGTGTCCGTGCCTGCAGCTCCGACAGC gi|41327737|ref|NM_005228.3| ATGTGGTGACAGATCACGGCTCGTGCGTCCGAGCCTGTGGGGCCGACAGC gi|6478867|gb|M37394.2|RATEGFR ACGTGGTGACAGATCACGGCTCGTGTGTCCGGGCCTGTGGGCCAGACTAC gi|24657088|ref|NM_057410.3| ---AAGATGGACAAGGGGGGC------GAGTGTGTGCCCTGCAATGGACC gi|24657104|ref|NM_057411.3| ---AAGATGGACAAGGGGGGC------GAGTGTGTGCCCTGCAATGGACC gi|302179500|gb|HM749883.1| CAGGAGGTAGAGGAAGACGGTGTCCGCAAGTGTAAAAAGTGTGACGGGCC gi|47522839|ref|NM_214007.1| TACGAGGTGGAGGAGGACGGCGTCCGCAAGTGTAAAAAGTGTGACGGGCC gi|41327737|ref|NM_005228.3| TATGAGATGGAGGAAGACGGCGTCCGCAAGTGTAAGAAGTGCGAAGGGCC gi|6478867|gb|M37394.2|RATEGFR TATGAAGTAGAAGAAGATGGAGTCAGCAAGTGTAAAAAATGTGACGGGCC gi|24657088|ref|NM_057410.3| GTGCCCCAAAACCTGCCCGGGCGTTACTGTC------------------- gi|24657104|ref|NM_057411.3| GTGCCCCAAAACCTGCCCGGGCGTTACTGTC------------------- gi|302179500|gb|HM749883.1| TTGTGGCAAAGTTTGTAACGGAATAGGAATCGGTGAGTTTAAAGACACAC gi|47522839|ref|NM_214007.1| CTGCGGCAAAGTTTGTAACGGGATAGGGATTGGCGAGTTTAAAGACACAC gi|41327737|ref|NM_005228.3| TTGCCGCAAAGTGTGTAACGGAATAGGTATTGGTGAATTTAAAGACTCAC gi|6478867|gb|M37394.2|RATEGFR CTGCCGCAAAGTTTGCAATGGCATAGGCATTGGTGAATTTAAAGACACAC gi|24657088|ref|NM_057410.3| -----CTGCATGCCGGCAACATTGACTCGTTCCGGAATTGTACGGTGATC gi|24657104|ref|NM_057411.3| -----CTGCATGCCGGCAACATTGACTCGTTCCGGAATTGTACGGTGATC gi|302179500|gb|HM749883.1| TTTCCATAAATGCTACAAACATTAAACACTTCAGAAACTGCACATCCATC gi|47522839|ref|NM_214007.1| TTTCCATAAATGCTACGAATATCAAGCACTTCAGGAACTGCACCTCGATC gi|41327737|ref|NM_005228.3| TCTCCATAAATGCTACGAATATTAAACACTTCAAAAACTGCACCTCCATC gi|6478867|gb|M37394.2|RATEGFR TCTCCATAAATGCTACAAACATCAAACACTTCAAGTACTGCACTGCCATC gi|24657088|ref|NM_057410.3| GATGGCAACATTCGCATTTTGGATCAGACCTTCTCGGGCTTCCAGGATGT gi|24657104|ref|NM_057411.3| GATGGCAACATTCGCATTTTGGATCAGACCTTCTCGGGCTTCCAGGATGT gi|302179500|gb|HM749883.1| AGTGGAGATCTTCATATCCTGCCAGTAGCATTTAGGGGT----------- gi|47522839|ref|NM_214007.1| AGCGGAGATCTTCATATCCTGCCGGTAGCATTTAGGGGT----------- gi|41327737|ref|NM_005228.3| AGTGGCGATCTCCACATCCTGCCGGTGGCATTTAGGGGT----------- gi|6478867|gb|M37394.2|RATEGFR AGTGGGGACCTCCACATCCTGCCAGTGGCCTTTAAGGGG----------- gi|24657088|ref|NM_057410.3| CTATGCCAACTACACGATGGGACCACGATACATACCGCTGGATCCCGAGC gi|24657104|ref|NM_057411.3| CTATGCCAACTACACGATGGGACCACGATACATACCGCTGGATCCCGAGC gi|302179500|gb|HM749883.1| ----GACTCCTTCACACGTACTGCA---------CCTCTGGACCCGAAAG gi|47522839|ref|NM_214007.1| ----GACTCCTTCACACGCACGCCG---------CCTCTGGACCCCAAGG gi|41327737|ref|NM_005228.3| ----GACTCCTTCACACATACTCCT---------CCTCTGGATCCACAGG gi|6478867|gb|M37394.2|RATEGFR ----GATTCTTTCACCCGCACTCCT---------CCTCTAGACCCACGGG gi|24657088|ref|NM_057410.3| GACTGGAGGTGTTCTCCACGGTGAAGGAGATCACCGGGTATCTGAATATC gi|24657104|ref|NM_057411.3| GACTGGAGGTGTTCTCCACGGTGAAGGAGATCACCGGGTATCTGAATATC gi|302179500|gb|HM749883.1| AACTGGACATTCTAAGAACTGTAAAAGAAATAACAGGGTTTTTGCTGATT gi|47522839|ref|NM_214007.1| AACTGGACATCCTGAAAACCGTGAAGGAAATAACAGGGTTTTTACTGATT gi|41327737|ref|NM_005228.3| AACTGGATATTCTGAAAACCGTAAAGGAAATCACAGGGTTTTTGCTGATT gi|6478867|gb|M37394.2|RATEGFR AACTAGAAATTCTCAAAACTGTGAAGGAAATAACAGGGTTTTTGCTGATT gi|24657088|ref|NM_057410.3| GAGGGAACCCACCCGCAGTTCCGGAATCTGTCGTACTTCCGCAATCTGGA gi|24657104|ref|NM_057411.3| GAGGGAACCCACCCGCAGTTCCGGAATCTGTCGTACTTCCGCAATCTGGA gi|302179500|gb|HM749883.1| CAGGCCTGGCCCGAAAACAGGACTGACCTCCATGCTTTTGAGAACCTGGA gi|47522839|ref|NM_214007.1| CAGGCCTGGCCTGAAAACAGGACTGGCCTCCATGCTTTTGAGAACCTGGA gi|41327737|ref|NM_005228.3| CAGGCTTGGCCTGAAAACAGGACGGACCTCCATGCCTTTGAGAACCTAGA gi|6478867|gb|M37394.2|RATEGFR CAGGCTTGGCCTGAAAACTGGACTGACCTCCATGCTTTTGAGAACCTAGA gi|24657088|ref|NM_057410.3| AACAATTCATGGCCGCCAGCTGATGGAGAGCATGTTTGCCGCTTTGGCGA gi|24657104|ref|NM_057411.3| AACAATTCATGGCCGCCAGCTGATGGAGAGCATGTTTGCCGCTTTGGCGA gi|302179500|gb|HM749883.1| AATCATACGTGGCAGAACGAAGCAGCATGGCCAGTTT---TCTCTTGCGG gi|47522839|ref|NM_214007.1| AATCATACGTGGCAGGACGAAGCAACATGGTCAGTTT---TCCCTCGCGG gi|41327737|ref|NM_005228.3| AATCATACGCGGCAGGACCAAGCAACATGGTCAGTTT---TCTCTTGCAG gi|6478867|gb|M37394.2|RATEGFR AATAATTCGTGGCAGAACAAAGCAACATGGTCAGTTT---TCTCTGGCGG gi|24657088|ref|NM_057410.3| TCGTTAAGTCATCCCTGTACAGCCTGGAGATGCGCAATCTGAAGCAGATT gi|24657104|ref|NM_057411.3| TCGTTAAGTCATCCCTGTACAGCCTGGAGATGCGCAATCTGAAGCAGATT gi|302179500|gb|HM749883.1| TTGTCGGCCTGGATATAACATCTTTGGGATTACGCTCCCTCAAGGAGATA gi|47522839|ref|NM_214007.1| TTGTTGGCCTGGACATAGCGTCCTTGGGGATGCGCTCCCTCAAGGAGATC gi|41327737|ref|NM_005228.3| TCGTCAGCCTGAACATAACATCCTTGGGATTACGCTCCCTCAAGGAGATA gi|6478867|gb|M37394.2|RATEGFR TTGTCGGCCTGAACATAACATCGCTGGGGTTGCGTTCCCTCAAGGAGATC gi|24657088|ref|NM_057410.3| AGTTCCGGCAGTGTGGTCATCCAGCATAATAGAGACCTCTGCTACGTAAG gi|24657104|ref|NM_057411.3| AGTTCCGGCAGTGTGGTCATCCAGCATAATAGAGACCTCTGCTACGTAAG gi|302179500|gb|HM749883.1| AGTGATGGTGATGTGATAATTTCAGGAAATCGAAACTTGTGCTATGCAGA gi|47522839|ref|NM_214007.1| AGCGACGGAGACGTGATCGTCTCAGGAAACCGAAACCTGTGCTATGCAAA gi|41327737|ref|NM_005228.3| AGTGATGGAGATGTGATAATTTCAGGAAACAAAAATTTGTGCTATGCAAA gi|6478867|gb|M37394.2|RATEGFR AGTGATGGGGATGTGATTATTTCTGGGAACCGAAATTTGTGCTACGCAAA gi|24657088|ref|NM_057410.3| CAATATCCGTTGGCCGGCCATTCAGAAGGAGCCCGAACAGAAGGTGTGGG gi|24657104|ref|NM_057411.3| CAATATCCGTTGGCCGGCCATTCAGAAGGAGCCCGAACAGAAGGTGTGGG gi|302179500|gb|HM749883.1| TACAATACGCTGGAAAAAACTTTTTGGGACCTCAACTCAGAAAACCAAAA gi|47522839|ref|NM_214007.1| TACAATCAGCTGGAAAAAACTATTTGGGACCGCAAGTCAGAAAACCAAAA gi|41327737|ref|NM_005228.3| TACAATAAACTGGAAAAAACTGTTTGGGACCTCCGGTCAGAAAACCAAAA gi|6478867|gb|M37394.2|RATEGFR CACTATAAACTGGAAAAAACTCTTCGGGACGCCCAATCAAAAGACCAAAA gi|24657088|ref|NM_057410.3| TCAACGAGAATCTCAGGGCGGATCTATGCGAGAAAAATGGAACCATTTGC gi|24657104|ref|NM_057411.3| TCAACGAGAATCTCAGGGCGGATCTATGCGAGAAAAATGGAACCATTTGC gi|302179500|gb|HM749883.1| TTTTAAACAACAGGAGTGAAAAACAGTGCAAGGCCGCAGGCCACATCTGT gi|47522839|ref|NM_214007.1| TTATAAACAACAGGAGCGAAAAAGAGTGCAAAGCCATGGGCCACATCTGT gi|41327737|ref|NM_005228.3| TTATAAGCAACAGAGGTGAAAACAGCTGCAAGGCCACAGGCCAGGTCTGC gi|6478867|gb|M37394.2|RATEGFR TCATGAACAACAGAGCTGAAAAGGACTGCAAGGCCACGAACCACGTCTGT gi|24657088|ref|NM_057410.3| TCGGATCAGTGCAACGAGGACGGCTGCTGGGGAGCTGGCACGGATCAGTG gi|24657104|ref|NM_057411.3| TCGGATCAGTGCAACGAGGACGGCTGCTGGGGAGCTGGCACGGATCAGTG gi|302179500|gb|HM749883.1| CACCCGCTGTGCTCATCAGAGGGCTGCTGGGGACCGGGACCCAAATACTG gi|47522839|ref|NM_214007.1| AACCCGCTGTGCTCATCAGAGGGCTGCTGGGGCCCTGAACCCAGAGACTG gi|41327737|ref|NM_005228.3| CATGCCTTGTGCTCCCCCGAGGGCTGCTGGGGCCCGGAGCCCAGGGACTG gi|6478867|gb|M37394.2|RATEGFR AATCCTTTATGCTCCTCGGAAGGCTGCTGGGGCCCTGAGCCCACGGACTG gi|24657088|ref|NM_057410.3| CCTTACCTGCAAGAACTTCAATTTCAATGGCACCTGCATCGCCGACTGTG gi|24657104|ref|NM_057411.3| CCTTACCTGCAAGAACTTCAATTTCAATGGCACCTGCATCGCCGACTGTG gi|302179500|gb|HM749883.1| CATGTCCTGCCAGAACTTCAGTCGTGGCAAGGAGTGTGTGGGAAAGTGCA gi|47522839|ref|NM_214007.1| CATGTCCTGTCGAAACTTTAGCCGCGGCAAGGAATGTGTGGAGAAGTGCA gi|41327737|ref|NM_005228.3| CGTCTCTTGCCGGAATGTCAGCCGAGGCAGGGAATGCGTGGACAAGTGCA gi|6478867|gb|M37394.2|RATEGFR TGTCTCCTGCCAGAATGTGAGCAGAGGCAGGGAGTGCGTGGACAAGTGCA gi|24657088|ref|NM_057410.3| GTTATATATCCAATGCCTACAAG------TTTGACAATAGAACGTGCAAG gi|24657104|ref|NM_057411.3| GTTATATATCCAATGCCTACAAG------TTTGACAATAGAACGTGCAAG gi|302179500|gb|HM749883.1| ACATTCTAGAGGGAGAGCCCAGAGAATTCGTGGAGAACTCCGAGTGTGTG gi|47522839|ref|NM_214007.1| ACGTTCTGGAGGGGGAGCCGAGAGAGTTCGTGGAGAATGCCGAGTGTGTG gi|41327737|ref|NM_005228.3| ACCTTCTGGAGGGTGAGCCAAGGGAGTTTGTGGAGAACTCTGAGTGCATA gi|6478867|gb|M37394.2|RATEGFR ACATCCTGGAGGGGGAACCGAGGGAGTTTGTGGAAAATTCTGAATGCATC gi|24657088|ref|NM_057410.3| ATATGCCATCCAGAGTGCCGG------------------ACTTGCAATGG gi|24657104|ref|NM_057411.3| ATATGCCATCCAGAGTGCCGG------------------ACTTGCAATGG gi|302179500|gb|HM749883.1| CAGTGCCATCCAGAATGCCTGCCCCAGGCCATGAACGTGACCTGCACTGG gi|47522839|ref|NM_214007.1| CAGTGCCACCCGGAGTGCCTGCCCCAGGCCAAGAACGTGACCTGCATGGG gi|41327737|ref|NM_005228.3| CAGTGCCACCCAGAGTGCCTGCCTCAGGCCATGAACATCACCTGCACAGG gi|6478867|gb|M37394.2|RATEGFR CAGTGCCATCCAGAATGTCTGCCCCAGACCATGAACATCACCTGTACAGG gi|24657088|ref|NM_057410.3| AGCTGGAGCAGATCACTGCCAGGAGTGCGTCCATGTGAGGGACGGTCAGC gi|24657104|ref|NM_057411.3| AGCTGGAGCAGATCACTGCCAGGAGTGCGTCCATGTGAGGGACGGTCAGC gi|302179500|gb|HM749883.1| ACGCGGACCAGGCAACTGTGTAAAGTGCGCCCACTACATTGATGGCCCTC gi|47522839|ref|NM_214007.1| ACGCGGACCGGACAGCTGTGTCCGGTGTGCTCACTACATCGACGGCCCTC gi|41327737|ref|NM_005228.3| ACGGGGACCAGACAACTGTATCCAGTGTGCCCACTACATTGACGGCCCCC gi|6478867|gb|M37394.2|RATEGFR CCGGGGGCCAGACAACTGCATCAAGTGTGCCCACTATGTTGATGGTCCCC gi|24657088|ref|NM_057410.3| ACTGTGTGTCCGAGTGCCCGAAGAACAAGTACAACGATCGTGGTGTCTGC gi|24657104|ref|NM_057411.3| ACTGTGTGTCCGAGTGCCCGAAGAACAAGTACAACGATCGTGGTGTCTGC gi|302179500|gb|HM749883.1| ACTGCGTCAAGACCTGCCCT------------------------------ gi|47522839|ref|NM_214007.1| ACTGTGTCAAGACCTGCCCC------------------------------ gi|41327737|ref|NM_005228.3| ACTGCGTCAAGACCTGCCCG------------------------------ gi|6478867|gb|M37394.2|RATEGFR ACTGTGTCAAGACCTGCCCT------------------------------ gi|24657088|ref|NM_057410.3| CGAGAGTGCCACGCCACCTGCGATGGATGCACTGGGCCCAAGGACACCAT gi|24657104|ref|NM_057411.3| CGAGAGTGCCACGCCACCTGCGATGGATGCACTGGGCCCAAGGACACCAT gi|302179500|gb|HM749883.1| ---------------------GCTGGAGTCGCGGGAGAGAATGGCACCCT gi|47522839|ref|NM_214007.1| ---------------------GCGGGAATCGCAGGAGAAAACAGCACCCT gi|41327737|ref|NM_005228.3| ---------------------GCAGGAGTCATGGGAGAAAACAACACCCT gi|6478867|gb|M37394.2|RATEGFR ---------------------TCGGGCATCATGGGGGAGAACAACACCCT gi|24657088|ref|NM_057410.3| CGGCATTGGAGCGTGTACAACGTGCAATTTGGCCATTATCAACAATGACG gi|24657104|ref|NM_057411.3| CGGCATTGGAGCGTGTACAACGTGCAATTTGGCCATTATCAACAATGACG gi|302179500|gb|HM749883.1| GATC---------------------------------------------- gi|47522839|ref|NM_214007.1| CATC---------------------------------------------- gi|41327737|ref|NM_005228.3| GGTC---------------------------------------------- gi|6478867|gb|M37394.2|RATEGFR GGTC---------------------------------------------- gi|24657088|ref|NM_057410.3| CCACAGTAAAACGCTGCCTGCTGAAGGACGACAAGTGCCCCGATGGGTAC gi|24657104|ref|NM_057411.3| CCACAGTAAAACGCTGCCTGCTGAAGGACGACAAGTGCCCCGATGGGTAC gi|302179500|gb|HM749883.1| -------------------------------------------------- gi|47522839|ref|NM_214007.1| -------------------------------------------------- gi|41327737|ref|NM_005228.3| -------------------------------------------------- gi|6478867|gb|M37394.2|RATEGFR -------------------------------------------------- gi|24657088|ref|NM_057410.3| TTCTGGGAGTATGTGCATCCACAAGAGCAGGGATCGCTAAAGCCATTGGC gi|24657104|ref|NM_057411.3| TTCTGGGAGTATGTGCATCCACAAGAGCAGGGATCGCTAAAGCCATTGGC gi|302179500|gb|HM749883.1| ---TGGAAGTTTGCA----------------------------------- gi|47522839|ref|NM_214007.1| ---TGGAAGTTTGCG----------------------------------- gi|41327737|ref|NM_005228.3| ---TGGAAGTACGCA----------------------------------- gi|6478867|gb|M37394.2|RATEGFR ---TGGAAGTTTGCA----------------------------------- gi|24657088|ref|NM_057410.3| CGGCAGAGCAGTTTGCCGAAAGTGCCATCCCCTTTGCGAGCTGTGCACCA gi|24657104|ref|NM_057411.3| CGGCAGAGCAGTTTGCCGAAAGTGCCATCCCCTTTGCGAGCTGTGCACCA gi|302179500|gb|HM749883.1| -------------------GATGCCAACCACGTGTGTCTCCTG------- gi|47522839|ref|NM_214007.1| -------------------GATGCCAACCACGTGTGTCACCTG------- gi|41327737|ref|NM_005228.3| -------------------GACGCCGGCCATGTGTGCCACCTG------- gi|6478867|gb|M37394.2|RATEGFR -------------------GATGCCAATAACGTCTGCCACCTC------- gi|24657088|ref|NM_057410.3| ACTACGGATACCATGAACAGGTGTGCTCCAAGTGCACCCACTACAAGCGA gi|24657104|ref|NM_057411.3| ACTACGGATACCATGAACAGGTGTGCTCCAAGTGCACCCACTACAAGCGA gi|302179500|gb|HM749883.1| -------------------------------------------------- gi|47522839|ref|NM_214007.1| -------------------------------------------------- gi|41327737|ref|NM_005228.3| -------------------------------------------------- gi|6478867|gb|M37394.2|RATEGFR -------------------------------------------------- gi|24657088|ref|NM_057410.3| CGAGAGCAGTGCGAGACCGAGTGTCCGGCCGATCACTACACGGATGAGGA gi|24657104|ref|NM_057411.3| CGAGAGCAGTGCGAGACCGAGTGTCCGGCCGATCACTACACGGATGAGGA gi|302179500|gb|HM749883.1| -------------------------------------------------- gi|47522839|ref|NM_214007.1| -------------------------------------------------- gi|41327737|ref|NM_005228.3| -------------------------------------------------- gi|6478867|gb|M37394.2|RATEGFR -------------------------------------------------- gi|24657088|ref|NM_057410.3| GCAGCGCGAGTGCTTCCAGTGCCACCCAGAATGCAAC---GGTTGCACTG gi|24657104|ref|NM_057411.3| GCAGCGCGAGTGCTTCCAGTGCCACCCAGAATGCAAC---GGTTGCACTG gi|302179500|gb|HM749883.1| -------------------TGCCACCCCAACTGCACCTATGGCTGTGAAG gi|47522839|ref|NM_214007.1| -------------------TGCCACCCCAACTGCACCTACGGCTGTGTCG gi|41327737|ref|NM_005228.3| -------------------TGCCATCCAAACTGCACCTACGGATGCACTG gi|6478867|gb|M37394.2|RATEGFR -------------------TGCCATGCAAACTGTACCTATGGATGTGCTG gi|24657088|ref|NM_057410.3| GTCCGGGTGCCGACGATTGCAAGTCTTGTCGCAACTTCAAGTTGTTCGAC gi|24657104|ref|NM_057411.3| GTCCGGGTGCCGACGATTGCAAGTCTTGTCGCAACTTCAAGTTGTTCGAC gi|302179500|gb|HM749883.1| GGCCAGGTCTCGAAGGCTGTCCACAA---AAAGGGCCCAAGATC------ gi|47522839|ref|NM_214007.1| GACCAGGTCTCGAGGGCTGTGCGGTG---GACAGGCCCAAGATC------ gi|41327737|ref|NM_005228.3| GGCCAGGTCTTGAAGGCTGTCCAACG---AATGGGCCTAAGATC------ gi|6478867|gb|M37394.2|RATEGFR GGCCAGGCCTTAAAGGATGTCAACAACCAGAAGGGCCAAAGATC------ gi|24657088|ref|NM_057410.3| GCGAATGAGACGGGTCCCTATGTGAACTCCACGATGTTCAATTGCACCTC gi|24657104|ref|NM_057411.3| GCGAATGAGACGGGTCCCTATGTGAACTCCACGATGTTCAATTGCACCTC gi|302179500|gb|HM749883.1| ---------------CCGTCCATTGCCACGGGCATCGTG----------- gi|47522839|ref|NM_214007.1| ---------------CCGTCCATCGCCACCGGGATAGTG----------- gi|41327737|ref|NM_005228.3| ---------------CCGTCCATCGCCACTGGGATGGTG----------- gi|6478867|gb|M37394.2|RATEGFR ---------------CCATCCATCGCCACTGGGATTGTG----------- gi|24657088|ref|NM_057410.3| GAAGTGTCCCTTGGAGATGCGACATGTGAACTATCAGTACACGGCCATTG gi|24657104|ref|NM_057411.3| GAAGTGTCCCTTGGAGATGCGACATGTGAACTATCAGTACACGGCCATTG gi|302179500|gb|HM749883.1| -------------------------------------------------- gi|47522839|ref|NM_214007.1| -------------------------------------------------- gi|41327737|ref|NM_005228.3| -------------------------------------------------- gi|6478867|gb|M37394.2|RATEGFR -------------------------------------------------- gi|24657088|ref|NM_057410.3| GACCCTACTGTGCAGCTAGTCCGCCGAGGAGCAGCAAGATAACTGCCAAT gi|24657104|ref|NM_057411.3| GACCCTACTGTGCAGCTAGTCCGCCGAGGAGCAGCAAGATAACTGCCAAT gi|302179500|gb|HM749883.1| -------------------------------------------------- gi|47522839|ref|NM_214007.1| -------------------------------------------------- gi|41327737|ref|NM_005228.3| -------------------------------------------------- gi|6478867|gb|M37394.2|RATEGFR -------------------------------------------------- gi|24657088|ref|NM_057410.3| CTGGATGTGAACATGATCTTCATTATCACTGGTGCTGTTCTGGTGCCGAC gi|24657104|ref|NM_057411.3| CTGGATGTGAACATGATCTTCATTATCACTGGTGCTGTTCTGGTGCCGAC gi|302179500|gb|HM749883.1| ------------------------------GGCGGCCTGCTGCTGGTGGT gi|47522839|ref|NM_214007.1| ------------------------------GGGGGCCTGCTTCTGGCCGT gi|41327737|ref|NM_005228.3| ------------------------------GGGGCCCTCCTCTTGCTGCT gi|6478867|gb|M37394.2|RATEGFR ------------------------------GGTGGCCTCCTCTTCATAGT gi|24657088|ref|NM_057410.3| GATCTGCATCCTCTGCGTGGTCACATACATTTGTCGGCAAAAGCAAAAGG gi|24657104|ref|NM_057411.3| GATCTGCATCCTCTGCGTGGTCACATACATTTGTCGGCAAAAGCAAAAGG gi|302179500|gb|HM749883.1| GGTGCTGGCCCTGAGCGTCGGCCTCTTCATG---CGCAGGCGCCACATCG gi|47522839|ref|NM_214007.1| GGTGCTGGCCCTGGGGGTCGGCCTCTTTCTG---CGCAGGCGCCACATCG gi|41327737|ref|NM_005228.3| GGTGGTGGCCCTGGGGATCGGCCTCTTCATG---CGAAGGCGCCACATCG gi|6478867|gb|M37394.2|RATEGFR AGTGGTGGCCCTTGGGATCGGCCTCTTCATG---CGTCGACGTCAGCTTG gi|24657088|ref|NM_057410.3| CCAAGAAAGAAACAGTGAAGATGACCATGGCTCTGTCCGGCTGTGAGGAT gi|24657104|ref|NM_057411.3| CCAAGAAAGAAACAGTGAAGATGACCATGGCTCTGTCCGGCTGTGAGGAT gi|302179500|gb|HM749883.1| TGCGCAAGCGCACACTGCGCCGGCTG------CTGCAGGAGCGTGAGCTC gi|47522839|ref|NM_214007.1| TCCGCAAGCGCACGCTGCGCCGGCTG------CTGCAGGAGCGGGAGCTG gi|41327737|ref|NM_005228.3| TTCGGAAGCGCACGCTGCGGAGGCTG------CTGCAGGAGAGGGAGCTT gi|6478867|gb|M37394.2|RATEGFR TCCGAAAACGTACACTACGCCGCCTG------CTTCAAGAGAGAGAGCTC gi|24657088|ref|NM_057410.3| TCCGAGCCGCTGCGTCCCTCGAACATTGGAGCCAATCTATGCAAGTTGCG gi|24657104|ref|NM_057411.3| TCCGAGCCGCTGCGTCCCTCGAACATTGGAGCCAATCTATGCAAGTTGCG gi|302179500|gb|HM749883.1| GTGGAGCCTCTGACGCCCAGCGGAGAAGCTCCCAACCAAGCTCTCTTGAG gi|47522839|ref|NM_214007.1| GTTGAGCCTCTCACACCCAGTGGAGAAGCTCCCAACCAAGCTCTCTTGAG gi|41327737|ref|NM_005228.3| GTGGAGCCTCTTACACCCAGTGGAGAAGCTCCCAACCAAGCTCTCTTGAG gi|6478867|gb|M37394.2|RATEGFR GTGGAACCTCTCACACCCAGCGGAGAAGCTCCGAACCAAGCCCACTTGAG gi|24657088|ref|NM_057410.3| CATTGTCAAGGACGCCGAGTTGCGCAAGGGCGGAGTCCTCGGAATGGGAG gi|24657104|ref|NM_057411.3| CATTGTCAAGGACGCCGAGTTGCGCAAGGGCGGAGTCCTCGGAATGGGAG gi|302179500|gb|HM749883.1| GATCCTAAAGGAAACAGAATTCAAGAAGGTCAAGGTGCTGGGCTCGGGAG gi|47522839|ref|NM_214007.1| GATCCTGAAGGAGACGGAATTCAAAAAGGTCAAGGTGCTGGGCTCCGGCG gi|41327737|ref|NM_005228.3| GATCTTGAAGGAAACTGAATTCAAAAAGATCAAAGTGCTGGGCTCCGGTG gi|6478867|gb|M37394.2|RATEGFR GATATTAAAGGAAACAGAATTCAAAAAGATCAAAGTTCTGGGTTCAGGAG gi|24657088|ref|NM_057410.3| CCTTTGGACGAGTGTACAAGGGCGTTTGGGTGCCGGAGGGTGAGAACGTC gi|24657104|ref|NM_057411.3| CCTTTGGACGAGTGTACAAGGGCGTTTGGGTGCCGGAGGGTGAGAACGTC gi|302179500|gb|HM749883.1| CATTTGGCACCGTGTACAAGGGACTCTGGATCCCAGAAGGCGAGAAGGTT gi|47522839|ref|NM_214007.1| CGTTCGGCACGGTGTACAAGGGCCTCTGGATCCCAGAAGGTGAGAAGGTG gi|41327737|ref|NM_005228.3| CGTTCGGCACGGTGTATAAGGGACTCTGGATCCCAGAAGGTGAGAAAGTT gi|6478867|gb|M37394.2|RATEGFR CATTTGGCACAGTGTATAAGGGTCTCTGGATCCCAGAAGGCGAGAAAGTG gi|24657088|ref|NM_057410.3| AAGATTCCAGTGGCCATTAAGGAGCTGCTCAAGTCCACAGGCGCCGAGTC gi|24657104|ref|NM_057411.3| AAGATTCCAGTGGCCATTAAGGAGCTGCTCAAGTCCACAGGCGCCGAGTC gi|302179500|gb|HM749883.1| AAAATTCCTGTAGCTATCAAGGAATTAAGAGAAGCCACATCTCCAAAAGC gi|47522839|ref|NM_214007.1| AAAATTCCTGTGGCTATCAAGGAATTAAGAGAAGCCACTTCTCCAAAAGC gi|41327737|ref|NM_005228.3| AAAATTCCCGTCGCTATCAAGGAATTAAGAGAAGCAACATCTCCGAAAGC gi|6478867|gb|M37394.2|RATEGFR AAAATCCCTGTGGCCATCAAGGAGTTAAGAGAAGCCACATCTCCCAAAGC gi|24657088|ref|NM_057410.3| AAGCGAAGAGTTCCTCCGCGAAGCCTACATCATGGCCTCTGTGGAGCACG gi|24657104|ref|NM_057411.3| AAGCGAAGAGTTCCTCCGCGAAGCCTACATCATGGCCTCTGTGGAGCACG gi|302179500|gb|HM749883.1| CAACAAGGAAATTCTTGATGAGGCCTACGTGATGGCCAGTGTGGACAACC gi|47522839|ref|NM_214007.1| CAACAAGGAAATTCTTGACGAAGCCTACGTGATGGCCAGTGTGGACAATC gi|41327737|ref|NM_005228.3| CAACAAGGAAATCCTCGATGAAGCCTACGTGATGGCCAGCGTGGACAACC gi|6478867|gb|M37394.2|RATEGFR CAACAAGGAAATCCTTGATGAAGCCTACGTGATGGCCAGTGTGGACAACC gi|24657088|ref|NM_057410.3| TTAATCTGCTGAAGCTCCTGGCCGTCTGCATGTCCTCACAAATGATGCTA gi|24657104|ref|NM_057411.3| TTAATCTGCTGAAGCTCCTGGCCGTCTGCATGTCCTCACAAATGATGCTA gi|302179500|gb|HM749883.1| CCCATGTGTGCCGCCTCCTGGGCATCTGCCTGACCTCCACCGTGCAGCTC gi|47522839|ref|NM_214007.1| CTCATGTGTGCCGCCTCCTGGGCATCTGCCTGACCTCCACGGTGCAGCTC gi|41327737|ref|NM_005228.3| CCCACGTGTGCCGCCTGCTGGGCATCTGCCTCACCTCCACCGTGCAGCTC gi|6478867|gb|M37394.2|RATEGFR CTCATGTATGCCGCCTCCTGGGCATCTGTCTGACCTCCACTGTCCAGCTC gi|24657088|ref|NM_057410.3| ATCACGCAACTGATGCCGCTTGGCTGCCTGTTGGACTATGTGCGAAATAA gi|24657104|ref|NM_057411.3| ATCACGCAACTGATGCCGCTTGGCTGCCTGTTGGACTATGTGCGAAATAA gi|302179500|gb|HM749883.1| ATCACACAGCTCATGCCCTTCGGCTGCCTGCTGGACTACGTCCGCGAGCA gi|47522839|ref|NM_214007.1| ATCACGCAGCTCATGCCCTTCGGCTGCCTCCTGGACTACGTCCGCGAGCA gi|41327737|ref|NM_005228.3| ATCACGCAGCTCATGCCCTTCGGCTGCCTCCTGGACTATGTCCGGGAACA gi|6478867|gb|M37394.2|RATEGFR ATTACACAACTCATGCCCTATGGTTGCCTCCTGGACTATGTCCGAGAACA gi|24657088|ref|NM_057410.3| CCGGGACAAGATCGGCTCTAAGGCTCTGCTCAACTGGAGCACGCAAATCG gi|24657104|ref|NM_057411.3| CCGGGACAAGATCGGCTCTAAGGCTCTGCTCAACTGGAGCACGCAAATCG gi|302179500|gb|HM749883.1| CAAGGACAATGTCGGCTCCCAGTACCTGCTCAACTGGTGTGTGCAGATCG gi|47522839|ref|NM_214007.1| CAAGGACAACATCGGCTCCCAGCACCTGCTCAACTGGTGTGTGCAGATCG gi|41327737|ref|NM_005228.3| CAAAGACAATATTGGCTCCCAGTACCTGCTCAACTGGTGTGTGCAGATCG gi|6478867|gb|M37394.2|RATEGFR TAAGGACAACATTGGCTCCCAGTACCTACTCAACTGGTGTGTGCAGATTG gi|24657088|ref|NM_057410.3| CCAAGGGCATGTCGTATCTGGAGGAGAAGCGACTGGTCCACAGAGACTTG gi|24657104|ref|NM_057411.3| CCAAGGGCATGTCGTATCTGGAGGAGAAGCGACTGGTCCACAGAGACTTG gi|302179500|gb|HM749883.1| CAAAGGGCATGAATTACCTGGAAGACCGGCGCTTGGTGCATAGGGACCTG gi|47522839|ref|NM_214007.1| CAAAGGGCATGAACTATCTGGAAGACCGGCGCTTGGTGCACCGAGACCTG gi|41327737|ref|NM_005228.3| CAAAGGGCATGAACTACTTGGAGGACCGTCGCTTGGTGCACCGCGACCTG gi|6478867|gb|M37394.2|RATEGFR CAAAGGGCATGAACTACCTGGAAGACCGGCGTTTGGTACACCGTGACTTG gi|24657088|ref|NM_057410.3| GCTGCCCGCAATGTCCTGGTGCAGACTCCCTCGCTGGTGAAGATCACCGA gi|24657104|ref|NM_057411.3| GCTGCCCGCAATGTCCTGGTGCAGACTCCCTCGCTGGTGAAGATCACCGA gi|302179500|gb|HM749883.1| GCAGCCAGGAACGTGCTGGTGAAGACGCCGCAGCACGTGAAGATCACAGA gi|47522839|ref|NM_214007.1| GCGGCCAGGAATGTGCTGGTGAAGACACCGCAGCATGTCAAGATCACTGA gi|41327737|ref|NM_005228.3| GCAGCCAGGAACGTACTGGTGAAAACACCGCAGCATGTCAAGATCACAGA gi|6478867|gb|M37394.2|RATEGFR GCAGCCAGGAATGTACTGGTAAAGACACCACAGCATGTCAAGATCACAGA gi|24657088|ref|NM_057410.3| CTTTGGGCTGGCCAAGTTGCTGAGCAGCGATTCCAATGAGTACAAGGCTG gi|24657104|ref|NM_057411.3| CTTTGGGCTGGCCAAGTTGCTGAGCAGCGATTCCAATGAGTACAAGGCTG gi|302179500|gb|HM749883.1| CTTCGGGCTGGCCAAGCTGCTGGGTGCCGAGGAGAAGGAGTATCATGCAG gi|47522839|ref|NM_214007.1| CTTTGGGCTGGCCAAGCTGCTGGGCGCCGAGGAGAAAGAGTACCACGCGG gi|41327737|ref|NM_005228.3| TTTTGGGCTGGCCAAACTGCTGGGTGCGGAAGAGAAAGAATACCATGCAG gi|6478867|gb|M37394.2|RATEGFR TTTTGGACTGGCCAAACTGCTTGGTGCTGAGGAGAAAGAATACCATGCAG gi|24657088|ref|NM_057410.3| CTGGCGGCAAGATGCCCATCAAGTGGTTGGCACTGGAGTGCATTCGCAAT gi|24657104|ref|NM_057411.3| CTGGCGGCAAGATGCCCATCAAGTGGTTGGCACTGGAGTGCATTCGCAAT gi|302179500|gb|HM749883.1| AAGGAGGCAAGGTCCCTATCAAATGGATGGCTTTGGAATCAATTTTACAC gi|47522839|ref|NM_214007.1| AAGGAGGCAAAGTGCCCATCAAGTGGCTGGCTCTAGAGTCAATCCTGCAC gi|41327737|ref|NM_005228.3| AAGGAGGCAAAGTGCCTATCAAGTGGATGGCATTGGAATCAATTTTACAC gi|6478867|gb|M37394.2|RATEGFR AGGGGGGCAAAGTGCCTATCAAGTGGATGGCTTTGGAATCAATTTTACAC gi|24657088|ref|NM_057410.3| CGTGTATTCACCAGCAAGTCCGATGTCTGGGCCTTTGGTGTGACAATTTG gi|24657104|ref|NM_057411.3| CGTGTATTCACCAGCAAGTCCGATGTCTGGGCCTTTGGTGTGACAATTTG gi|302179500|gb|HM749883.1| CGAATTTATACCCATCAGAGTGATGTCTGGAGCTATGGAGTCACTGTTTG gi|47522839|ref|NM_214007.1| CGTGTATACACCCACCAGAGTGACGTCTGGAGCTACGGAGTCACCGTTTG gi|41327737|ref|NM_005228.3| AGAATCTATACCCACCAGAGTGATGTCTGGAGCTACGGGGTGACCGTTTG gi|6478867|gb|M37394.2|RATEGFR CGAATTTATACACACCAAAGCGACGTCTGGAGCTATGGAGTCACCGTGTG gi|24657088|ref|NM_057410.3| GGAACTGCTGACCTTTGGCCAGCGTCCACACGAGAACATCCCCGCTAAGG gi|24657104|ref|NM_057411.3| GGAACTGCTGACCTTTGGCCAGCGTCCACACGAGAACATCCCCGCTAAGG gi|302179500|gb|HM749883.1| GGAGTTGATGACCTTTGGATCCAAGCCTTACGATGGAATCCCTGCGAGTG gi|47522839|ref|NM_214007.1| GGAGCTGATGACCTTTGGGTCCAAGCCTTATGACGGGATCCCCGCGAGTG gi|41327737|ref|NM_005228.3| GGAGTTGATGACCTTTGGATCCAAGCCATATGACGGAATCCCTGCCAGCG gi|6478867|gb|M37394.2|RATEGFR GGAACTGATGACCTTTGGGTCCAAGCCTTATGATGGGATCCCTGCAAGTG gi|24657088|ref|NM_057410.3| ATATTCCCGATCTTATTGAAGTCGGTCTGAAGCTGGAGCAGCCGGAGATT gi|24657104|ref|NM_057411.3| ATATTCCCGATCTTATTGAAGTCGGTCTGAAGCTGGAGCAGCCGGAGATT gi|302179500|gb|HM749883.1| AGATCTCGACTGTCCTGGAGAAAGGAGAGCGCCTCCCACAGCCACCCATC gi|47522839|ref|NM_214007.1| AGATCTCGACCGTCCTGGAGAAGGGAGAGCGCCTCCCGCAGCCCCCCATC gi|41327737|ref|NM_005228.3| AGATCTCCTCCATCCTGGAGAAAGGAGAACGCCTCCCTCAGCCACCCATA gi|6478867|gb|M37394.2|RATEGFR AGATCTCATCCATCCTAGAGAAAGGAGAGCGCCTTCCACAGCCACCTATC gi|24657088|ref|NM_057410.3| TGTTCGCTGGACATTTACTGCACACTTCTCTCGTGCTGGCACTTGGATGC gi|24657104|ref|NM_057411.3| TGTTCGCTGGACATTTACTGCACACTTCTCTCGTGCTGGCACTTGGATGC gi|302179500|gb|HM749883.1| TGCACCATCGACGTCTACATGATCATGGTCAAGTGCTGGATGATAGATGC gi|47522839|ref|NM_214007.1| TGCACCATTGATGTCTACATGATCATGGTCAAGTGCTGGATGATAGATGC gi|41327737|ref|NM_005228.3| TGTACCATCGATGTCTACATGATCATGGTCAAGTGCTGGATGATAGACGC gi|6478867|gb|M37394.2|RATEGFR TGCACCATCGACGTCTACATGATCATGGTCAAGTGCTGGATGATAGATGC gi|24657088|ref|NM_057410.3| CGCCATGCGTCCAACCTTCAAGCAGCTGACTACGGTCTTTGCTGAGTTCG gi|24657104|ref|NM_057411.3| CGCCATGCGTCCAACCTTCAAGCAGCTGACTACGGTCTTTGCTGAGTTCG gi|302179500|gb|HM749883.1| AGACAGTCGCCCAAAGTTCCGTGAGTTGATCCTTGAATTCTCCAAGATGG gi|47522839|ref|NM_214007.1| TGATAGTCGCCCAAAGTTCCGTGAGCTGATCATCGAATTCTCCAAAATGG gi|41327737|ref|NM_005228.3| AGATAGTCGCCCAAAGTTCCGTGAGTTGATCATCGAATTCTCCAAAATGG gi|6478867|gb|M37394.2|RATEGFR TGATAGCCGCCCAAAGTTCCGAGAGTTGATTCTCGAATTCTCCAAAATGG gi|24657088|ref|NM_057410.3| CCAGAGATCCGGGTCGCTATCTGGCCATTCCCGGGGATAAGTTCACCCGG gi|24657104|ref|NM_057411.3| CCAGAGATCCGGGTCGCTATCTGGCCATTCCCGGGGATAAGTTCACCCGG gi|302179500|gb|HM749883.1| CCCGAGACCCCCAGCGCTACCTTGTCATCCAGGGGGACGAGAGAATGCAT gi|47522839|ref|NM_214007.1| CCCGAGACCCCCAGCGCTACCTTGTCATCCAGGGAGACGAGCGAATGCAC gi|41327737|ref|NM_005228.3| CCCGAGACCCCCAGCGCTACCTTGTCATTCAGGGGGATGAAAGAATGCAT gi|6478867|gb|M37394.2|RATEGFR CCAGAGACCCACAGCGCTACCTTGTTATCCAGGGGGATGAAAGGATGCAT gi|24657088|ref|NM_057410.3| CTGCCGGCCTACACGAGTCAGGATGAGAAGGATCTCATCCGAAAATTGGC gi|24657104|ref|NM_057411.3| CTGCCGGCCTACACGAGTCAGGATGAGAAGGATCTCATCCGAAAATTGGC gi|302179500|gb|HM749883.1| TTGCCA---------AGCCCTACGGACTCCAACTTCTACCGCGCCCTGAT gi|47522839|ref|NM_214007.1| TTGCCA---------AGCCCTACGGACTCCAACTTCTACCGCGCCCTGAT gi|41327737|ref|NM_005228.3| TTGCCA---------AGTCCTACAGACTCCAACTTCTACCGTGCCCTGAT gi|6478867|gb|M37394.2|RATEGFR TTGCCG---------AGCCCTACAGACTCCAACTTTTACCGAGCCCTGAT gi|24657088|ref|NM_057410.3| TCCCACCACCGATGGGTCCGAAGCCATTGCGGAACCCGATGACTACCTGC gi|24657104|ref|NM_057411.3| TCCCACCACCGATGGGTCCGAAGCCATTGCGGAACCCGATGACTACCTGC gi|302179500|gb|HM749883.1| GGATGAGGAGGAC---ATGGAGGATGTTGTGGATGCCGATGAGTACCTCG gi|47522839|ref|NM_214007.1| GGACGAGGAGGAC---ATGGAGGATGTGGTGGACGCCGACGAGTACCTCG gi|41327737|ref|NM_005228.3| GGATGAAGAAGAC---ATGGACGACGTGGTGGATGCCGACGAGTACCTCA gi|6478867|gb|M37394.2|RATEGFR GGAGGAGGAGGAC---ATGGAAGACGTAGTTGATGCTGATGAATACCTCA gi|24657088|ref|NM_057410.3| AACCCAAGGCAGCACCTGGTCCTAGTCACAGAACCGACTGCACGGATGAG gi|24657104|ref|NM_057411.3| AACCCAAGGCAGCACCTGGTCCTAGTCACAGAACCGACTGCACGGATGAG gi|302179500|gb|HM749883.1| TCCCCCAGCAGGGCTTCTTCCACAGCCCCACCACCTCCCGGACACCCCTC gi|47522839|ref|NM_214007.1| TCCCCCAGCAGGGCTTCTTCCACAGCCCCGCCACCTCCCGGACGCCGCTG gi|41327737|ref|NM_005228.3| TCCCACAGCAGGGCTTCTTCAGCAGCCCCTCCACGTCACGGACTCCCCTC gi|6478867|gb|M37394.2|RATEGFR TCCCACAGCAAGGCTTCTTCAACAGCCCATCCACGTCACGGACTCCACTC gi|24657088|ref|NM_057410.3| ATACCCAAGCTGAACCGCTACTGCAAGGATCCTAGC------------AA gi|24657104|ref|NM_057411.3| ATACCCAAGCTGAACCGCTACTGCAAGGATCCTAGC------------AA gi|302179500|gb|HM749883.1| CTCAGCTCGCTGAGCACCTCCAGCAACACTCCCACTGTGACTTGCGTTGA gi|47522839|ref|NM_214007.1| CTCAGCTCTCTGAGCGCCACCAGCAGCACCCCCGCTGTGGCTTGCGTTGA gi|41327737|ref|NM_005228.3| CTGAGCTCTCTGAGTGCAACCAGCAACAATTCCACCGTGGCTTGCATTGA gi|6478867|gb|M37394.2|RATEGFR TTGAGCTCTCTGAGTGCAAATAGCAACAGTTCCACTGTGGCTTGCATTAA gi|24657088|ref|NM_057410.3| CAAGAATTCG------------AGTACCGGAGACGATGAGACGGATTCGA gi|24657104|ref|NM_057411.3| CAAGAATTCG------------AGTACCGGAGACGATGAGACGGATTCGA gi|302179500|gb|HM749883.1| TAGAAATGGG------AGCTACCCTCTCAAGGAAGACAGCTTCCTGCAGC gi|47522839|ref|NM_214007.1| CAGAAACGGG---CAGAGTTATCCCCTCAAGGAAGACAGCTTCCTGCAGC gi|41327737|ref|NM_005228.3| TAGAAATGGGCTGCAAAGCTGTCCCATCAAGGAAGACAGCTTCTTGCAGC gi|6478867|gb|M37394.2|RATEGFR TAGAAATGGG------AGCTGCCGTGTCAAAGAAGACGCCTTCTTGCAAC gi|24657088|ref|NM_057410.3| GTGCCCGGGAAGTGGGCGTGGGTAATCTGCGCCTCGAT------------ gi|24657104|ref|NM_057411.3| GTGCCCGGGAAGTGGGCGTGGGTAATCTGCGCCTCGAT------------ gi|302179500|gb|HM749883.1| GCTACAGCTCAGACCCCACTGGTGCCCTCATCGAGGACAGCATGGACGAC gi|47522839|ref|NM_214007.1| GGTACAGCTCCGACCCCACTGGCGCCCTGACCGAGGACAGCCTAGACGAC gi|41327737|ref|NM_005228.3| GATACAGCTCAGACCCCACAGGCGCCTTGACTGAGGACAGCATAGACGAC gi|6478867|gb|M37394.2|RATEGFR GGTATAGCTCCGATCCCACCAGCGTCCTGACAGAGGACAACATAGATGAC gi|24657088|ref|NM_057410.3| ------CTACCAGTCGATGAGGATGATTACCTGATGCCCACATGCCAACC gi|24657104|ref|NM_057411.3| ------CTACCAGTCGATGAGGATGATTACCTGATGCCCACATGCCAACC gi|302179500|gb|HM749883.1| GCTTTCCTCCCAGTACCCGAA------TATGTAAACCAATCTGTTCCCAA gi|47522839|ref|NM_214007.1| ACTTTTCTCCCAGCACCCGAA------TATGTAAACCAGTCTGTTCCCAA gi|41327737|ref|NM_005228.3| ACCTTCCTCCCAGTGCCTGAA------TACATAAACCAGTCCGTTCCCAA gi|6478867|gb|M37394.2|RATEGFR ACATTCCTTCCCGTGCCTGAA------TATATAAACCAATCTGTTCCCAA gi|24657088|ref|NM_057410.3| GGGGCCCAACAACAACAACAACATAAATAATCCC---------AATCAAA gi|24657104|ref|NM_057411.3| GGGGCCCAACAACAACAACAACATAAATAATCCC---------AATCAAA gi|302179500|gb|HM749883.1| AAGACCC------GCAGGCTCTGTCCAGAACCCTGTCTATCACAATCAGC gi|47522839|ref|NM_214007.1| GAGGCCC------GCGGGCTCCGTCCAGAACCCTGTCTACCACAATCAGC gi|41327737|ref|NM_005228.3| AAGGCCC------GCTGGCTCTGTGCAGAATCCTGTCTATCACAATCAGC gi|6478867|gb|M37394.2|RATEGFR GAGGCCG------GCTGGCTCTGTGCAGAACCCAGTCTATCACAATCAGC gi|24657088|ref|NM_057410.3| ACAATATGGCAGCTGTGGGCGTGGCTGCCGGCTACATGGATCTCATCGGA gi|24657104|ref|NM_057411.3| ACAATATGGCAGCTGTGGGCGTGGCTGCCGGCTACATGGATCTCATCGGA gi|302179500|gb|HM749883.1| CTCTATATCCAGCTCCTGGCAGAGACCCTCAGTACCAAAAT------TCA gi|47522839|ref|NM_214007.1| CTCTCAGTGCAGCTCCTGGCCGGGACCCCCACTACCAGAAC------TCC gi|41327737|ref|NM_005228.3| CTCTGAACCCCGCGCCCAGCAGAGACCCACACTACCAGGAC------CCC gi|6478867|gb|M37394.2|RATEGFR CCCTGCATCCAGCTCCTGGAAGAGACCTGCATTATCAAAAT------CCC gi|24657088|ref|NM_057410.3| GTGCCCGTTAGTGTGGACAATCCGGAGTATCTGCTAAACGCGCAGACACT gi|24657104|ref|NM_057411.3| GTGCCCGTTAGTGTGGACAATCCGGAGTATCTGCTAAACGCGCAGACACT gi|302179500|gb|HM749883.1| CTCAGCAACGCCGTGGACAACCCTGAGTATCTCAACACCACCCATCCTGC gi|47522839|ref|NM_214007.1| CACAGCAATGCCGTGGGCAACCCTGAGTATCTCAACACCCCCCGCCCCGC gi|41327737|ref|NM_005228.3| CACAGCACTGCAGTGGGCAACCCCGAGTATCTCAACACTGTCCAGCCCAC gi|6478867|gb|M37394.2|RATEGFR CATAGCAATGCGGTGAGCAACCCTGAGTATCTCAACACTGCCCAGCCGAC gi|24657088|ref|NM_057410.3| GGGTGTTGGG---------GAGTCGCCGATACCCACCCAGACCATCGGGA gi|24657104|ref|NM_057411.3| GGGTGTTGGG---------GAGTCGCCGATACCCACCCAGACCATCGGGA gi|302179500|gb|HM749883.1| CTGTATCAATGGTGTGCTCGACGGCCCTGCCCTCTGGGCTCAGAAGGGCA gi|47522839|ref|NM_214007.1| CTGCATCAACGGAGGACTGGACGGCCCTGCCTTCTGGGCACAGACAGGCA gi|41327737|ref|NM_005228.3| CTGTGTCAACAGCACATTCGACAGCCCTGCCCACTGGGCCCAGAAAGGCA gi|6478867|gb|M37394.2|RATEGFR CTGCCTCAGTAGTGGGTTTGACAGCTCTGCCCTCTGGATCCAGAAAGGCA gi|24657088|ref|NM_057410.3| TACCGGTGATGGGAGTCCCGGGCACCATGGAGGTCAAGGTGCCAATGCCA gi|24657104|ref|NM_057411.3| TACCGGTGATGGGAGTCCCGGGCACCATGGAGGTCAAGGTGCCAATGCCA gi|302179500|gb|HM749883.1| GTCACCAATTTAGCCTAGACAACCCTGACTACCAGCAGGCCTTCTTTCCC gi|47522839|ref|NM_214007.1| GCCACCAGATTAATCTGGACAACCCAGACTACCAGCAGGCCTTCTTCCCC gi|41327737|ref|NM_005228.3| GCCACCAAATTAGCCTGGACAACCCTGACTACCAGCAGGACTTCTTTCCC gi|6478867|gb|M37394.2|RATEGFR GCCACCAAATGAGCCTGGACAACCCTGACTACCAGCAGGACTTCTTTCCC gi|24657088|ref|NM_057410.3| GGCAGTGAGCCAACGAGCTCCGATCACGAGTACTACAATGATACCCAACG gi|24657104|ref|NM_057411.3| GGCAGTGAGCCAACGAGCTCCGATCACGAGTACTACAATGATACCCAACG gi|302179500|gb|HM749883.1| AAGGAAGCCAAGTCGAATGGCATCTTTAAGGGGCCTGCAGCTGAAAATGC gi|47522839|ref|NM_214007.1| AAGGAAGCCAAGTCAAACGGCATCTGTAAGGGTCCCGCCGCCGAAAACGC gi|41327737|ref|NM_005228.3| AAGGAAGCCAAGCCAAATGGCATCTTTAAGGGCTCCACAGCTGAAAATGC gi|6478867|gb|M37394.2|RATEGFR AAAGAAGCCAAGCCGAATGGCATCTTTAAGGGCCCCACAGCTGAAAATGC gi|24657088|ref|NM_057410.3| GGAGTTGCAGCCACTGCATCGAAACCGCAACACGGAGACGAGGGTG gi|24657104|ref|NM_057411.3| GGAGTTGCAGCCACTGCATCGAAACCGCAACACGGAGACGAGGGTG gi|302179500|gb|HM749883.1| AGAATACCTGCGGGCAGCACCAGCAGGCAGTGACTTTACTGGGGCC gi|47522839|ref|NM_214007.1| AGAGTACCTAAGGGCGGCACCAGCCAGCAGTGACCTTACTGGGGCA gi|41327737|ref|NM_005228.3| AGAATACCTAAGGGTCGCGCCACAAAGCAGTGAATTTATTGGAGCA gi|6478867|gb|M37394.2|RATEGFR AGAGTACCTGCGGGTGGCACCGCCAAGCAGTGAGTTTAGTGGAGCA """, ) pairwise_alignment = alignment[:2] dN, dS = calculate_dn_ds(pairwise_alignment, method="NG86") self.assertAlmostEqual(dN, 0.0209, places=4) self.assertAlmostEqual(dS, 0.0178, places=4) dN, dS = calculate_dn_ds(pairwise_alignment, method="LWL85") self.assertAlmostEqual(dN, 0.0203, places=4) self.assertAlmostEqual(dS, 0.0164, places=4) try: import scipy except ImportError: # Silently skip the rest of the test return # This should be present: from scipy.linalg import expm dN, dS = calculate_dn_ds(pairwise_alignment, method="YN00") self.assertAlmostEqual(dN, 0.0198, places=4) self.assertAlmostEqual(dS, 0.0222, places=4) try: # New in scipy v0.11 from scipy.optimize import minimize dN, dS = calculate_dn_ds(pairwise_alignment, method="ML") self.assertAlmostEqual(dN, 0.0194, places=4) self.assertAlmostEqual(dS, 0.0217, places=4) except ImportError: pass # NG86 method with default codon table dn_correct = [ 0, 0.02090783050583131, 0, 0.6115239249238438, 0.6102203266798018, 0, 0.6140350835631757, 0.6040168621204747, 0.041180350405913294, 0, 0.6141532531400524, 0.6018263135601294, 0.06701051445629494, 0.061470360954086874, 0, 0.6187088340904762, 0.6068687248870475, 0.07386903034833081, 0.07357890927918581, 0.05179847072570129, 0, ] ds_correct = [ 0, 0.01783718763890243, 0, 2.9382055377913687, 3.0375115405379267, 0, 2.008913071877126, 2.0182088023715616, 0.5638033197005285, 0, 2.771425931736778, 2.7353083173058295, 0.6374483799734671, 0.723542095485497, 0, -1, -1, 0.953865978141643, 1.182154857347706, 0.843182957978177, 0, ] dn, ds = calculate_dn_ds_matrix(alignment) dn_list = [] for i in dn.matrix: dn_list.extend(i) for dn_cal, dn_corr in zip(dn_list, dn_correct): self.assertAlmostEqual(dn_cal, dn_corr, places=4) ds_list = [] for i in ds.matrix: ds_list.extend(i) for ds_cal, ds_corr in zip(ds_list, ds_correct): self.assertAlmostEqual(ds_cal, ds_corr, places=4) # YN00 method with user specified codon table dn_correct = [ 0, 0.019701773284646867, 0, 0.6109649819852769, 0.6099903856901369, 0, 0.6114499930666559, 0.6028068208599121, 0.045158286242251426, 0, 0.6151835071687592, 0.6053227393422296, 0.07034397741651377, 0.06956967795096626, 0, 0.6103850655769698, 0.5988716898831496, 0.07905930042150053, 0.08203052937107111, 0.05659346894088538, 0, ] ds_correct = [ 0, 0.01881718550096053, 0, 1.814457265482046, 1.8417575124882066, 0, 1.5627041719628896, 1.563930819079887, 0.4748890153032888, 0, 1.6754828466084355, 1.6531212012501901, 0.5130923627791538, 0.5599667707191436, 0, 2.0796114236540943, 2.1452591651827304, 0.7243066372971764, 0.8536617406770075, 0.6509203399899367, 0, ] dn, ds = calculate_dn_ds_matrix( alignment, method="LWL85", codon_table=CodonTable.unambiguous_dna_by_id[3] ) dn_list = [] for i in dn.matrix: dn_list.extend(i) for dn_cal, dn_corr in zip(dn_list, dn_correct): self.assertAlmostEqual(dn_cal, dn_corr, places=4) ds_list = [] for i in ds.matrix: ds_list.extend(i) for ds_cal, ds_corr in zip(ds_list, ds_correct): self.assertAlmostEqual(ds_cal, ds_corr, places=4) class Test_MK(unittest.TestCase): def test_mk(self): aligner = CodonAligner() nucleotide_records = SeqIO.index("codonalign/drosophila.fasta", "fasta") protein_alignment = Align.read("codonalign/adh.aln", "clustal") self.assertEqual(len(protein_alignment.sequences), 27) codon_alignments = [] protein_record = protein_alignment.sequences[0] nucleotide_record = nucleotide_records[protein_record.id] self.assertEqual(nucleotide_record.id, protein_record.id) alignments = aligner.align(protein_record, nucleotide_record) self.assertEqual(len(alignments), 1) alignment = next(alignments) codon_alignments.append(alignment) self.assertTrue( np.array_equal(alignment.coordinates, np.array([[0, 256], [0, 768]])) ) self.assertEqual( str(alignment), """\ gi|9217|e 0 M A F T L T N K N V V F V A G L G G I G gi|9217|e 0 ATGGCGTTTACCTTGACCAACAAGAACGTGGTTTTCGTGGCCGGTCTGGGAGGCATTGGT gi|9217|e 20 L D T S K E L V K R D L K N L V I L D R gi|9217|e 60 CTGGACACCAGCAAGGAGCTGGTCAAGCGGGACCTGAAGAACCTGGTGATCCTCGACCGC gi|9217|e 40 I E N P A A I A E L K A I N P K V T V T gi|9217|e 120 ATTGAGAACCCGGCTGCCATCGCCGAGCTGAAGGCAATCAATCCAAAGGTGACCGTCACC gi|9217|e 60 F Y P Y D V T V P I A E T T K L L K T I gi|9217|e 180 TTCTACCCCTATGATGTGACCGTGCCCATTGCCGAGACCACCAAGCTGCTGAAGACCATC gi|9217|e 80 F A Q L K T I D V L I N G A G I L D D H gi|9217|e 240 TTCGCCCAGCTGAAGACCATCGATGTCCTGATCAACGGAGCTGGCATCCTGGACGATCAC gi|9217|e 100 Q I E R T I A V N Y T G L V N T T T A I gi|9217|e 300 CAGATCGAGCGCACCATCGCCGTCAACTACACCGGCCTGGTGAACACCACGACTGCCATC gi|9217|e 120 L D F W D K R K G G P G G I I C N I G S gi|9217|e 360 CTGGACTTCTGGGACAAGCGCAAGGGTGGACCCGGTGGTATCATCTGCAACATTGGATCC gi|9217|e 140 V T G F N A I Y Q V P V Y S G T K A A V gi|9217|e 420 GTGACTGGATTCAACGCCATCTACCAGGTGCCCGTTTACTCCGGCACCAAGGCTGCCGTG gi|9217|e 160 V N F T S S L A K L A P I T G V T A Y T gi|9217|e 480 GTCAACTTCACCAGCTCCCTGGCGAAACTGGCCCCCATCACCGGCGTGACCGCTTACACC gi|9217|e 180 V N P G I T R T T L V H K F N S W L D V gi|9217|e 540 GTGAACCCCGGCATCACCCGCACCACCCTGGTGCACAAGTTCAACTCCTGGCTGGATGTT gi|9217|e 200 E P Q V A E K L L A H P T Q P S L A C A gi|9217|e 600 GAGCCCCAGGTGGCCGAGAAGCTCCTGGCTCACCCCACCCAGCCCTCGTTGGCCTGCGCC gi|9217|e 220 Q N F V K A I E L N Q N G A I W K L D L gi|9217|e 660 CAGAACTTTGTGAAGGCCATCGAGCTGAACCAGAACGGTGCCATCTGGAAACTGGACTTG gi|9217|e 240 G T L E A I Q W S K H W D S G I 256 gi|9217|e 720 GGCACCCTGGAGGCCATCCAGTGGTCCAAGCACTGGGACTCCGGCATC 768 """, ) protein_record = protein_alignment.sequences[1] nucleotide_record = nucleotide_records[protein_record.id] self.assertEqual(nucleotide_record.id, protein_record.id) alignments = aligner.align(protein_record, nucleotide_record) self.assertEqual(len(alignments), 1) alignment = next(alignments) codon_alignments.append(alignment) self.assertTrue( np.array_equal(alignment.coordinates, np.array([[0, 256], [0, 768]])) ) self.assertEqual( str(alignment), """\ gi|9219|e 0 M A F T L T N K N V V F V A G L G G I G gi|9219|e 0 ATGGCGTTTACCTTGACCAACAAGAACGTGGTTTTCGTGGCCGGTCTGGGAGGCATTGGT gi|9219|e 20 L D T S K E L V K R D L K N L V I L D R gi|9219|e 60 CTGGACACCAGCAAGGAGCTGGTCAAGCGGGACCTGAAGAACCTGGTGATCCTCGACCGC gi|9219|e 40 I E N P A A I A E L K A I N P K V T V T gi|9219|e 120 ATTGAGAACCCGGCTGCCATCGCCGAGCTGAAGGCAATCAATCCAAAGGTGACCGTCACC gi|9219|e 60 F Y P Y D V T V P I A E T T K L L K T I gi|9219|e 180 TTCTACCCCTATGATGTGACCGTGCCCATTGCCGAGACCACCAAGCTGCTGAAGACCATC gi|9219|e 80 F A Q L K T I D V L I N G A G I L D D H gi|9219|e 240 TTCGCCCAGCTGAAGACCATCGATGTCCTGATCAACGGAGCTGGCATCCTGGACGATCAC gi|9219|e 100 Q I E R T I A V N Y T G L V N T T T A I gi|9219|e 300 CAGATCGAGCGCACCATCGCCGTCAACTACACCGGCCTGGTGAACACCACGACTGCCATC gi|9219|e 120 L D F W D K R K G G P G G I I C N I G S gi|9219|e 360 CTGGACTTCTGGGACAAGCGCAAGGGTGGACCCGGTGGTATCATCTGCAACATTGGATCC gi|9219|e 140 V T G F N A I Y Q V P V Y S G T K A A V gi|9219|e 420 GTGACTGGATTCAACGCCATCTACCAGGTGCCCGTTTACTCCGGCACCAAGGCTGCCGTG gi|9219|e 160 V N F T S S L A K L A P I T G V T A Y T gi|9219|e 480 GTCAACTTCACCAGCTCCCTGGCGAAACTGGCCCCCATCACCGGCGTGACCGCTTACACC gi|9219|e 180 V N P G I T R T T L V H K F N S W L D V gi|9219|e 540 GTGAACCCCGGCATCACCCGCACCACCCTGGTGCACAAGTTCAACTCCTGGCTGGATGTT gi|9219|e 200 E P Q V A E K L L A H P T Q P S L A C A gi|9219|e 600 GAGCCCCAGGTGGCCGAGAAGCTCCTGGCTCACCCCACCCAGCCCTCGTTGGCCTGCGCC gi|9219|e 220 Q N F V K A I E L N Q N G A I W K L D L gi|9219|e 660 CAGAACTTTGTGAAGGCCATCGAGCTGAACCAGAACGGTGCCATCTGGAAACTGGACTTG gi|9219|e 240 G T L E A I Q W S K H W D S G I 256 gi|9219|e 720 GGCACCCTGGAGGCCATCCAGTGGTCCAAGCACTGGGACTCCGGCATC 768 """, ) protein_record = protein_alignment.sequences[2] nucleotide_record = nucleotide_records[protein_record.id] self.assertEqual(nucleotide_record.id, protein_record.id) alignments = aligner.align(protein_record, nucleotide_record) self.assertEqual(len(alignments), 1) alignment = next(alignments) codon_alignments.append(alignment) self.assertTrue( np.array_equal(alignment.coordinates, np.array([[0, 256], [0, 768]])) ) self.assertEqual( str(alignment), """\ gi|9221|e 0 M A F T L T N K N V V F V A G L G G I G gi|9221|e 0 ATGGCGTTTACCTTGACCAACAAGAACGTGGTTTTCGTGGCCGGTCTGGGAGGCATTGGT gi|9221|e 20 L D T S K E L V K R D L K N L V I L D R gi|9221|e 60 CTGGACACCAGCAAGGAGCTGGTCAAGCGCGACCTGAAGAACCTGGTGATCCTCGACCGC gi|9221|e 40 I E N P A A I A E L K A I N P K V T V T gi|9221|e 120 ATTGAGAACCCGGCTGCCATCGCCGAGCTGAAGGCAATCAATCCAAAGGTGACCGTCACC gi|9221|e 60 F Y P Y D V T V P I A E T T K L L K T I gi|9221|e 180 TTCTACCCCTATGATGTGACCGTGCCCATTGCCGAGACCACCAAGCTGCTGAAGACCATC gi|9221|e 80 F A Q L K T I D V L I N G A G I L D D H gi|9221|e 240 TTCGCCCAGCTGAAGACCATCGATGTCCTGATCAACGGAGCTGGCATCCTGGACGATCAC gi|9221|e 100 Q I E R T I A V N Y T G L V N T T T A I gi|9221|e 300 CAGATCGAGCGCACCATCGCCGTCAACTACACCGGCCTGGTGAACACAACGACGGCCATC gi|9221|e 120 L D F W D K R K G G P G G I I C N I G S gi|9221|e 360 CTGGACTTCTGGGACAAGCGCAAGGGTGGACCCGGTGGTATAATCTGCAACATTGGATCC gi|9221|e 140 V T G F N A I Y Q V P V Y S G T K A A V gi|9221|e 420 GTGACTGGATTCAACGCCATCTACCAGGTGCCCGTTTACTCCGGCACCAAGGCTGCCGTG gi|9221|e 160 V N F T S S L A K L A P I T G V T A Y T gi|9221|e 480 GTCAACTTCACCAGCTCCCTGGCGAAACTGGCCCCCATCACCGGCGTGACCGCTTACACC gi|9221|e 180 V N P G I T R T T L V H K F N S W L D V gi|9221|e 540 GTGAACCCCGGCATCACCCGCACCACCCTGGTGCACAAGTTCAACTCCTGGCTGGATGTT gi|9221|e 200 E P Q V A E K L L A H P T Q P S L A C A gi|9221|e 600 GAGCCCCAGGTGGCCGAGAAGCTCCTGGCTCACCCCACCCAGCCCTCGTTGGCCTGCGCC gi|9221|e 220 Q N F V K A I E L N Q N G A I W K L D L gi|9221|e 660 CAGAACTTTGTCAAGGCCATCGAGCTGAACCAGAACGGTGCCATCTGGAAACTGGACTTG gi|9221|e 240 G T L E A I Q W S K H W D S G I 256 gi|9221|e 720 GGTACCCTGGAGGCCATCCAGTGGTCCAAGCACTGGGACTCCGGCATC 768 """, ) protein_record = protein_alignment.sequences[3] nucleotide_record = nucleotide_records[protein_record.id] self.assertEqual(nucleotide_record.id, protein_record.id) alignments = aligner.align(protein_record, nucleotide_record) self.assertEqual(len(alignments), 1) alignment = next(alignments) codon_alignments.append(alignment) self.assertTrue( np.array_equal(alignment.coordinates, np.array([[0, 256], [0, 768]])) ) self.assertEqual( str(alignment), """\ gi|9223|e 0 M A F T L T N K N V V F V A G L G G I G gi|9223|e 0 ATGGCGTTTACCTTGACCAACAAGAACGTGGTTTTCGTGGCCGGTCTGGGAGGCATTGGT gi|9223|e 20 L D T S K E L V K R D L K N L V I L D R gi|9223|e 60 CTGGACACCAGCAAGGAGCTGGTCAAGCGGGACCTGAAGAACCTGGTGATCCTCGACCGC gi|9223|e 40 I E N P A A I A E L K A I N P K V T V T gi|9223|e 120 ATTGAGAACCCGGCTGCCATCGCCGAGCTGAAGGCAATCAATCCAAAGGTGACCGTCACC gi|9223|e 60 F Y P Y D V T V P I A E T T K L L K T I gi|9223|e 180 TTCTACCCCTATGATGTGACCGTGCCCATTGCCGAGACCACCAAGCTGCTGAAGACCATC gi|9223|e 80 F A Q L K T I D V L I N G A G I L D D H gi|9223|e 240 TTCGCCCAGCTGAAGACCATCGATGTCCTGATCAACGGAGCTGGCATCCTGGACGATCAC gi|9223|e 100 Q I E R T I A V N Y T G L V N T T T A I gi|9223|e 300 CAGATCGAGCGCACCATCGCCGTCAACTACACCGGCCTGGTGAACACCACGACTGCCATC gi|9223|e 120 L D F W D K R K G G P G G I I C N I G S gi|9223|e 360 CTGGACTTCTGGGACAAGCGCAAGGGTGGACCCGGTGGTATCATCTGCAACATTGGATCC gi|9223|e 140 V T G F N A I Y Q V P V Y S G T K A A V gi|9223|e 420 GTGACTGGATTCAACGCCATCTACCAGGTGCCCGTTTACTCCGGCACCAAGGCTGCCGTG gi|9223|e 160 V N F T S S L A K L A P I T G V T A Y T gi|9223|e 480 GTCAACTTCACCAGCTCCCTGGCGAAACTGGCCCCCATCACCGGCGTGACCGCTTACACC gi|9223|e 180 V N P G I T R T T L V H K F N S W L D V gi|9223|e 540 GTGAACCCCGGCATCACCCGCACCACCCTGGTGCACAAGTTCAACTCCTGGCTGGATGTT gi|9223|e 200 E P Q V A E K L L A H P T Q P S L A C A gi|9223|e 600 GAGCCCCAGGTGGCCGAGAAGCTCCTGGCTCACCCCACCCAGCCCTCGTTGGCCTGCGCC gi|9223|e 220 Q N F V K A I E L N Q N G A I W K L D L gi|9223|e 660 CAGAACTTTGTGAAGGCCATCGAGCTGAACCAGAACGGTGCCATCTGGAAACTGGACTTG gi|9223|e 240 G T L E A I Q W S K H W D S G I 256 gi|9223|e 720 GGCACCCTGGAGGCCATCCAGTGGTCCAAGCACTGGGACTCCGGCATC 768 """, ) protein_record = protein_alignment.sequences[4] nucleotide_record = nucleotide_records[protein_record.id] self.assertEqual(nucleotide_record.id, protein_record.id) alignments = aligner.align(protein_record, nucleotide_record) self.assertEqual(len(alignments), 1) alignment = next(alignments) codon_alignments.append(alignment) self.assertTrue( np.array_equal(alignment.coordinates, np.array([[0, 256], [0, 768]])) ) self.assertEqual( str(alignment), """\ gi|9225|e 0 M A F T L T N K N V V F V A G L G G I G gi|9225|e 0 ATGGCGTTTACCTTGACCAACAAGAACGTGGTTTTCGTGGCCGGTCTGGGAGGCATTGGT gi|9225|e 20 L D T S K E L V K R D L K N L V I L D R gi|9225|e 60 CTGGACACCAGCAAGGAGCTGGTCAAGCGGGACCTGAAGAACCTGGTGATCCTCGACCGC gi|9225|e 40 I E N P A A I A E L K A I N P K V T V T gi|9225|e 120 ATTGAGAACCCGGCTGCCATCGCCGAGCTGAAGGCAATCAATCCAAAGGTGACCGTAACC gi|9225|e 60 F Y P Y D V T V P I A E T T K L L K T I gi|9225|e 180 TTCTACCCCTATGATGTGACAGTGCCCATTGCCGAGACCACCAAGCTGCTGAAGACCATC gi|9225|e 80 F A Q L K T I D V L I N G A G I L D D H gi|9225|e 240 TTCGCCCAGCTGAAGACCATCGATGTCCTGATCAACGGAGCTGGCATCTTGGACGATCAC gi|9225|e 100 Q I E R T I A V N Y T G L V N T T T A I gi|9225|e 300 CAGATCGAGCGCACCATCGCCGTCAACTACACCGGCCTGGTGAACACCACGACGGCCATC gi|9225|e 120 L D F W D K R K G G P G G I I C N I G S gi|9225|e 360 CTGGACTTCTGGGACAAGCGCAAGGGTGGACCCGGTGGTATCATCTGCAACATTGGATCC gi|9225|e 140 V T G F N A I Y Q V P V Y S G T K A A V gi|9225|e 420 GTGACTGGATTCAACGCCATCTACCAGGTGCCCGTTTACTCCGGCACCAAGGCTGCCGTG gi|9225|e 160 V N F T S S L A K L A P I T G V T A Y T gi|9225|e 480 GTCAACTTCACCAGCTCCCTGGCGAAACTGGCCCCCATCACCGGCGTGACCGCTTACACC gi|9225|e 180 V N P G I T R T T L V H K F N S W L D V gi|9225|e 540 GTGAACCCCGGCATCACCCGCACCACCCTGGTGCACAAGTTCAACTCCTGGCTGGATGTT gi|9225|e 200 E P Q V A E K L L A H P T Q P S L A C A gi|9225|e 600 GAGCCCCAGGTGGCTGAGAAGCTCCTGGCTCACCCAACCCAGCCCTCGTTGGCCTGCGCC gi|9225|e 220 Q N F V K A I E L N Q N G A I W K L D L gi|9225|e 660 CAGAACTTTGTCAAGGCCATCGAGCTGAACCAGAACGGTGCCATCTGGAAACTGGACTTG gi|9225|e 240 G T L E A I Q W S K H W D S G I 256 gi|9225|e 720 GGTACCCTGGAGGCCATCCAGTGGTCCAAGCACTGGGACTCCGGCATC 768 """, ) protein_record = protein_alignment.sequences[5] nucleotide_record = nucleotide_records[protein_record.id] self.assertEqual(nucleotide_record.id, protein_record.id) alignments = aligner.align(protein_record, nucleotide_record) self.assertEqual(len(alignments), 1) alignment = next(alignments) codon_alignments.append(alignment) self.assertTrue( np.array_equal(alignment.coordinates, np.array([[0, 256], [0, 768]])) ) self.assertEqual( str(alignment), """\ gi|9227|e 0 M A F T L T N K N V V F V A G L G G I G gi|9227|e 0 ATGGCGTTTACCTTGACCAACAAGAACGTGGTTTTCGTGGCCGGTCTGGGAGGCATTGGT gi|9227|e 20 L D T S K E L V K R D L K N L V I L D R gi|9227|e 60 CTGGACACCAGCAAGGAGCTGGTCAAGCGAGACCTGAAGAACCTGGTGATCCTCGACCGC gi|9227|e 40 I E N P A A I A E L K A I N P K V T V T gi|9227|e 120 ATTGAGAACCCGGCTGCCATCGCCGAGCTGAAGGCAATCAATCCAAAGGTGACCGTCACC gi|9227|e 60 F Y P Y D V T V P I A E T T K L L K T I gi|9227|e 180 TTCTACCCCTATGATGTGACCGTGCCCATTGCCGAGACCACCAAGCTGCTGAAGACCATC gi|9227|e 80 F A Q L K T I D V L I N G A G I L D D H gi|9227|e 240 TTCGCCCAGCTGAAGACCATCGATGTCCTGATCAACGGAGCTGGCATCCTGGACGATCAC gi|9227|e 100 Q I E R T I A V N Y T G L V N T T T A I gi|9227|e 300 CAGATCGAGCGCACCATCGCCGTCAACTACACCGGCCTGGTGAACACCACGACGGCCATC gi|9227|e 120 L D F W D K R K G G P G G I I C N I G S gi|9227|e 360 CTGGACTTCTGGGACAAGCGCAAGGGTGGACCCGGTGGTATCATCTGCAACATTGGATCC gi|9227|e 140 V T G F N A I Y Q V P V Y S G T K A A V gi|9227|e 420 GTGACTGGATTCAACGCCATCTACCAGGTGCCCGTTTACTCCGGCACCAAGGCTGCCGTG gi|9227|e 160 V N F T S S L A K L A P I T G V T A Y T gi|9227|e 480 GTCAACTTCACCAGCTCCCTGGCGAAACTGGCCCCCATTACCGGCGTGACCGCTTACACC gi|9227|e 180 V N P G I T R T T L V H K F N S W L D V gi|9227|e 540 GTGAACCCCGGCATCACCCGCACCACCCTGGTGCACAAGTTCAACTCCTGGCTGGATGTT gi|9227|e 200 E P Q V A E K L L A H P T Q P S L A C A gi|9227|e 600 GAGCCCCAGGTGGCCGAGAAGCTCCTGGCTCACCCCACCCAGCCCTCGTTGGCCTGCGCC gi|9227|e 220 Q N F V K A I E L N Q N G A I W K L D L gi|9227|e 660 CAGAACTTTGTGAAGGCCATCGAGCTGAACCAGAACGGTGCCATCTGGAAACTGGACTTG gi|9227|e 240 G T L E A I Q W S K H W D S G I 256 gi|9227|e 720 GGCACCCTGGAGGCCATCCAGTGGTCCAAGCACTGGGACTCCGGCATC 768 """, ) protein_record = protein_alignment.sequences[6] nucleotide_record = nucleotide_records[protein_record.id] self.assertEqual(nucleotide_record.id, protein_record.id) alignments = aligner.align(protein_record, nucleotide_record) self.assertEqual(len(alignments), 1) alignment = next(alignments) codon_alignments.append(alignment) self.assertTrue( np.array_equal(alignment.coordinates, np.array([[0, 256], [0, 768]])) ) self.assertEqual( str(alignment), """\ gi|9229|e 0 M A F T L T N K N V V F V A G L G G I G gi|9229|e 0 ATGGCGTTTACCTTGACCAACAAGAACGTGGTTTTCGTGGCCGGTCTGGGAGGCATTGGT gi|9229|e 20 L D T S K E L V K R D L K N L V I L D R gi|9229|e 60 CTGGACACCAGCAAGGAGCTGGTCAAGCGGGACCTGAAGAACCTGGTGATCCTCGACCGC gi|9229|e 40 I E N P A A I A E L K A I N P K V T V T gi|9229|e 120 ATTGAGAACCCGGCTGCCATCGCCGAGCTGAAGGCAATCAATCCAAAGGTGACCGTCACC gi|9229|e 60 F Y P Y D V T V P I A E T T K L L K T I gi|9229|e 180 TTCTACCCCTATGATGTGACCGTGCCCATTGCCGAGACCACCAAGCTGCTGAAGACCATC gi|9229|e 80 F A Q L K T I D V L I N G A G I L D D H gi|9229|e 240 TTCGCCCAGCTGAAGACCATCGATGTCCTGATCAACGGAGCTGGCATCCTGGACGATCAC gi|9229|e 100 Q I E R T I A V N Y T G L V N T T T A I gi|9229|e 300 CAGATCGAGCGCACCATCGCCGTCAACTACACCGGCCTGGTGAACACCACGACTGCCATC gi|9229|e 120 L D F W D K R K G G P G G I I C N I G S gi|9229|e 360 CTGGACTTCTGGGACAAGCGCAAGGGTGGACCCGGTGGTATCATCTGCAACATTGGATCC gi|9229|e 140 V T G F N A I Y Q V P V Y S G T K A A V gi|9229|e 420 GTGACTGGATTCAACGCCATCTACCAGGTGCCCGTTTACTCCGGCACCAAGGCTGCCGTG gi|9229|e 160 V N F T S S L A K L A P I T G V T A Y T gi|9229|e 480 GTCAACTTCACCAGCTCCCTGGCGAAACTGGCCCCCATCACCGGCGTGACCGCTTACACC gi|9229|e 180 V N P G I T R T T L V H K F N S W L D V gi|9229|e 540 GTGAACCCCGGCATCACCCGCACCACCCTGGTGCACAAGTTCAACTCCTGGCTGGATGTT gi|9229|e 200 E P Q V A E K L L A H P T Q P S L A C A gi|9229|e 600 GAGCCCCAGGTGGCCGAGAAGCTCCTGGCTCACCCCACCCAGCCCTCGTTGGCCTGCGCC gi|9229|e 220 Q N F V K A I E L N Q N G A I W K L D L gi|9229|e 660 CAGAACTTTGTGAAGGCCATCGAGCTGAACCAGAACGGTGCCATCTGGAAACTGGACTTG gi|9229|e 240 G T L E A I Q W S K H W D S G I 256 gi|9229|e 720 GGCACCCTGGAGGCCATCCAGTGGTCCAAGCACTGGGACTCCGGCATC 768 """, ) protein_record = protein_alignment.sequences[7] nucleotide_record = nucleotide_records[protein_record.id] self.assertEqual(nucleotide_record.id, protein_record.id) alignments = aligner.align(protein_record, nucleotide_record) self.assertEqual(len(alignments), 1) alignment = next(alignments) codon_alignments.append(alignment) self.assertTrue( np.array_equal(alignment.coordinates, np.array([[0, 256], [0, 768]])) ) self.assertEqual( str(alignment), """\ gi|9231|e 0 M A F T L T N K N V V F V A G L G G I G gi|9231|e 0 ATGGCGTTTACCTTGACCAACAAGAACGTGGTTTTCGTGGCCGGTCTGGGAGGCATTGGT gi|9231|e 20 L D T S K E L V K R D L K N L V I L D R gi|9231|e 60 CTGGACACCAGCAAGGAGCTGGTCAAGCGCGACCTGAAGAACCTGGTGATCCTCGACCGC gi|9231|e 40 I E N P A A I A E L K A I N P K V T V T gi|9231|e 120 ATTGAGAACCCGGCTGCCATCGCCGAGCTGAAGGCAATCAATCCAAAGGTGACCGTCACC gi|9231|e 60 F Y P Y D V T V P I A E T T K L L K T I gi|9231|e 180 TTCTACCCCTATGATGTGACCGTGCCCATTGCCGAGACCACCAAGCTGCTGAAGACCATC gi|9231|e 80 F A Q L K T I D V L I N G A G I L D D H gi|9231|e 240 TTCGCCCAGCTGAAGACCATCGATGTCCTGATCAACGGAGCTGGCATCCTGGACGATCAC gi|9231|e 100 Q I E R T I A V N Y T G L V N T T T A I gi|9231|e 300 CAGATCGAGCGCACCATCGCCGTCAACTACACCGGCCTGGTGAACACCACGACTGCCATC gi|9231|e 120 L D F W D K R K G G P G G I I C N I G S gi|9231|e 360 CTGGACTTCTGGGACAAGCGCAAGGGTGGACCCGGTGGTATCATCTGCAACATTGGATCC gi|9231|e 140 V T G F N A I Y Q V P V Y S G T K A A V gi|9231|e 420 GTGACTGGATTCAACGCCATCTACCAGGTGCCCGTTTACTCCGGCACCAAGGCTGCCGTG gi|9231|e 160 V N F T S S L A K L A P I T G V T A Y T gi|9231|e 480 GTCAACTTCACCAGCTCCCTGGCGAAACTGGCCCCCATCACCGGCGTGACCGCTTACACC gi|9231|e 180 V N P G I T R T T L V H K F N S W L D V gi|9231|e 540 GTGAACCCCGGCATCACCCGCACCACCCTGGTGCACAAGTTCAACTCCTGGCTGGATGTT gi|9231|e 200 E P Q V A E K L L A H P T Q P S L A C A gi|9231|e 600 GAGCCCCAGGTGGCCGAGAAGCTCCTGGCTCACCCCACCCAGCCCTCGTTGGCCTGCGCC gi|9231|e 220 Q N F V K A I E L N Q N G A I W K L D L gi|9231|e 660 CAGAACTTTGTGAAGGCCATCGAGCTGAACCAGAACGGTGCTATCTGGAAACTGGACTTG gi|9231|e 240 G T L E A I Q W S K H W D S G I 256 gi|9231|e 720 GGCACCCTGGAGGCCATCCAGTGGTCCAAGCACTGGGACTCCGGCATC 768 """, ) protein_record = protein_alignment.sequences[8] nucleotide_record = nucleotide_records[protein_record.id] self.assertEqual(nucleotide_record.id, protein_record.id) alignments = aligner.align(protein_record, nucleotide_record) self.assertEqual(len(alignments), 1) alignment = next(alignments) codon_alignments.append(alignment) self.assertTrue( np.array_equal(alignment.coordinates, np.array([[0, 256], [0, 768]])) ) self.assertEqual( str(alignment), """\ gi|9233|e 0 M A F T L T N K N V V F V A G L G G I G gi|9233|e 0 ATGGCGTTTACCTTGACCAACAAGAACGTGGTTTTCGTGGCCGGTCTGGGAGGCATTGGT gi|9233|e 20 L D T S K E L V K R D L K N L V I L D R gi|9233|e 60 CTGGACACCAGCAAGGAGCTGGTCAAGCGGGACCTGAAGAACCTGGTGATCCTCGACCGC gi|9233|e 40 I E N P A A I A E L K A I N P K V T V T gi|9233|e 120 ATTGAGAACCCGGCTGCCATCGCCGAGCTGAAGGCAATCAATCCAAAGGTGACCGTCACC gi|9233|e 60 F Y P Y D V T V P I A E T T K L L K T I gi|9233|e 180 TTCTACCCATACGATGTGACCGTGCCCATTGCCGAGACCACCAAGCTGCTGAAGACCATC gi|9233|e 80 F A Q L K T I D V L I N G A G I L D D H gi|9233|e 240 TTCGCCCAGCTGAAGACCATCGATGTCCTGATCAACGGAGCTGGCATCCTGGACGATCAC gi|9233|e 100 Q I E R T I A V N Y T G L V N T T T A I gi|9233|e 300 CAGATCGAGCGCACCATCGCCGTCAACTACACCGGCCTGGTGAACACCACGACGGCCATC gi|9233|e 120 L D F W D K R K G G P G G I I C N I G S gi|9233|e 360 CTGGACTTCTGGGACAAGCGCAAGGGTGGACCCGGTGGTATCATCTGCAACATTGGATCC gi|9233|e 140 V T G F N A I Y Q V P V Y S G T K A A V gi|9233|e 420 GTGACTGGATTCAACGCCATCTACCAGGTGCCCGTTTACTCCGGCACCAAGGCTGCCGTG gi|9233|e 160 V N F T S S L A K L A P I T G V T A Y T gi|9233|e 480 GTCAACTTCACCAGCTCCCTGGCGAAACTGGCCCCCATCACCGGCGTGACCGCTTACACC gi|9233|e 180 V N P G I T R T T L V H K F N S W L D V gi|9233|e 540 GTGAACCCCGGCATCACCCGCACCACCCTGGTGCACAAGTTCAACTCCTGGCTGGATGTT gi|9233|e 200 E P Q V A E K L L A H P T Q P S L A C A gi|9233|e 600 GAGCCCCAGGTGGCCGAGAAGCTCCTGGCTCACCCCACCCAGCCCTCGTTGGCCTGCGCC gi|9233|e 220 Q N F V K A I E L N Q N G A I W K L D L gi|9233|e 660 CAGAACTTTGTGAAGGCCATCGAGCTGAACCAGAACGGTGCCATCTGGAAACTGGACTTG gi|9233|e 240 G T L E A I Q W S K H W D S G I 256 gi|9233|e 720 GGCACCCTGGAGGCCATCCAGTGGTCCAAGCACTGGGACTCCGGCATC 768 """, ) protein_record = protein_alignment.sequences[9] nucleotide_record = nucleotide_records[protein_record.id] self.assertEqual(nucleotide_record.id, protein_record.id) alignments = aligner.align(protein_record, nucleotide_record) self.assertEqual(len(alignments), 1) alignment = next(alignments) codon_alignments.append(alignment) self.assertTrue( np.array_equal(alignment.coordinates, np.array([[0, 256], [0, 768]])) ) self.assertEqual( str(alignment), """\ gi|9235|e 0 M A F T L T N K N V V F V A G L G G I G gi|9235|e 0 ATGGCGTTTACCTTGACCAACAAGAACGTGGTTTTCGTGGCCGGTCTGGGAGGCATTGGT gi|9235|e 20 L D T S K E L V K R D L K N L V I L D R gi|9235|e 60 CTGGACACCAGCAAGGAGCTGGTCAAGCGGGACCTGAAGAACCTGGTGATCCTCGACCGC gi|9235|e 40 I E N P A A I A E L K A I N P K V T V T gi|9235|e 120 ATTGAGAACCCGGCTGCCATCGCCGAGCTGAAGGCAATCAATCCAAAGGTGACCGTCACC gi|9235|e 60 F Y P Y D V T V P I A E T T K L L K T I gi|9235|e 180 TTCTACCCCTATGATGTGACCGTGCCCATTGCCGAGACCACCAAGCTGCTGAAGACCATC gi|9235|e 80 F A Q L K T I D V L I N G A G I L D D H gi|9235|e 240 TTCGCCCAGCTGAAGACCATCGATGTCCTGATCAACGGAGCTGGCATCCTGGACGATCAC gi|9235|e 100 Q I E R T I A V N Y T G L V N T T T A I gi|9235|e 300 CAGATCGAGCGCACCATCGCCGTCAACTACACCGGCCTGGTGAACACCACGACTGCCATC gi|9235|e 120 L D F W D K R K G G P G G I I C N I G S gi|9235|e 360 CTGGACTTCTGGGACAAGCGCAAGGGTGGACCCGGTGGTATCATCTGCAACATTGGATCC gi|9235|e 140 V T G F N A I Y Q V P V Y S G T K A A V gi|9235|e 420 GTGACTGGATTCAACGCCATCTACCAGGTGCCCGTTTACTCCGGCACCAAGGCTGCCGTG gi|9235|e 160 V N F T S S L A K L A P I T G V T A Y T gi|9235|e 480 GTCAACTTCACCAGCTCCCTGGCGAAACTGGCCCCCATCACCGGCGTGACCGCTTACACC gi|9235|e 180 V N P G I T R T T L V H K F N S W L D V gi|9235|e 540 GTGAACCCCGGCATCACCCGCACCACCCTGGTGCACAAGTTCAACTCCTGGCTGGATGTT gi|9235|e 200 E P Q V A E K L L A H P T Q P S L A C A gi|9235|e 600 GAGCCCCAGGTGGCCGAGAAGCTCCTGGCTCACCCCACCCAGCCCTCGTTGGCCTGCGCC gi|9235|e 220 Q N F V K A I E L N Q N G A I W K L D L gi|9235|e 660 CAGAACTTTGTGAAGGCCATCGAGCTGAACCAGAACGGTGCCATCTGGAAACTGGACTTG gi|9235|e 240 G T L E A I Q W S K H W D S G I 256 gi|9235|e 720 GGCACCCTGGAGGCCATCCAGTGGTCCAAGCATTGGGACTCCGGCATC 768 """, ) protein_record = protein_alignment.sequences[10] nucleotide_record = nucleotide_records[protein_record.id] self.assertEqual(nucleotide_record.id, protein_record.id) alignments = aligner.align(protein_record, nucleotide_record) self.assertEqual(len(alignments), 1) alignment = next(alignments) codon_alignments.append(alignment) self.assertTrue( np.array_equal(alignment.coordinates, np.array([[0, 256], [0, 768]])) ) self.assertEqual( str(alignment), """\ gi|9237|e 0 M A F T L T N K N V V F V A G L G G I G gi|9237|e 0 ATGGCGTTTACCTTGACCAACAAGAACGTGGTTTTCGTGGCCGGTCTGGGAGGCATTGGT gi|9237|e 20 L D T S K E L V K R D L K N L V I L D R gi|9237|e 60 CTGGACACCAGCAAGGAGCTGGTCAAGCGGGACCTGAAGAACCTGGTGATCCTCGACCGC gi|9237|e 40 I E N P A A I A E L K A I N P K V T V T gi|9237|e 120 ATTGAGAACCCGGCTGCCATCGCCGAGCTGAAGGCAATCAATCCAAAGGTGACCGTCACC gi|9237|e 60 F Y P Y D V T V P I A E T T K L L K T I gi|9237|e 180 TTCTACCCCTACGATGTGACCGTGCCCATTGCCGAGACCACCAAGCTGCTGAAGACCATC gi|9237|e 80 F A Q L K T I D V L I N G A G I L D D H gi|9237|e 240 TTCGCCCAGCTGAAGACCATCGATGTCCTGATCAACGGAGCTGGCATCCTGGACGATCAC gi|9237|e 100 Q I E R T I A V N Y T G L V N T T T A I gi|9237|e 300 CAGATCGAGCGCACCATCGCCGTCAACTACACCGGACTGGTGAACACCACGACGGCCATC gi|9237|e 120 L D F W D K R K G G P G G I I C N I G S gi|9237|e 360 CTGGACTTCTGGGACAAGCGCAAGGGTGGACCCGGTGGTATCATCTGCAACATTGGATCC gi|9237|e 140 V T G F N A I Y Q V P V Y S G T K A A V gi|9237|e 420 GTGACTGGATTCAACGCCATCTACCAGGTGCCCGTTTACTCCGGCACCAAGGCTGCCGTG gi|9237|e 160 V N F T S S L A K L A P I T G V T A Y T gi|9237|e 480 GTCAACTTCACCAGCTCCCTGGCGAAACTGGCCCCCATCACCGGCGTGACCGCTTACACC gi|9237|e 180 V N P G I T R T T L V H K F N S W L D V gi|9237|e 540 GTGAACCCCGGCATCACCCGCACCACCCTGGTGCACAAGTTCAACTCCTGGCTGGATGTT gi|9237|e 200 E P Q V A E K L L A H P T Q P S L A C A gi|9237|e 600 GAGCCCCAGGTGGCCGAGAAGCTCCTGGCTCACCCCACCCAGCCCTCGTTGGCCTGCGCC gi|9237|e 220 Q N F V K A I E L N Q N G A I W K L D L gi|9237|e 660 CAGAACTTTGTGAAGGCCATCGAGCTGAACCAGAACGGTGCCATCTGGAAACTGGACTTG gi|9237|e 240 G T L E A I Q W S K H W D S G I 256 gi|9237|e 720 GGCACCCTGGAGGCCATCCAGTGGTCCAAGCACTGGGACTCCGGCATC 768 """, ) protein_record = protein_alignment.sequences[11] nucleotide_record = nucleotide_records[protein_record.id] self.assertEqual(nucleotide_record.id, protein_record.id) alignments = aligner.align(protein_record, nucleotide_record) self.assertEqual(len(alignments), 1) alignment = next(alignments) codon_alignments.append(alignment) self.assertTrue( np.array_equal(alignment.coordinates, np.array([[0, 256], [0, 768]])) ) self.assertEqual( str(alignment), """\ gi|9239|e 0 M A F T L T N K N V V F V A G L G G I G gi|9239|e 0 ATGGCGTTTACCTTGACCAACAAGAACGTGGTTTTCGTGGCCGGTCTGGGAGGCATTGGT gi|9239|e 20 L D T S K E L V K R D L K N L V I L D R gi|9239|e 60 CTGGACACCAGCAAGGAGCTGGTCAAGCGGGACCTGAAGAACCTGGTGATCCTCGACCGC gi|9239|e 40 I E N P A A I A E L K A I N P K V T V T gi|9239|e 120 ATTGAGAACCCGGCTGCCATCGCCGAGCTGAAGGCAATCAATCCAAAGGTGACCGTCACC gi|9239|e 60 F Y P Y D V T V P I A E T T K L L K T I gi|9239|e 180 TTCTACCCCTACGATGTGACCGTGCCCATTGCCGAGACCACCAAGCTGCTGAAGACCATC gi|9239|e 80 F A Q L K T I D V L I N G A G I L D D H gi|9239|e 240 TTCGCCCAGCTGAAGACCATCGATGTCCTGATCAACGGAGCTGGCATCCTGGACGATCAC gi|9239|e 100 Q I E R T I A V N Y T G L V N T T T A I gi|9239|e 300 CAGATCGAGCGCACCATCGCCGTCAACTACACCGGCCTGGTGAACACCACGACGGCCATC gi|9239|e 120 L D F W D K R K G G P G G I I C N I G S gi|9239|e 360 CTGGACTTCTGGGACAAGCGCAAGGGTGGACCCGGTGGTATCATCTGCAACATTGGATCC gi|9239|e 140 V T G F N A I Y Q V P V Y S G T K A A V gi|9239|e 420 GTGACTGGATTCAACGCCATCTACCAGGTGCCCGTTTACTCCGGCACCAAGGCTGCCGTG gi|9239|e 160 V N F T S S L A K L A P I T G V T A Y T gi|9239|e 480 GTCAACTTCACCAGCTCCCTGGCGAAACTGGCCCCCATCACCGGCGTGACCGCTTACACC gi|9239|e 180 V N P G I T R T T L V H K F N S W L D V gi|9239|e 540 GTGAACCCCGGCATCACCCGCACCACCCTGGTGCACAAGTTCAACTCCTGGCTGGATGTT gi|9239|e 200 E P Q V A E K L L A H P T Q P S L A C A gi|9239|e 600 GAGCCCCAGGTGGCCGAGAAGCTCCTGGCTCACCCCACCCAGCCCTCGTTGGCCTGCGCC gi|9239|e 220 Q N F V K A I E L N Q N G A I W K L D L gi|9239|e 660 CAGAACTTTGTCAAGGCCATCGAGCTGAACCAGAACGGTGCCATCTGGAAACTGGACTTG gi|9239|e 240 G T L E A I Q W S K H W D S G I 256 gi|9239|e 720 GGCACCCTGGAGGCCATCCAGTGGTCCAAGCACTGGGACTCCGGCATC 768 """, ) protein_record = protein_alignment.sequences[12] nucleotide_record = nucleotide_records[protein_record.id] self.assertEqual(nucleotide_record.id, protein_record.id) alignments = aligner.align(protein_record, nucleotide_record) self.assertEqual(len(alignments), 1) alignment = next(alignments) codon_alignments.append(alignment) self.assertTrue( np.array_equal(alignment.coordinates, np.array([[0, 256], [0, 768]])) ) self.assertEqual( str(alignment), """\ gi|9097|e 0 M A F T L T N K N V I F V A G L G G I G gi|9097|e 0 ATGGCGTTTACTTTGACCAACAAGAACGTGATTTTCGTTGCCGGTCTGGGAGGCATTGGT gi|9097|e 20 L D T S K E L L K R D L K N L V I L D R gi|9097|e 60 CTGGACACCAGCAAGGAGCTGCTCAAGCGCGACCTGAAGAACCTGGTGATCCTCGACCGC gi|9097|e 40 I E N P A A I A E L K A I N P K V T V T gi|9097|e 120 ATTGAGAACCCTGCTGCCATTGCCGAGCTGAAGGCAATCAATCCAAAGGTGACCGTCACC gi|9097|e 60 F Y P Y D V T V P I A E T T K L L K T I gi|9097|e 180 TTCTACCCCTATGATGTGACCGTGCCCATTGCCGAGACCACCAAGCTGCTGAAGACCATC gi|9097|e 80 F A K L K T V D V L I N G A G I L D D H gi|9097|e 240 TTCGCCAAGCTGAAGACCGTCGATGTCCTGATCAACGGAGCTGGTATCCTGGACGATCAC gi|9097|e 100 Q I E R T I A V N Y T G L V N T T T A I gi|9097|e 300 CAGATCGAGCGCACCATTGCCGTCAACTACACTGGCCTGGTCAACACCACGACGGCCATT gi|9097|e 120 L D F W D K R K G G P G G I I C N I G S gi|9097|e 360 TTGGACTTCTGGGACAAGCGCAAGGGTGGTCCCGGTGGTATCATCTGCAACATTGGATCC gi|9097|e 140 V T G F N A I Y Q V P V Y S G T K A A V gi|9097|e 420 GTCACTGGATTCAATGCCATCTACCAGGTGCCCGTCTACTCCGGCACCAAGGCTGCCGTG gi|9097|e 160 V N F T S S L A K L A P I T G V T A Y T gi|9097|e 480 GTCAACTTCACCAGCTCCCTGGCGAAACTGGCCCCCATTACCGGCGTGACCGCTTACACC gi|9097|e 180 V N P G I T R T T L V H K F N S W L D V gi|9097|e 540 GTGAACCCCGGCATCACCCGCACCACCCTGGTGCACAAGTTCAACTCCTGGCTGGATGTT gi|9097|e 200 E P Q V A E K L L A H P T Q P S L A C A gi|9097|e 600 GAGCCCCAGGTTGCCGAGAAGCTCCTGGCTCATCCCACCCAGCCCTCGTTGGCCTGCGCC gi|9097|e 220 E N F V K A I E L N Q N G A I W K L D L gi|9097|e 660 GAGAACTTCGTCAAGGCTATCGAGCTGAACCAGAACGGAGCCATCTGGAAACTGGACTTG gi|9097|e 240 G T L E A I Q W T K H W D S G I 256 gi|9097|e 720 GGCACCCTGGAGGCCATCCAGTGGACCAAGCACTGGGACTCCGGCATC 768 """, ) protein_record = protein_alignment.sequences[13] nucleotide_record = nucleotide_records[protein_record.id] self.assertEqual(nucleotide_record.id, protein_record.id) alignments = aligner.align(protein_record, nucleotide_record) self.assertEqual(len(alignments), 1) alignment = next(alignments) codon_alignments.append(alignment) self.assertTrue( np.array_equal(alignment.coordinates, np.array([[0, 256], [0, 768]])) ) self.assertEqual( str(alignment), """\ gi|9099|e 0 M A F T L T N K N V I F V A G L G G I G gi|9099|e 0 ATGGCGTTTACTTTGACCAACAAGAACGTGATTTTCGTTGCCGGTCTGGGAGGCATTGGT gi|9099|e 20 L D T S K E L L K R D L K N L V I L D R gi|9099|e 60 CTGGACACCAGCAAGGAGCTGCTCAAGCGCGACCTGAAGAACCTGGTGATCCTCGACCGC gi|9099|e 40 I E N P A A I A E L K A I N P K V T V T gi|9099|e 120 ATTGAGAACCCTGCTGCCATTGCCGAGCTGAAGGCAATCAATCCAAAGGTGACCGTCACC gi|9099|e 60 F Y P Y D V T V P I A E T T K L L K T I gi|9099|e 180 TTCTACCCCTATGATGTGACCGTGCCCATTGCCGAGACCACCAAGCTGCTGAAGACCATC gi|9099|e 80 F A K L K T V D V L I N G A G I L D D H gi|9099|e 240 TTCGCCAAGCTGAAGACCGTCGATGTCCTGATCAACGGAGCTGGTATCCTGGACGATCAC gi|9099|e 100 Q I E R T I A V N Y T G L V N T T T A I gi|9099|e 300 CAGATCGAGCGCACCATTGCCGTCAACTACACTGGCCTGGTCAACACCACGACGGCCATT gi|9099|e 120 L D F W D K R K G G P G G I I C N I G S gi|9099|e 360 CTGGACTTCTGGGACAAGCGCAAGGGTGGTCCCGGTGGTATCATCTGCAACATTGGATCC gi|9099|e 140 V T G F N A I Y Q V P V Y S G T K A A V gi|9099|e 420 GTCACTGGTTTCAATGCCATCTACCAGGTGCCCGTCTACTCCGGCACCAAGGCTGCCGTG gi|9099|e 160 V N F T S S L A K L A P I T G V T A Y T gi|9099|e 480 GTCAACTTCACCAGCTCCCTGGCGAAACTGGCCCCCATTACCGGCGTGACCGCTTACACC gi|9099|e 180 V N P G I T R T T L V H K F N S W L D V gi|9099|e 540 GTGAACCCCGGCATCACCCGCACCACCCTGGTGCACAAGTTCAACTCCTGGCTGGATGTT gi|9099|e 200 E P Q V A E K L L A H P T Q P S L A C A gi|9099|e 600 GAGCCCCAGGTTGCCGAGAAGCTCCTGGCTCATCCCACTCAGCCCTCATTGGCCTGCGCC gi|9099|e 220 E N F V K A I E L N Q N G A I W K L D L gi|9099|e 660 GAGAACTTCGTCAAGGCCATCGAGCTGAACCAGAACGGAGCCATCTGGAAACTGGACTTG gi|9099|e 240 G T L E A I Q W T K H W D S G I 256 gi|9099|e 720 GGCACCCTGGAGGCCATCCAGTGGACCAAGCACTGGGACTCCGGCATC 768 """, ) protein_record = protein_alignment.sequences[14] nucleotide_record = nucleotide_records[protein_record.id] self.assertEqual(nucleotide_record.id, protein_record.id) alignments = aligner.align(protein_record, nucleotide_record) self.assertEqual(len(alignments), 1) alignment = next(alignments) codon_alignments.append(alignment) self.assertTrue( np.array_equal(alignment.coordinates, np.array([[0, 256], [0, 768]])) ) self.assertEqual( str(alignment), """\ gi|9101|e 0 M A F T L T N K N V I F V A G L G G I G gi|9101|e 0 ATGGCGTTTACTTTGACCAACAAGAACGTGATTTTCGTTGCCGGTCTGGGAGGCATTGGT gi|9101|e 20 L D T S K E L L K R D L K N L V I L D R gi|9101|e 60 CTGGACACCAGCAAGGAGCTGCTCAAGCGCGACCTGAAGAACCTGGTGATCCTCGACCGC gi|9101|e 40 I E N P A A I A E L K A I N P K V T V T gi|9101|e 120 ATTGAGAACCCTGCTGCCATTGCCGAGCTGAAGGCAATCAATCCAAAGGTGACCGTCACC gi|9101|e 60 F Y P Y D V T V P I A E T T K L L K T I gi|9101|e 180 TTCTACCCCTATGATGTGACCGTGCCCATTGCCGAGACCACCAAGCTGCTGAAGACCATC gi|9101|e 80 F A K L K T V D V L I N G A G I L D D H gi|9101|e 240 TTCGCCAAGCTGAAGACCGTCGATGTCCTGATCAACGGAGCTGGTATCCTGGACGATCAC gi|9101|e 100 Q I E R T I A V N Y T G L V N T T T A I gi|9101|e 300 CAGATCGAGCGCACCATTGCCGTCAACTACACTGGCCTGGTCAACACCACGACGGCCATT gi|9101|e 120 L D F W D K R K G G P G G I I C N I G S gi|9101|e 360 CTGGACTTCTGGGACAAGCGCAAGGGTGGTCCCGGTGGTATCATCTGCAACATTGGATCC gi|9101|e 140 V T G F N A I Y Q V P V Y S G T K A A V gi|9101|e 420 GTCACTGGATTCAATGCCATCTACCAGGTGCCCGTCTACTCTGGCACCAAGGCCGCCGTG gi|9101|e 160 V N F T S S L A K L A P I T G V T A Y T gi|9101|e 480 GTCAACTTCACCAGCTCCCTGGCGAAACTGGCCCCCATTACCGGCGTGACCGCTTACACC gi|9101|e 180 V N P G I T R T T L V H K F N S W L D V gi|9101|e 540 GTGAACCCCGGCATCACCCGCACCACCCTGGTGCACAAGTTCAACTCCTGGCTGGATGTT gi|9101|e 200 E P Q V A E K L L A H P T Q P S L A C A gi|9101|e 600 GAGCCCCAGGTTGCCGAGAAGCTCCTGGCTCATCCCACCCAGCCCTCGTTGGCCTGCGCC gi|9101|e 220 E N F V K A I E L N Q N G A I W K L D L gi|9101|e 660 GAGAACTTCGTCAAGGCCATCGAGCTGAACCAGAACGGAGCCATCTGGAAACTGGACTTG gi|9101|e 240 G T L E A I Q W T K H W D S G I 256 gi|9101|e 720 GGCACCCTGGAGGCCATCCAGTGGACCAAGCACTGGGACTCCGGCATC 768 """, ) protein_record = protein_alignment.sequences[15] nucleotide_record = nucleotide_records[protein_record.id] self.assertEqual(nucleotide_record.id, protein_record.id) alignments = aligner.align(protein_record, nucleotide_record) self.assertEqual(len(alignments), 1) alignment = next(alignments) codon_alignments.append(alignment) self.assertTrue( np.array_equal(alignment.coordinates, np.array([[0, 256], [0, 768]])) ) self.assertEqual( str(alignment), """\ gi|9103|e 0 M A F T L T N K N V I F V A G L G G I G gi|9103|e 0 ATGGCGTTTACTTTGACCAACAAGAACGTGATTTTCGTTGCCGGTCTGGGAGGCATCGGT gi|9103|e 20 L D T S K E L L K R D L K N L V I L D R gi|9103|e 60 CTGGACACCAGCAAGGAGCTGCTCAAGCGCGACCTGAAGAACCTGGTGATCCTCGACCGC gi|9103|e 40 I E N P A A I A E L K A I N P K V T V T gi|9103|e 120 ATTGAGAACCCTGCTGCCATTGCCGAGCTGAAGGCAATCAATCCAAAGGTGACCGTCACC gi|9103|e 60 F Y P Y D V T V P I A E T T K L L K T I gi|9103|e 180 TTCTACCCCTATGATGTGACCGTGCCCATTGCCGAGACCACCAAGCTGCTGAAGACCATC gi|9103|e 80 F A K L K T V D V L I N G A G I L D D H gi|9103|e 240 TTCGCCAAGCTGAAGACCGTCGATGTCCTGATCAACGGAGCTGGTATCCTGGACGATCAC gi|9103|e 100 Q I E R T I A V N Y T G L V N T T T A I gi|9103|e 300 CAGATCGAGCGCACCATTGCCGTCAACTACACTGGCCTGGTCAACACCACGACGGCCATT gi|9103|e 120 L D F W D K R K G G P G G I I C N I G S gi|9103|e 360 CTGGACTTCTGGGACAAGCGCAAGGGTGGTCCCGGTGGTATCATCTGCAACATTGGATCC gi|9103|e 140 V T G F N A I Y Q V P V Y S G T K A A V gi|9103|e 420 GTCACTGGATTCAATGCCATCTACCAGGTGCCCGTCTACTCCGGCACCAAGGCCGCCGTG gi|9103|e 160 V N F T S S L A K L A P I T G V T A Y T gi|9103|e 480 GTCAACTTCACCAGCTCCCTGGCGAAACTGGCCCCCATTACCGGCGTGACCGCTTACACC gi|9103|e 180 V N P G I T R T T L V H K F N S W L D V gi|9103|e 540 GTGAACCCCGGCATCACCCGCACCACCCTGGTGCACAAGTTCAACTCCTGGCTGGATGTT gi|9103|e 200 E P Q V A E K L L A H P T Q P S L A C A gi|9103|e 600 GAGCCCCAGGTTGCCGAGAAGCTCCTGGCTCATCCCACCCAGCCCTCGTTGGCCTGCGCC gi|9103|e 220 E N F V K A I E L N Q N G A I W K L D L gi|9103|e 660 GAGAACTTCGTCAAGGCCATCGAGCTGAACCAGAACGGAGCCATCTGGAAACTGGACTTG gi|9103|e 240 G T L E A I Q W T K H W D S G I 256 gi|9103|e 720 GGCACCCTGGAGGCCATCCAGTGGACCAAGCACTGGGACTCCGGCATC 768 """, ) protein_record = protein_alignment.sequences[16] nucleotide_record = nucleotide_records[protein_record.id] self.assertEqual(nucleotide_record.id, protein_record.id) alignments = aligner.align(protein_record, nucleotide_record) self.assertEqual(len(alignments), 1) alignment = next(alignments) codon_alignments.append(alignment) self.assertTrue( np.array_equal(alignment.coordinates, np.array([[0, 256], [0, 768]])) ) self.assertEqual( str(alignment), """\ gi|156879 0 M S F T L T N K N V I F V A G L G G I G gi|156879 0 ATGTCGTTTACTTTGACCAACAAGAACGTGATTTTCGTGGCCGGTCTGGGAGGCATTGGT gi|156879 20 L D T S K E L L K R D L K N L V I L D R gi|156879 60 CTGGACACCAGCAAGGAGCTGCTCAAGCGCGATCTGAAGAACCTGGTGATCCTCGACCGC gi|156879 40 I E N P A A I A E L K A I N P K V T V T gi|156879 120 ATTGAGAACCCGGCTGCCATTGCCGAGCTGAAGGCAATCAATCCAAAGGTGACCGTCACC gi|156879 60 F Y P Y D V T V P I A E T T K L L K T I gi|156879 180 TTCTACCCCTATGATGTGACCGTGCCCATTGCCGAGACCACCAAGCTGCTGAAGACCATC gi|156879 80 F A Q L K T V D V L I N G A G I L D D H gi|156879 240 TTCGCCCAGCTGAAGACCGTCGATGTCCTGATCAACGGAGCTGGTATCCTGGACGATCAC gi|156879 100 Q I E R T I A V N Y T G L V N T T T A I gi|156879 300 CAGATCGAGCGCACCATTGCCGTCAACTACACTGGCCTGGTCAACACCACGACGGCCATT gi|156879 120 L D F W D K R K G G P G G I I C N I G S gi|156879 360 CTGGACTTCTGGGACAAGCGCAAGGGCGGTCCAGGTGGTATCATCTGCAACATTGGATCC gi|156879 140 V T G F N A I Y Q V P V Y S G T K A A V gi|156879 420 GTCACTGGATTCAATGCCATCTACCAGGTGCCCGTCTACTCCGGCACCAAGGCCGCCGTG gi|156879 160 V N F T S S L A K L A P I T G V T A Y T gi|156879 480 GTCAACTTCACCAGCTCCCTGGCGAAACTGGCCCCCATTACCGGCGTGACGGCTTACACT gi|156879 180 V N P G I T R T T L V H T F N S W L D V gi|156879 540 GTGAACCCCGGCATCACCCGCACCACCCTGGTGCACACGTTCAACTCCTGGTTGGATGTT gi|156879 200 E P Q V A E K L L A H P T Q P S L A C A gi|156879 600 GAGCCTCAGGTTGCCGAGAAGCTCCTGGCTCATCCCACCCAGCCCTCGTTGGCCTGCGCC gi|156879 220 E N F V K A I E L N Q N G A I W K L D L gi|156879 660 GAGAACTTCGTCAAGGCTATCGAGCTGAACCAGAACGGAGCCATCTGGAAACTGGACTTG gi|156879 240 G T L E A I Q W T K H W D S G I 256 gi|156879 720 GGCACCCTGGAGGCCATCCAGTGGACCAAGCACTGGGACTCCGGCATC 768 """, ) protein_record = protein_alignment.sequences[17] nucleotide_record = nucleotide_records[protein_record.id] self.assertEqual(nucleotide_record.id, protein_record.id) alignments = aligner.align(protein_record, nucleotide_record) self.assertEqual(len(alignments), 1) alignment = next(alignments) codon_alignments.append(alignment) self.assertTrue( np.array_equal(alignment.coordinates, np.array([[0, 256], [0, 768]])) ) self.assertEqual( str(alignment), """\ gi|156877 0 M S F T L T N K N V I F V A G L G G I G gi|156877 0 ATGTCGTTTACTTTGACCAACAAGAACGTGATTTTCGTGGCCGGTCTGGGAGGCATTGGT gi|156877 20 L D T S K E L L K R D L K N L V I L D R gi|156877 60 CTGGACACCAGCAAGGAGCTGCTCAAGCGCGATCTGAAGAACCTGGTGATCCTCGACCGC gi|156877 40 I E N P A A I A E L K A I N P K V T V T gi|156877 120 ATTGAGAACCCGGCTGCCATTGCCGAGCTGAAGGCAATCAATCCAAAGGTGACCGTCACC gi|156877 60 F Y P Y D V T V P I A E T T K L L K T I gi|156877 180 TTCTACCCCTATGATGTGACCGTGCCCATTGCCGAGACCACCAAGCTGCTGAAGACCATC gi|156877 80 F A Q L K T V D V L I N G A G I L D D H gi|156877 240 TTCGCCCAGCTGAAGACCGTCGATGTCCTGATCAACGGAGCTGGTATCCTGGACGATCAC gi|156877 100 Q I E R T I A V N Y T G L V N T T T A I gi|156877 300 CAGATCGAGCGCACCATTGCCGTCAACTACACTGGCCTGGTCAACACCACGACGGCCATT gi|156877 120 L D F W D K R K G G P G G I I C N I G S gi|156877 360 CTGGACTTCTGGGACAAGCGCAAGGGCGGTCCCGGTGGTATCATCTGCAACATTGGATCC gi|156877 140 V T G F N A I Y Q V P V Y S G T K A A V gi|156877 420 GTCACTGGATTCAATGCCATCTACCAGGTGCCCGTCTACTCCGGCACCAAGGCCGCCGTG gi|156877 160 V N F T S S L A K L A P I T G V T A Y T gi|156877 480 GTCAACTTCACCAGCTCCCTGGCGAAACTGGCCCCCATTACCGGCGTGACGGCTTACACT gi|156877 180 V N P G I T R T T L V H T F N S W L D V gi|156877 540 GTGAACCCCGGCATCACCCGCACCACCCTGGTGCACACGTTCAACTCCTGGTTGGATGTT gi|156877 200 E P Q V A E K L L A H P T Q P S L A C A gi|156877 600 GAGCCTCAGGTTGCCGAGAAGCTCCTGGCTCATCCCACCCAGCCCTCGTTGGCCTGCGCC gi|156877 220 E N F V K A I E L N Q N G A I W K L D L gi|156877 660 GAGAACTTCGTCAAGGCTATCGAGCTGAACCAGAACGGAGCCATCTGGAAACTGGACTTG gi|156877 240 G T L E A I Q W T K H W D S G I 256 gi|156877 720 GGCACCCTGGAGGCCATCCAGTGGACCAAGCACTGGGACTCCGGCATC 768 """, ) protein_record = protein_alignment.sequences[18] nucleotide_record = nucleotide_records[protein_record.id] self.assertEqual(nucleotide_record.id, protein_record.id) alignments = aligner.align(protein_record, nucleotide_record) self.assertEqual(len(alignments), 1) alignment = next(alignments) codon_alignments.append(alignment) self.assertTrue( np.array_equal(alignment.coordinates, np.array([[0, 256], [0, 768]])) ) self.assertEqual( str(alignment), """\ gi|156875 0 M S F T L T N K N V I F V A G L G G I G gi|156875 0 ATGTCGTTTACTTTGACCAACAAGAACGTGATTTTCGTGGCCGGTCTGGGAGGCATTGGT gi|156875 20 L D T S K E L L K R D L K N L V I L D R gi|156875 60 CTGGACACCAGCAAGGAGCTGCTCAAGCGCGATCTGAAGAACCTGGTGATCCTCGACCGC gi|156875 40 I E N P A A I A E L K A I N P K V T V T gi|156875 120 ATTGAGAACCCGGCTGCCATTGCCGAGCTGAAGGCAATCAATCCAAAGGTGACCGTCACC gi|156875 60 F Y P Y D V T V P I A E T T K L L K T I gi|156875 180 TTCTACCCCTATGATGTGACCGTGCCCATTGCCGAGACCACCAAGCTGCTGAAGACCATC gi|156875 80 F A Q L K T V D V L I N G A G I L D D H gi|156875 240 TTCGCCCAGCTGAAGACCGTCGATGTCCTGATCAACGGAGCTGGTATCCTGGACGATCAC gi|156875 100 Q I E R T I A V N Y T G L V N T T T A I gi|156875 300 CAGATCGAGCGCACCATTGCCGTCAACTACACTGGCCTGGTCAACACCACGACGGCCATT gi|156875 120 L D F W D K R K G G P G G I I C N I G S gi|156875 360 CTGGACTTCTGGGACAAGCGCAAGGGCGGTCCCGGTGGTATCATCTGCAACATTGGATCC gi|156875 140 V T G F N A I Y Q V P V Y S G T K A A V gi|156875 420 GTCACTGGATTCAATGCCATCTACCAGGTGCCCGTCTACTCCGGCACCAAGGCCGCCGTG gi|156875 160 V N F T S S L A K L A P I T G V T A Y T gi|156875 480 GTCAACTTCACCAGCTCCCTGGCGAAACTGGCCCCCATTACCGGCGTGACGGCTTACACT gi|156875 180 V N P G I T R T T L V H T F N S W L D V gi|156875 540 GTGAACCCCGGCATCACCCGCACCACCCTGGTGCACACGTTCAACTCCTGGTTGGATGTT gi|156875 200 E P Q V A E K L L A H P T Q P S L A C A gi|156875 600 GAGCCTCAGGTTGCCGAGAAGCTCCTGGCTCATCCCACCCAGCCCTCGTTGGCCTGCGCC gi|156875 220 E N F V K A I E L N Q N G A I W K L D L gi|156875 660 GAGAACTTCGTCAAGGCTATCGAGCTGAACCAGAACGGAGCCATCTGGAAACTGGACTTG gi|156875 240 G T L E A I Q W T K H W D S G I 256 gi|156875 720 GGCACCCTGGAGGCCATCCAGTGGACCAAGCACTGGGACTCCGGCATC 768 """, ) protein_record = protein_alignment.sequences[19] nucleotide_record = nucleotide_records[protein_record.id] self.assertEqual(nucleotide_record.id, protein_record.id) alignments = aligner.align(protein_record, nucleotide_record) self.assertEqual(len(alignments), 1) alignment = next(alignments) codon_alignments.append(alignment) self.assertTrue( np.array_equal(alignment.coordinates, np.array([[0, 256], [0, 768]])) ) self.assertEqual( str(alignment), """\ gi|156873 0 M S F T L T N K N V I F V A G L G G I G gi|156873 0 ATGTCGTTTACTTTGACCAACAAGAACGTGATTTTCGTGGCCGGTCTGGGAGGCATTGGT gi|156873 20 L D T S K E L L K R D L K N L V I L D R gi|156873 60 CTGGACACCAGCAAGGAGCTGCTCAAGCGCGATCTGAAGAACCTGGTGATCCTCGACCGC gi|156873 40 I E N P A A I A E L K A I N P K V T V T gi|156873 120 ATTGAGAACCCGGCTGCCATTGCCGAGCTGAAGGCAATCAATCCAAAGGTGACCGTCACC gi|156873 60 F Y P Y D V T V P I A E T T K L L K T I gi|156873 180 TTCTACCCCTATGATGTGACCGTGCCCATTGCCGAGACCACCAAGCTGCTGAAGACCATC gi|156873 80 F A Q L K T V D V L I N G A G I L D D H gi|156873 240 TTCGCCCAGCTGAAGACCGTCGATGTCCTGATCAACGGAGCTGGTATCCTGGACGATCAC gi|156873 100 Q I E R T I A V N Y T G L V N T T T A I gi|156873 300 CAGATCGAGCGCACCATTGCCGTCAACTACACTGGCCTGGTCAACACCACGACGGCCATT gi|156873 120 L D F W D K R K G G P G G I I C N I G S gi|156873 360 CTGGACTTCTGGGACAAGCGCAAGGGCGGTCCCGGTGGTATCATCTGCAACATTGGATCC gi|156873 140 V T G F N A I Y Q V P V Y S G T K A A V gi|156873 420 GTCACTGGATTCAATGCCATCTACCAGGTGCCCGTCTACTCCGGCACCAAGGCCGCCGTG gi|156873 160 V N F T S S L A K L A P I T G V T A Y T gi|156873 480 GTCAACTTCACCAGCTCCCTGGCGAAACTGGCCCCCATTACCGGCGTGACGGCTTACACT gi|156873 180 V N P G I T R T T L V H T F N S W L D V gi|156873 540 GTGAACCCCGGCATCACCCGCACCACCCTGGTGCACACGTTCAACTCCTGGTTGGATGTT gi|156873 200 E P Q V A E K L L A H P T Q P S L A C A gi|156873 600 GAGCCTCAGGTTGCCGAGAAGCTCCTGGCTCATCCCACCCAGCCCTCGTTGGCCTGCGCC gi|156873 220 E N F V K A I E L N Q N G A I W K L D L gi|156873 660 GAGAACTTCGTCAAGGCTATCGAGCTGAACCAGAACGGAGCCATCTGGAAACTGGACTTG gi|156873 240 G T L E A I Q W T K H W D S G I 256 gi|156873 720 GGCACCCTGGAGGCCATCCAGTGGACCAAGCACTGGGACTCCGGCATC 768 """, ) protein_record = protein_alignment.sequences[20] nucleotide_record = nucleotide_records[protein_record.id] self.assertEqual(nucleotide_record.id, protein_record.id) alignments = aligner.align(protein_record, nucleotide_record) self.assertEqual(len(alignments), 1) alignment = next(alignments) codon_alignments.append(alignment) self.assertTrue( np.array_equal(alignment.coordinates, np.array([[0, 256], [0, 768]])) ) self.assertEqual( str(alignment), """\ gi|156871 0 M S F T L T N K N V I F V A G L G G I G gi|156871 0 ATGTCGTTTACTTTGACCAACAAGAACGTGATTTTCGTGGCCGGTCTGGGAGGCATTGGT gi|156871 20 L D T S K E L L K R D L K N L V I L D R gi|156871 60 CTGGACACCAGCAAGGAGCTGCTCAAGCGCGATCTGAAGAACCTGGTGATCCTCGACCGC gi|156871 40 I E N P A A I A E L K A I N P K V T V T gi|156871 120 ATTGAGAACCCGGCTGCCATTGCCGAGCTGAAGGCAATCAATCCAAAGGTGACCGTCACC gi|156871 60 F Y P Y D V T V P I A E T T K L L K T I gi|156871 180 TTCTACCCCTATGATGTGACCGTGCCCATTGCCGAGACCACCAAGCTGCTGAAGACCATC gi|156871 80 F A Q L K T V D V L I N G A G I L D D H gi|156871 240 TTCGCCCAGCTGAAGACCGTCGATGTCCTGATCAACGGAGCTGGTATCCTGGACGATCAC gi|156871 100 Q I E R T I A V N Y T G L V N T T T A I gi|156871 300 CAGATCGAGCGCACCATTGCCGTCAACTACACTGGCCTGGTCAACACCACGACGGCCATT gi|156871 120 L D F W D K R K G G P G G I I C N I G S gi|156871 360 CTGGACTTCTGGGACAAGCGCAAGGGCGGTCCCGGTGGTATCATCTGCAACATTGGATCC gi|156871 140 V T G F N A I Y Q V P V Y S G T K A A V gi|156871 420 GTCACTGGATTCAATGCCATCTACCAGGTGCCCGTCTACTCCGGCACCAAGGCCGCCGTG gi|156871 160 V N F T S S L A K L A P I T G V T A Y T gi|156871 480 GTCAACTTCACCAGCTCCCTGGCGAAACTGGCCCCCATTACCGGCGTGACGGCTTACACT gi|156871 180 V N P G I T R T T L V H T F N S W L D V gi|156871 540 GTGAACCCCGGCATCACCCGCACCACCCTGGTGCACACGTTCAACTCCTGGTTGGATGTT gi|156871 200 E P Q V A E K L L A H P T Q P S L A C A gi|156871 600 GAGCCTCAGGTTGCCGAGAAGCTCCTGGCTCATCCCACCCAGCCCTCGTTGGCCTGCGCC gi|156871 220 E N F V K A I E L N Q N G A I W K L D L gi|156871 660 GAGAACTTCGTCAAGGCTATCGAGCTGAACCAGAACGGAGCCATCTGGAAACTGGACTTG gi|156871 240 G T L E A I Q W T K H W D S G I 256 gi|156871 720 GGCACCCTGGAGGCCATCCAGTGGACCAAGCACTGGGACTCCGGCATC 768 """, ) protein_record = protein_alignment.sequences[21] nucleotide_record = nucleotide_records[protein_record.id] self.assertEqual(nucleotide_record.id, protein_record.id) alignments = aligner.align(protein_record, nucleotide_record) self.assertEqual(len(alignments), 1) alignment = next(alignments) codon_alignments.append(alignment) self.assertTrue( np.array_equal(alignment.coordinates, np.array([[0, 256], [0, 768]])) ) self.assertEqual( str(alignment), """\ gi|156863 0 M S F T L T N K N V I F V A G L G G I G gi|156863 0 ATGTCGTTTACTTTGACCAACAAGAACGTGATTTTCGTTGCCGGTCTGGGAGGCATTGGT gi|156863 20 L D T S K E L L K R D L K N L V I L D R gi|156863 60 CTGGACACCAGCAAGGAGCTGCTCAAGCGCGATCTGAAGAACCTGGTGATCCTCGACCGC gi|156863 40 I E N P A A I A E L K A I N P K V T V T gi|156863 120 ATTGAGAACCCGGCTGCCATTGCCGAGCTGAAGGCAATCAATCCAAAGGTGACCGTCACC gi|156863 60 F Y P Y D V T V P I A E T T K L L K T I gi|156863 180 TTCTACCCCTATGATGTGACCGTGCCCATTGCCGAGACCACCAAGCTGCTGAAGACCATC gi|156863 80 F A Q L K T V D V L I N G A G I L D D H gi|156863 240 TTCGCCCAGCTGAAGACCGTCGATGTCCTGATCAACGGAGCTGGTATCCTGGACGATCAC gi|156863 100 Q I E R T I A V N Y T G L V N T T T A I gi|156863 300 CAGATCGAGCGCACCATTGCCGTCAACTACACTGGCCTGGTCAACACCACGACGGCCATT gi|156863 120 L D F W D K R K G G P G G I I C N I G S gi|156863 360 CTGGACTTCTGGGACAAGCGCAAGGGCGGTCCCGGTGGTATCATCTGCAACATTGGATCC gi|156863 140 V T G F N A I Y Q V P V Y S G T K A A V gi|156863 420 GTCACTGGATTCAATGCCATCTACCAGGTGCCCGTCTACTCCGGCACCAAGGCCGCCGTG gi|156863 160 V N F T S S L A K L A P I T G V T A Y T gi|156863 480 GTCAACTTCACCAGCTCCCTGGCGAAACTGGCCCCCATTACCGGCGTGACCGCTTACACC gi|156863 180 V N P G I T R T T L V H K F N S W L D V gi|156863 540 GTGAACCCCGGCATCACCCGCACCACCCTGGTGCACAAGTTCAACTCCTGGTTGGATGTT gi|156863 200 E P Q V A E K L L A H P T Q P S L A C A gi|156863 600 GAGCCCCAGGTTGCTGAGAAGCTCCTGGCTCATCCCACCCAGCCATCGTTGGCCTGCGCC gi|156863 220 E N F V K A I E L N Q N G A I W K L D L gi|156863 660 GAGAACTTCGTCAAGGCTATCGAACTGAACCAGAACGGAGCCATCTGGAAACTGGACTTG gi|156863 240 G T L E A I Q W T K H W D S G I 256 gi|156863 720 GGCACCCTGGAGGCCATCCAGTGGACCAAGCACTGGGACTCCGGCATC 768 """, ) protein_record = protein_alignment.sequences[22] nucleotide_record = nucleotide_records[protein_record.id] self.assertEqual(nucleotide_record.id, protein_record.id) alignments = aligner.align(protein_record, nucleotide_record) self.assertEqual(len(alignments), 1) alignment = next(alignments) codon_alignments.append(alignment) self.assertTrue( np.array_equal(alignment.coordinates, np.array([[0, 256], [0, 768]])) ) self.assertEqual( str(alignment), """\ gi|156869 0 M S F T L T N K N V I F V A G L G G I G gi|156869 0 ATGTCGTTTACTTTGACCAACAAGAACGTGATTTTCGTGGCCGGTCTGGGAGGCATTGGT gi|156869 20 L D T S K E L L K R D L K N L V I L D R gi|156869 60 CTGGACACCAGCAAGGAGCTGCTCAAGCGCGATCTGAAGAACCTGGTGATCCTCGACCGC gi|156869 40 I E N P A A I A E L K A I N P K V T V T gi|156869 120 ATTGAGAACCCGGCTGCCATTGCCGAGCTGAAGGCAATCAATCCAAAGGTGACCGTCACC gi|156869 60 F Y P Y D V T V P I A E T T K L L K T I gi|156869 180 TTCTACCCCTATGATGTGACCGTGCCCATTGCCGAGACCACCAAGCTGCTGAAGACCATC gi|156869 80 F A Q L K T V D V L I N G A G I L D D H gi|156869 240 TTCGCCCAGCTGAAGACCGTCGATGTCCTGATCAACGGAGCTGGTATCCTGGACGATCAC gi|156869 100 Q I E R T I A V N Y T G L V N T T T A I gi|156869 300 CAGATCGAGCGCACCATTGCCGTCAACTACACTGGCCTGGTCAACACCACGACGGCCATT gi|156869 120 L D F W D K R K G G P G G I I C N I G S gi|156869 360 CTGGACTTCTGGGACAAGCGCAAGGGCGGTCCCGGTGGTATCATCTGCAACATTGGATCC gi|156869 140 V T G F N A I Y Q V P V Y S G T K A A V gi|156869 420 GTCACTGGATTCAATGCCATCTACCAGGTGCCCGTCTACTCCGGCACCAAGGCCGCCGTG gi|156869 160 V N F T S S L A K L A P I T G V T A Y T gi|156869 480 GTCAACTTCACCAGCTCCCTGGCGAAACTGGCCCCCATTACCGGCGTGACCGCTTACACT gi|156869 180 V N P G I T R T T L V H K F N S W L D V gi|156869 540 GTGAACCCCGGCATCACCCGCACCACCCTGGTGCACAAGTTCAACTCCTGGTTGGATGTT gi|156869 200 E P Q V A E K L L A H P T Q P S L A C A gi|156869 600 GAGCCTCAGGTTGCTGAGAAGCTCCTGGCTCATCCCACCCAGCCCTCGTTGGCCTGCGCC gi|156869 220 E N F V K A I E L N Q N G A I W K L D L gi|156869 660 GAGAACTTCGTCAAGGCTATCGAACTGAACCAGAACGGAGCCATCTGGAAACTGGACTTG gi|156869 240 G T L E A I Q W T K H W D S G I 256 gi|156869 720 GGCACCCTGGAGGCCATCCAGTGGACCAAGCACTGGGACTCCGGCATC 768 """, ) protein_record = protein_alignment.sequences[23] nucleotide_record = nucleotide_records[protein_record.id] self.assertEqual(nucleotide_record.id, protein_record.id) alignments = aligner.align(protein_record, nucleotide_record) self.assertEqual(len(alignments), 1) alignment = next(alignments) codon_alignments.append(alignment) self.assertTrue( np.array_equal(alignment.coordinates, np.array([[0, 256], [0, 768]])) ) self.assertEqual( str(alignment), """\ gi|156867 0 M S F T L T N K N V I F V A G L G G I G gi|156867 0 ATGTCGTTTACTTTGACCAACAAGAACGTGATTTTCGTGGCCGGTCTGGGAGGCATTGGT gi|156867 20 L D T S K E L L K R D L K N L V I L D R gi|156867 60 CTGGACACCAGCAAGGAGCTGCTCAAGCGCGATCTGAAGAACCTGGTGATCCTCGACCGC gi|156867 40 I E N P A A I A E L K A I N P K V T V T gi|156867 120 ATTGAGAACCCGGCTGCCATTGCCGAGCTGAAGGCAATCAATCCAAAGGTGACCGTCACC gi|156867 60 F Y P Y D V T V P I A E T T K L L K T I gi|156867 180 TTCTACCCCTATGATGTGACCGTGCCCATTGCCGAGACCACCAAGCTGCTGAAGACCATC gi|156867 80 F A Q L K T V D V L I N G A G I L D D H gi|156867 240 TTCGCCCAGCTGAAGACCGTCGATGTCCTGATCAACGGAGCTGGTATCCTGGACGATCAC gi|156867 100 Q I E R T I A V N Y T G L V N T T T A I gi|156867 300 CAGATCGAGCGCACCATTGCCGTCAACTACACTGGCCTGGTCAACACCACGACGGCCATT gi|156867 120 L D F W D K R K G G P G G I I C N I G S gi|156867 360 CTGGACTTCTGGGACAAGCGCAAGGGCGGTCCCGGTGGTATCATCTGCAACATTGGATCC gi|156867 140 V T G F N A I Y Q V P V Y S G T K A A V gi|156867 420 GTCACTGGATTCAATGCCATCTACCAGGTGCCCGTCTACTCCGGCACCAAGGCCGCCGTG gi|156867 160 V N F T S S L A K L A P I T G V T A Y T gi|156867 480 GTCAACTTCACCAGCTCCCTGGCGAAACTGGCCCCCATTACCGGCGTGACCGCTTACACC gi|156867 180 V N P G I T R T T L V H K F N S W L D V gi|156867 540 GTGAACCCCGGCATCACCCGCACCACCCTGGTGCACAAGTTCAACTCCTGGTTGGATGTT gi|156867 200 E P Q V A E K L L A H P T Q P S L A C A gi|156867 600 GAGCCCCAGGTTGCTGAGAAGCTCCTGGCTCATCCCACCCAGCCATCGTTGGCCTGCGCC gi|156867 220 E N F V K A I E L N Q N G A I W K L D L gi|156867 660 GAGAACTTCGTCAAGGCTATCGAGCTGAACCAGAACGGAGCCATCTGGAAACTGGACTTG gi|156867 240 G T L E A I Q W T K H W D S G I 256 gi|156867 720 GGCACCCTGGAGGCCATCCAGTGGACCAAGCACTGGGACTCCGGCATC 768 """, ) protein_record = protein_alignment.sequences[24] nucleotide_record = nucleotide_records[protein_record.id] self.assertEqual(nucleotide_record.id, protein_record.id) alignments = aligner.align(protein_record, nucleotide_record) self.assertEqual(len(alignments), 1) alignment = next(alignments) codon_alignments.append(alignment) self.assertTrue( np.array_equal(alignment.coordinates, np.array([[0, 256], [0, 768]])) ) self.assertEqual( str(alignment), """\ gi|156865 0 M S F T L T N K N V I F V A G L G G I G gi|156865 0 ATGTCGTTTACTTTGACCAACAAGAACGTGATTTTCGTTGCCGGTCTGGGAGGCATTGGT gi|156865 20 L D T S K E L L K R D L K N L V I L D R gi|156865 60 CTGGACACCAGCAAGGAGCTGCTCAAGCGCGATCTGAAGAACCTGGTGATCCTCGACCGC gi|156865 40 I E N P A A I A E L K A I N P K V T V T gi|156865 120 ATTGAGAACCCGGCTGCCATTGCCGAGCTGAAGGCAATCAATCCAAAGGTGACCGTCACC gi|156865 60 F Y P Y D V T V P I A E T T K L L K T I gi|156865 180 TTCTACCCCTATGATGTGACCGTGCCCATTGCCGAGACCACCAAGCTGCTGAAGACCATC gi|156865 80 F A Q L K T V D V L I N G A G I L D D H gi|156865 240 TTCGCCCAGCTGAAGACCGTCGATGTCCTGATCAACGGAGCTGGTATCCTGGACGATCAC gi|156865 100 Q I E R T I A V N Y T G L V N T T T A I gi|156865 300 CAGATCGAGCGCACCATTGCCGTCAACTACACTGGCCTGGTCAACACCACGACGGCCATT gi|156865 120 L D F W D K R K G G P G G I I C N I G S gi|156865 360 CTGGACTTCTGGGACAAGCGCAAGGGCGGTCCCGGTGGTATCATCTGCAACATTGGATCC gi|156865 140 V T G F N A I Y Q V P V Y S G T K A A V gi|156865 420 GTCACTGGATTCAATGCCATCTACCAGGTGCCCGTCTACTCCGGCACCAAGGCCGCCGTG gi|156865 160 V N F T S S L A K L A P I T G V T A Y T gi|156865 480 GTCAACTTCACCAGCTCCCTGGCGAAACTGGCCCCCATTACCGGCGTGACCGCTTACACC gi|156865 180 V N P G I T R T T L V H K F N S W L D V gi|156865 540 GTGAACCCCGGCATCACCCGCACCACCCTGGTGCACAAGTTCAACTCCTGGTTGGATGTT gi|156865 200 E P Q V A E K L L A H P T Q P S L A C A gi|156865 600 GAGCCCCAGGTTGCTGAGAAGCTCCTGGCTCATCCCACCCAGCCATCGTTGGCCTGCGCC gi|156865 220 E N F V K A I E L N Q N G A I W K L D L gi|156865 660 GAGAACTTCGTCAAGGCTATCGAACTGAACCAGAACGGAGCCATCTGGAAACTGGACTTG gi|156865 240 G T L E A I Q W T K H W D S G I 256 gi|156865 720 GGCACCCTGGAGGCCATCCAGTGGACCAAGCACTGGGACTCCGGCATC 768 """, ) protein_record = protein_alignment.sequences[25] nucleotide_record = nucleotide_records[protein_record.id] self.assertEqual(nucleotide_record.id, protein_record.id) alignments = aligner.align(protein_record, nucleotide_record) self.assertEqual(len(alignments), 1) alignment = next(alignments) codon_alignments.append(alignment) self.assertTrue( np.array_equal(alignment.coordinates, np.array([[0, 256], [0, 768]])) ) self.assertEqual( str(alignment), """\ gi|156861 0 M S F T L T N K N V I F V A G L G G I G gi|156861 0 ATGTCGTTTACTTTGACCAACAAGAACGTGATTTTCGTTGCCGGTCTGGGAGGCATTGGT gi|156861 20 L D T S K E L L K R D L K N L V I L D R gi|156861 60 CTGGACACCAGCAAGGAGCTGCTCAAGCGCGATCTGAAGAACCTGGTGATCCTCGACCGC gi|156861 40 I E N P A A I A E L K A I N P K V T V T gi|156861 120 ATTGAGAACCCGGCTGCCATTGCCGAGCTGAAGGCAATCAATCCAAAGGTGACCGTCACC gi|156861 60 F Y P Y D V T V P I A E T T K L L K T I gi|156861 180 TTCTACCCCTATGATGTGACCGTGCCCATTGCCGAGACCACCAAGTTGCTGAAGACCATC gi|156861 80 F A Q L K T V D V L I N G A G I L D D H gi|156861 240 TTCGCCCAGCTGAAGACCGTCGATGTCCTGATCAACGGAGCTGGTATCCTGGACGATCAC gi|156861 100 Q I E R T I A V N Y T G L V N T T T A I gi|156861 300 CAGATCGAGCGCACCATTGCCGTCAACTACACTGGCCTGGTCAACACCACGACGGCTATT gi|156861 120 L D F W D K R K G G P G G I I C N I G S gi|156861 360 CTGGACTTCTGGGACAAGCGCAAGGGTGGTCCCGGTGGTATCATCTGCAACATTGGATCC gi|156861 140 V T G F N A I Y Q V P V Y S G T K A A V gi|156861 420 GTCACTGGATTCAATGCCATATACCAGGTGCCCGTCTACTCCGGCACCAAGGCCGCCGTG gi|156861 160 V N F T S S L A K L A P I T G V T A Y T gi|156861 480 GTCAACTTCACCAGCTCCCTGGCGAAACTGGCACCCATCACCGGCGTGACCGCTTACACC gi|156861 180 V N P G I T R T T L V H K F N S W L D V gi|156861 540 GTGAACCCCGGCATCACCCGCACCACCCTGGTGCACAAGTTCAACTCCTGGTTGGATGTT gi|156861 200 E P Q V A E K L L A H P T Q P S L A C A gi|156861 600 GAGCCCCAGGTTGCTGAGAAGCTCCTGGCTCATCCCACCCAGCCATCGTTGGCCTGCGCC gi|156861 220 E N F V K A I E L N Q N G A I W K L D L gi|156861 660 GAGAACTTCGTCAAGGCTATCGAGCTGAACCAGAACGGAGCCATCTGGAAACTGGACTTG gi|156861 240 G T L E A I Q W T K H W D S G I 256 gi|156861 720 GGCACCCTGGAGGCCATCCAGTGGACCAAGCACTGGGACTCCGGCATC 768 """, ) protein_record = protein_alignment.sequences[26] nucleotide_record = nucleotide_records[protein_record.id] self.assertEqual(nucleotide_record.id, protein_record.id) alignments = aligner.align(protein_record, nucleotide_record) self.assertEqual(len(alignments), 1) alignment = next(alignments) codon_alignments.append(alignment) self.assertTrue( np.array_equal(alignment.coordinates, np.array([[0, 256], [0, 768]])) ) self.assertEqual( str(alignment), """\ gi|156859 0 M S F T L T N K N V I F V A G L G G I G gi|156859 0 ATGTCGTTTACTTTGACCAACAAGAACGTGATTTTCGTTGCCGGTCTGGGAGGCATTGGT gi|156859 20 L D T S K E L L K R D L K N L V I L D R gi|156859 60 CTGGACACCAGCAAGGAGCTGCTCAAGCGCGATCTGAAGAACCTGGTGATCCTCGACCGC gi|156859 40 I E N P A A I A E L K A I N P K V T V T gi|156859 120 ATTGAGAACCCGGCTGCCATTGCCGAGCTGAAGGCAATCAATCCAAAGGTGACCGTCACC gi|156859 60 F Y P Y D V T V P I A E T T K L L K T I gi|156859 180 TTCTACCCCTATGATGTGACCGTGCCCATTGCCGAGACCACCAAGTTGCTGAAGACCATC gi|156859 80 F A Q L K T V D V L I N G A G I L D D H gi|156859 240 TTCGCCCAGCTGAAGACCGTCGATGTCCTGATCAACGGAGCTGGTATCCTGGACGATCAC gi|156859 100 Q I E R T I A V N Y T G L V N T T T A I gi|156859 300 CAGATCGAGCGCACCATTGCCGTCAACTACACTGGCCTGGTCAACACCACGACGGCCATT gi|156859 120 L D F W D K R K G G P G G I I C N I G S gi|156859 360 CTGGACTTCTGGGACAAGCGCAAGGGTGGTCCCGGTGGTATCATCTGCAACATTGGATCC gi|156859 140 V T G F N A I Y Q V P V Y S G T K A A V gi|156859 420 GTCACTGGATTCAATGCCATATACCAGGTGCCCGTCTACTCCGGCACCAAGGCCGCCGTG gi|156859 160 V N F T S S L A K L A P I T G V T A Y T gi|156859 480 GTCAACTTCACCAGCTCCCTGGCGAAACTGGCACCCATCACCGGCGTGACCGCTTACACC gi|156859 180 V N P G I T R T T L V H K F N S W L D V gi|156859 540 GTGAACCCCGGCATCACCCGCACCACCCTGGTGCACAAGTTCAACTCCTGGTTGGATGTT gi|156859 200 E P Q V A E K L L A H P T Q P S L A C A gi|156859 600 GAGCCCCAGGTTGCTGAGAAGCTCCTGGCTCATCCCACCCAGCCATCGTTGGCCTGCGCC gi|156859 220 E N F V K A I E L N Q N G A I W K L D L gi|156859 660 GAGAACTTCGTCAAGGCTATCGAGCTGAACCAGAACGGAGCCATCTGGAAACTGGACTTG gi|156859 240 G T L E A I Q W T K H W D S G I 256 gi|156859 720 GGCACCCTGGAGGCCATCCAGTGGACCAAGCACTGGGACTCCGGCATC 768 """, ) nucleotide_records.close() # Close indexed FASTA file alignment = protein_alignment.mapall(codon_alignments) unique_species = [ "Drosophila simulans", "Drosophila yakuba", "D.melanogaster", ] species = [] for record in alignment.sequences: description = record.description for s in unique_species: if s in description: break else: raise Exception(f"Failed to find species for {description}") species.append(s) pvalue = mktest(alignment, species) self.assertAlmostEqual(pvalue, 0.0020645725725430097) if __name__ == "__main__": runner = unittest.TextTestRunner(verbosity=2) unittest.main(testRunner=runner)