# Copyright 2000-2001 by Brad Chapman. All rights reserved. # Revisions copyright 2007-2003 by Peter Cock. All rights reserved. # 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. """Test alignment stuff. Right now we've got tests for: - Reading and Writing clustal format - Reading and Writing fasta format - Converting between formats """ # standard library import os import unittest import warnings from io import StringIO from Bio import Align from Bio import AlignIO # biopython from Bio import BiopythonDeprecationWarning from Bio import motifs from Bio.Align import AlignInfo from Bio.Align import Alignment from Bio.Align import MultipleSeqAlignment from Bio.Seq import Seq from Bio.SeqRecord import SeqRecord class TestBasics(unittest.TestCase): def test_empty_alignment(self): """Very simple tests on an empty alignment.""" alignment = MultipleSeqAlignment([]) self.assertEqual(alignment.get_alignment_length(), 0) self.assertEqual(len(alignment), 0) alignment = alignment.alignment # new-style Alignment object self.assertEqual(alignment.length, 0) self.assertEqual(len(alignment), 0) def test_basic_alignment(self): """Basic tests on a simple alignment of three sequences.""" msa = MultipleSeqAlignment([]) letters = "AbcDefGhiJklMnoPqrStuVwxYz" msa.append(SeqRecord(Seq(letters), id="mixed")) msa.append(SeqRecord(Seq(letters.lower()), id="lower")) msa.append(SeqRecord(Seq(letters.upper()), id="upper")) msa.append(SeqRecord(Seq(letters), id="duplicate")) del msa[3] self.assertEqual(msa.get_alignment_length(), 26) self.assertEqual(len(msa), 3) self.assertEqual(msa[0].seq, letters) self.assertEqual(msa[1].seq, letters.lower()) self.assertEqual(msa[2].seq, letters.upper()) self.assertEqual(msa[0].id, "mixed") self.assertEqual(msa[1].id, "lower") self.assertEqual(msa[2].id, "upper") for col, letter in enumerate(letters): self.assertEqual(msa[:, col], letter + letter.lower() + letter.upper()) # Check row extractions: self.assertEqual(msa[0].id, "mixed") self.assertEqual(msa[-1].id, "upper") # Check sub-alignment extraction by row slicing: self.assertIsInstance(msa[::-1], MultipleSeqAlignment) self.assertEqual(msa[::-1][0].id, "upper") self.assertEqual(msa[::-1][2].id, "mixed") # create a new-style Alignment object alignment = msa.alignment self.assertEqual(alignment.shape, (3, 26)) self.assertEqual(len(alignment), 3) self.assertEqual(alignment.sequences[0].seq, letters) self.assertEqual(alignment.sequences[1].seq, letters.lower()) self.assertEqual(alignment.sequences[2].seq, letters.upper()) self.assertEqual(alignment.sequences[0].id, "mixed") self.assertEqual(alignment.sequences[1].id, "lower") self.assertEqual(alignment.sequences[2].id, "upper") for col, letter in enumerate(letters): self.assertEqual( alignment[:, col], letter + letter.lower() + letter.upper() ) # Check row extractions: self.assertEqual(alignment[0], letters) self.assertEqual(alignment[-1], letters.upper()) # Check sub-alignment extraction by row slicing: self.assertIsInstance(alignment[::-1], Alignment) self.assertEqual(alignment[::-1].sequences[0].id, "upper") self.assertEqual(alignment[::-1].sequences[2].id, "mixed") class TestReading(unittest.TestCase): def test_read_clustal1(self): """Parse an alignment file and get an alignment object.""" opuntia_clustal_header = """\ CLUSTAL X (1.81) multiple sequence alignment """ opuntia_clustal_body = """\ gi|6273285|gb|AF191659.1|AF191 TATACATTAAAGAAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAA gi|6273284|gb|AF191658.1|AF191 TATACATTAAAGAAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAA gi|6273287|gb|AF191661.1|AF191 TATACATTAAAGAAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAA gi|6273286|gb|AF191660.1|AF191 TATACATAAAAGAAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAA gi|6273290|gb|AF191664.1|AF191 TATACATTAAAGGAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAA gi|6273289|gb|AF191663.1|AF191 TATACATTAAAGGAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAA gi|6273291|gb|AF191665.1|AF191 TATACATTAAAGGAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAA ******* **** ************************************* gi|6273285|gb|AF191659.1|AF191 TATATA----------ATATATTTCAAATTTCCTTATATACCCAAATATA gi|6273284|gb|AF191658.1|AF191 TATATATA--------ATATATTTCAAATTTCCTTATATACCCAAATATA gi|6273287|gb|AF191661.1|AF191 TATATA----------ATATATTTCAAATTTCCTTATATATCCAAATATA gi|6273286|gb|AF191660.1|AF191 TATATA----------ATATATTTATAATTTCCTTATATATCCAAATATA gi|6273290|gb|AF191664.1|AF191 TATATATATA------ATATATTTCAAATTCCCTTATATATCCAAATATA gi|6273289|gb|AF191663.1|AF191 TATATATATA------ATATATTTCAAATTCCCTTATATATCCAAATATA gi|6273291|gb|AF191665.1|AF191 TATATATATATATATAATATATTTCAAATTCCCTTATATATCCAAATATA ****** ******** **** ********* ********* gi|6273285|gb|AF191659.1|AF191 AAAATATCTAATAAATTAGATGAATATCAAAGAATCCATTGATTTAGTGT gi|6273284|gb|AF191658.1|AF191 AAAATATCTAATAAATTAGATGAATATCAAAGAATCTATTGATTTAGTGT gi|6273287|gb|AF191661.1|AF191 AAAATATCTAATAAATTAGATGAATATCAAAGAATCTATTGATTTAGTGT gi|6273286|gb|AF191660.1|AF191 AAAATATCTAATAAATTAGATGAATATCAAAGAATCTATTGATTTAGTGT gi|6273290|gb|AF191664.1|AF191 AAAATATCTAATAAATTAGATGAATATCAAAGAATCTATTGATTTAGTGT gi|6273289|gb|AF191663.1|AF191 AAAATATCTAATAAATTAGATGAATATCAAAGAATCTATTGATTTAGTAT gi|6273291|gb|AF191665.1|AF191 AAAATATCTAATAAATTAGATGAATATCAAAGAATCTATTGATTTAGTGT ************************************ *********** * gi|6273285|gb|AF191659.1|AF191 ACCAGA gi|6273284|gb|AF191658.1|AF191 ACCAGA gi|6273287|gb|AF191661.1|AF191 ACCAGA gi|6273286|gb|AF191660.1|AF191 ACCAGA gi|6273290|gb|AF191664.1|AF191 ACCAGA gi|6273289|gb|AF191663.1|AF191 ACCAGA gi|6273291|gb|AF191665.1|AF191 ACCAGA ****** """ # noqa : W291 opuntia_fasta = """\ >gi|6273285|gb|AF191659.1|AF191 TATACATTAAAGAAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAATATATA---- ------ATATATTTCAAATTTCCTTATATACCCAAATATAAAAATATCTAATAAATTAGA TGAATATCAAAGAATCCATTGATTTAGTGTACCAGA >gi|6273284|gb|AF191658.1|AF191 TATACATTAAAGAAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAATATATATA-- ------ATATATTTCAAATTTCCTTATATACCCAAATATAAAAATATCTAATAAATTAGA TGAATATCAAAGAATCTATTGATTTAGTGTACCAGA >gi|6273287|gb|AF191661.1|AF191 TATACATTAAAGAAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAATATATA---- ------ATATATTTCAAATTTCCTTATATATCCAAATATAAAAATATCTAATAAATTAGA TGAATATCAAAGAATCTATTGATTTAGTGTACCAGA >gi|6273286|gb|AF191660.1|AF191 TATACATAAAAGAAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAATATATA---- ------ATATATTTATAATTTCCTTATATATCCAAATATAAAAATATCTAATAAATTAGA TGAATATCAAAGAATCTATTGATTTAGTGTACCAGA >gi|6273290|gb|AF191664.1|AF191 TATACATTAAAGGAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAATATATATATA ------ATATATTTCAAATTCCCTTATATATCCAAATATAAAAATATCTAATAAATTAGA TGAATATCAAAGAATCTATTGATTTAGTGTACCAGA >gi|6273289|gb|AF191663.1|AF191 TATACATTAAAGGAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAATATATATATA ------ATATATTTCAAATTCCCTTATATATCCAAATATAAAAATATCTAATAAATTAGA TGAATATCAAAGAATCTATTGATTTAGTATACCAGA >gi|6273291|gb|AF191665.1|AF191 TATACATTAAAGGAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAATATATATATA TATATAATATATTTCAAATTCCCTTATATATCCAAATATAAAAATATCTAATAAATTAGA TGAATATCAAAGAATCTATTGATTTAGTGTACCAGA """ opuntia_fasta_oneline = """\ >gi|6273285|gb|AF191659.1|AF191 TATACATTAAAGAAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAATATATA----------ATATATTTCAAATTTCCTTATATACCCAAATATAAAAATATCTAATAAATTAGATGAATATCAAAGAATCCATTGATTTAGTGTACCAGA >gi|6273284|gb|AF191658.1|AF191 TATACATTAAAGAAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAATATATATA--------ATATATTTCAAATTTCCTTATATACCCAAATATAAAAATATCTAATAAATTAGATGAATATCAAAGAATCTATTGATTTAGTGTACCAGA >gi|6273287|gb|AF191661.1|AF191 TATACATTAAAGAAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAATATATA----------ATATATTTCAAATTTCCTTATATATCCAAATATAAAAATATCTAATAAATTAGATGAATATCAAAGAATCTATTGATTTAGTGTACCAGA >gi|6273286|gb|AF191660.1|AF191 TATACATAAAAGAAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAATATATA----------ATATATTTATAATTTCCTTATATATCCAAATATAAAAATATCTAATAAATTAGATGAATATCAAAGAATCTATTGATTTAGTGTACCAGA >gi|6273290|gb|AF191664.1|AF191 TATACATTAAAGGAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAATATATATATA------ATATATTTCAAATTCCCTTATATATCCAAATATAAAAATATCTAATAAATTAGATGAATATCAAAGAATCTATTGATTTAGTGTACCAGA >gi|6273289|gb|AF191663.1|AF191 TATACATTAAAGGAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAATATATATATA------ATATATTTCAAATTCCCTTATATATCCAAATATAAAAATATCTAATAAATTAGATGAATATCAAAGAATCTATTGATTTAGTATACCAGA >gi|6273291|gb|AF191665.1|AF191 TATACATTAAAGGAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAATATATATATATATATAATATATTTCAAATTCCCTTATATATCCAAATATAAAAATATCTAATAAATTAGATGAATATCAAAGAATCTATTGATTTAGTGTACCAGA """ opuntia_fasta_oneline_with_description = """\ >gi|6273285|gb|AF191659.1|AF191 gi|6273285|gb|AF191659.1|AF191 TATACATTAAAGAAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAATATATA----------ATATATTTCAAATTTCCTTATATACCCAAATATAAAAATATCTAATAAATTAGATGAATATCAAAGAATCCATTGATTTAGTGTACCAGA >gi|6273284|gb|AF191658.1|AF191 gi|6273284|gb|AF191658.1|AF191 TATACATTAAAGAAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAATATATATA--------ATATATTTCAAATTTCCTTATATACCCAAATATAAAAATATCTAATAAATTAGATGAATATCAAAGAATCTATTGATTTAGTGTACCAGA >gi|6273287|gb|AF191661.1|AF191 gi|6273287|gb|AF191661.1|AF191 TATACATTAAAGAAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAATATATA----------ATATATTTCAAATTTCCTTATATATCCAAATATAAAAATATCTAATAAATTAGATGAATATCAAAGAATCTATTGATTTAGTGTACCAGA >gi|6273286|gb|AF191660.1|AF191 gi|6273286|gb|AF191660.1|AF191 TATACATAAAAGAAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAATATATA----------ATATATTTATAATTTCCTTATATATCCAAATATAAAAATATCTAATAAATTAGATGAATATCAAAGAATCTATTGATTTAGTGTACCAGA >gi|6273290|gb|AF191664.1|AF191 gi|6273290|gb|AF191664.1|AF191 TATACATTAAAGGAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAATATATATATA------ATATATTTCAAATTCCCTTATATATCCAAATATAAAAATATCTAATAAATTAGATGAATATCAAAGAATCTATTGATTTAGTGTACCAGA >gi|6273289|gb|AF191663.1|AF191 gi|6273289|gb|AF191663.1|AF191 TATACATTAAAGGAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAATATATATATA------ATATATTTCAAATTCCCTTATATATCCAAATATAAAAATATCTAATAAATTAGATGAATATCAAAGAATCTATTGATTTAGTATACCAGA >gi|6273291|gb|AF191665.1|AF191 gi|6273291|gb|AF191665.1|AF191 TATACATTAAAGGAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAATATATATATATATATAATATATTTCAAATTCCCTTATATATCCAAATATAAAAATATCTAATAAATTAGATGAATATCAAAGAATCTATTGATTTAGTGTACCAGA """ path = os.path.join(os.getcwd(), "Clustalw", "opuntia.aln") msa = AlignIO.read(path, "clustal") opuntia_clustal = opuntia_clustal_header + opuntia_clustal_body self.assertEqual(format(msa, "clustal"), opuntia_clustal) self.assertEqual(format(msa, "fasta"), opuntia_fasta) # create a new-style Alignment object alignment = msa.alignment self.assertEqual(format(alignment, "clustal"), opuntia_clustal_body) # New-style Alignment objects generate FASTA format with the sequence # on one line. Also, the clustal parser in Bio.AlignIO generates # SeqRecords with an (identical) ID and a description; the clustal # parser in Bio.Align generates SeqRecords with an ID only. self.assertEqual( format(alignment, "fasta"), opuntia_fasta_oneline_with_description ) alignment = Align.read(path, "clustal") self.assertEqual(format(alignment, "fasta"), opuntia_fasta_oneline) def test_read_clustal2(self): """Parse an alignment file and get an alignment object.""" clustalw_clustal_header = """\ CLUSTAL X (1.81) multiple sequence alignment """ clustalw_clustal_body = """\ gi|4959044|gb|AAD34209.1|AF069 MENSDSNDKGSDQSAAQRRSQMDRLDREEAFYQFVNNLSEEDYRLMRDNN gi|671626|emb|CAA85685.1| ---------MSPQTETKASVGFKAGVKEYKLTYYTPEYETKDTDILAAFR * *: :: :. :* : :. : . :* :: . gi|4959044|gb|AAD34209.1|AF069 LLGTPGESTEEELLRRLQQIKEGPPPQSPDENRAGESSDDVTNSDSIIDW gi|671626|emb|CAA85685.1| VTPQPG-----------------VPPEEAGAAVAAESSTGT--------- : ** **:... *.*** .. gi|4959044|gb|AAD34209.1|AF069 LNSVRQTGNTTRSRQRGNQSWRAVSRTNPNSGDFRFSLEINVNRNNGSQT gi|671626|emb|CAA85685.1| WTTVWTDGLTSLDRYKG-----RCYHIEPVPG------------------ .:* * *: .* :* : :* .* gi|4959044|gb|AAD34209.1|AF069 SENESEPSTRRLSVENMESSSQRQMENSASESASARPSRAERNSTEAVTE gi|671626|emb|CAA85685.1| -EKDQCICYVAYPLDLFEEGSVTNMFTSIVGNVFGFKALRALRLEDLRIP *::. . .:: :*..* :* .* .. . : . : gi|4959044|gb|AAD34209.1|AF069 VPTTRAQRRARSRSPEHRRTRARAERSMSPLQPTSEIPRRAPTLEQSSEN gi|671626|emb|CAA85685.1| VAYVKTFQGPPHGIQVERDKLNKYGRPLLGCTIKPKLGLSAKNYGRAVYE *. .:: : . .* . : *.: ..:: * . :: : gi|4959044|gb|AAD34209.1|AF069 EPEGSSRTRHHVTLRQQISGPELLGRGLFAASGSRNPSQGTSSSDTGSNS gi|671626|emb|CAA85685.1| CLRGGLDFTKDDENVNSQPFMRWRDRFLFCAEAIYKAQAETGEIKGHYLN .*. :. :. . . .* **.*.. :.. *.. . . gi|4959044|gb|AAD34209.1|AF069 ESSGSGQRPPTIVLDLQVRRVRPGEYRQRDSIASRTRSRSQAPNNTVTYE gi|671626|emb|CAA85685.1| ATAG-----------------------TCEEMIKRAIFARELGVPIVMHD ::* :.: .*: : * :: gi|4959044|gb|AAD34209.1|AF069 SERGGFRRTFSRSERAGVRTYVSTIRIPIRRILNTGLSETTSVAIQTMLR gi|671626|emb|CAA85685.1| YLTGGFTANTSLAHYCRDNGLLLHIHRAMHAVIDRQKNHGMHFRVLAKAL *** . * :. . . : *: .:: ::: .. . : : gi|4959044|gb|AAD34209.1|AF069 QIMTGFGELSYFMYSDSDSEPSASVSSRNVERVESRNGRGSSGGGNSSGS gi|671626|emb|CAA85685.1| RLSGGDHIHSGTVVGKLEGERDITLGFVDLLRDDFIEKDRSRGIYFTQDW :: * * : .. :.* . ::. :: * : : * * :.. gi|4959044|gb|AAD34209.1|AF069 SSSSSPSPSSSGESSESSSKMFEGSSEGGSSGPSRKDGRHRAPVTFDESG gi|671626|emb|CAA85685.1| VSLPGVIPVASG-----------------------------GIHVWHMPA * .. * :** . .:. .. gi|4959044|gb|AAD34209.1|AF069 SLPFFSLAQFFLLNEDDEDQPRGLTKEQIDNLAMRSFGENDALKTCSVCI gi|671626|emb|CAA85685.1| LTEIFGDDSVLQFGGGTLGHPWGNAPGAVANRVA-----------VEACV :*. ..: :. . .:* * : : * . ..*: gi|4959044|gb|AAD34209.1|AF069 TEYTEGDKLRKLPCSHEFHVHCIDRWLSE-NSTCPICRRAVLSSGNRESV gi|671626|emb|CAA85685.1| KARNEG---RDLAAEGNAIIREACKWSPELAAACEVWKEIKFEFPAMD-- . .** *.*... : :: :* .* ::* : :. :. : gi|4959044|gb|AAD34209.1|AF069 V gi|671626|emb|CAA85685.1| - """ # noqa : W291 path = os.path.join(os.curdir, "Clustalw", "clustalw.aln") msa = AlignIO.read(path, "clustal") clustalw_clustal = clustalw_clustal_header + clustalw_clustal_body self.assertEqual(format(msa, "clustal"), clustalw_clustal) # create a new-style Alignment object alignment = msa.alignment self.assertEqual(format(alignment, "clustal"), clustalw_clustal_body) def test_read_write_clustal(self): """Test the base alignment stuff.""" path = os.path.join(os.getcwd(), "Clustalw", "opuntia.aln") msa = AlignIO.read(path, "clustal") self.assertEqual(len(msa), 7) seq_record = msa[0] self.assertEqual(seq_record.description, "gi|6273285|gb|AF191659.1|AF191") self.assertEqual( seq_record.seq, Seq( "TATACATTAAAGAAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAATATATA----------ATATATTTCAAATTTCCTTATATACCCAAATATAAAAATATCTAATAAATTAGATGAATATCAAAGAATCCATTGATTTAGTGTACCAGA" ), ) seq_record = msa[1] self.assertEqual(seq_record.description, "gi|6273284|gb|AF191658.1|AF191") self.assertEqual( seq_record.seq, "TATACATTAAAGAAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAATATATATA--------ATATATTTCAAATTTCCTTATATACCCAAATATAAAAATATCTAATAAATTAGATGAATATCAAAGAATCTATTGATTTAGTGTACCAGA", ) seq_record = msa[2] self.assertEqual(seq_record.description, "gi|6273287|gb|AF191661.1|AF191") self.assertEqual( seq_record.seq, "TATACATTAAAGAAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAATATATA----------ATATATTTCAAATTTCCTTATATATCCAAATATAAAAATATCTAATAAATTAGATGAATATCAAAGAATCTATTGATTTAGTGTACCAGA", ) seq_record = msa[3] self.assertEqual(seq_record.description, "gi|6273286|gb|AF191660.1|AF191") self.assertEqual( seq_record.seq, "TATACATAAAAGAAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAATATATA----------ATATATTTATAATTTCCTTATATATCCAAATATAAAAATATCTAATAAATTAGATGAATATCAAAGAATCTATTGATTTAGTGTACCAGA", ) seq_record = msa[4] self.assertEqual(seq_record.description, "gi|6273290|gb|AF191664.1|AF191") self.assertEqual( seq_record.seq, "TATACATTAAAGGAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAATATATATATA------ATATATTTCAAATTCCCTTATATATCCAAATATAAAAATATCTAATAAATTAGATGAATATCAAAGAATCTATTGATTTAGTGTACCAGA", ) seq_record = msa[5] self.assertEqual(seq_record.description, "gi|6273289|gb|AF191663.1|AF191") self.assertEqual( seq_record.seq, "TATACATTAAAGGAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAATATATATATA------ATATATTTCAAATTCCCTTATATATCCAAATATAAAAATATCTAATAAATTAGATGAATATCAAAGAATCTATTGATTTAGTATACCAGA", ) seq_record = msa[6] self.assertEqual(seq_record.description, "gi|6273291|gb|AF191665.1|AF191") self.assertEqual( seq_record.seq, "TATACATTAAAGGAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAATATATATATATATATAATATATTTCAAATTCCCTTATATATCCAAATATAAAAATATCTAATAAATTAGATGAATATCAAAGAATCTATTGATTTAGTGTACCAGA", ) self.assertEqual(msa.get_alignment_length(), 156) align_info = AlignInfo.SummaryInfo(msa) with self.assertWarns(BiopythonDeprecationWarning): consensus = align_info.dumb_consensus(ambiguous="N") self.assertIsInstance(consensus, Seq) self.assertEqual( consensus, "TATACATTAAAGNAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAATATATATATATATATAATATATTTCAAATTNCCTTATATATCCAAATATAAAAATATCTAATAAATTAGATGAATATCAAAGAATCTATTGATTTAGTGTACCAGA", ) with self.assertWarns(BiopythonDeprecationWarning): dictionary = align_info.replacement_dictionary( skip_chars=None, letters="ACGT" ) self.assertEqual(len(dictionary), 16) self.assertAlmostEqual(dictionary[("A", "A")], 1395.0, places=1) self.assertAlmostEqual(dictionary[("A", "C")], 3.0, places=1) self.assertAlmostEqual(dictionary[("A", "G")], 13.0, places=1) self.assertAlmostEqual(dictionary[("A", "T")], 6.0, places=1) self.assertAlmostEqual(dictionary[("C", "A")], 3.0, places=1) self.assertAlmostEqual(dictionary[("C", "C")], 271.0, places=1) self.assertAlmostEqual(dictionary[("C", "G")], 0, places=1) self.assertAlmostEqual(dictionary[("C", "T")], 16.0, places=1) self.assertAlmostEqual(dictionary[("G", "A")], 5.0, places=1) self.assertAlmostEqual(dictionary[("G", "C")], 0, places=1) self.assertAlmostEqual(dictionary[("G", "G")], 480.0, places=1) self.assertAlmostEqual(dictionary[("G", "T")], 0, places=1) self.assertAlmostEqual(dictionary[("T", "A")], 6.0, places=1) self.assertAlmostEqual(dictionary[("T", "C")], 12.0, places=1) self.assertAlmostEqual(dictionary[("T", "G")], 0, places=1) self.assertAlmostEqual(dictionary[("T", "T")], 874.0, places=1) alignment = msa.alignment dictionary = alignment.substitutions self.assertEqual(len(dictionary), 4) self.assertEqual(dictionary.shape, (4, 4)) self.assertEqual(len(dictionary.keys()), 16) self.assertAlmostEqual(dictionary[("A", "A")], 1395) self.assertAlmostEqual(dictionary[("A", "C")], 3) self.assertAlmostEqual(dictionary[("A", "G")], 13) self.assertAlmostEqual(dictionary[("A", "T")], 6) self.assertAlmostEqual(dictionary[("C", "A")], 3) self.assertAlmostEqual(dictionary[("C", "C")], 271) self.assertAlmostEqual(dictionary[("C", "G")], 0) self.assertAlmostEqual(dictionary[("C", "T")], 16) self.assertAlmostEqual(dictionary[("G", "A")], 5) self.assertAlmostEqual(dictionary[("G", "C")], 0) self.assertAlmostEqual(dictionary[("G", "G")], 480) self.assertAlmostEqual(dictionary[("G", "T")], 0) self.assertAlmostEqual(dictionary[("T", "A")], 6) self.assertAlmostEqual(dictionary[("T", "C")], 12) self.assertAlmostEqual(dictionary[("T", "G")], 0) self.assertAlmostEqual(dictionary[("T", "T")], 874) with self.assertWarns(BiopythonDeprecationWarning): matrix = align_info.pos_specific_score_matrix(consensus, ["N", "-"]) motif = motifs.Motif("ACGT", alignment) counts = motif.counts for i in range(alignment.length): for letter in "ACGT": self.assertAlmostEqual(counts[letter][i], matrix[i][letter]) self.assertEqual(counts.calculate_consensus(identity=0.7), consensus) self.assertEqual( str(matrix), """\ A C G T T 0.0 0.0 0.0 7.0 A 7.0 0.0 0.0 0.0 T 0.0 0.0 0.0 7.0 A 7.0 0.0 0.0 0.0 C 0.0 7.0 0.0 0.0 A 7.0 0.0 0.0 0.0 T 0.0 0.0 0.0 7.0 T 1.0 0.0 0.0 6.0 A 7.0 0.0 0.0 0.0 A 7.0 0.0 0.0 0.0 A 7.0 0.0 0.0 0.0 G 0.0 0.0 7.0 0.0 N 4.0 0.0 3.0 0.0 A 7.0 0.0 0.0 0.0 G 0.0 0.0 7.0 0.0 G 0.0 0.0 7.0 0.0 G 0.0 0.0 7.0 0.0 G 0.0 0.0 7.0 0.0 G 0.0 0.0 7.0 0.0 A 7.0 0.0 0.0 0.0 T 0.0 0.0 0.0 7.0 G 0.0 0.0 7.0 0.0 C 0.0 7.0 0.0 0.0 G 0.0 0.0 7.0 0.0 G 0.0 0.0 7.0 0.0 A 7.0 0.0 0.0 0.0 T 0.0 0.0 0.0 7.0 A 7.0 0.0 0.0 0.0 A 7.0 0.0 0.0 0.0 A 7.0 0.0 0.0 0.0 T 0.0 0.0 0.0 7.0 G 0.0 0.0 7.0 0.0 G 0.0 0.0 7.0 0.0 A 7.0 0.0 0.0 0.0 A 7.0 0.0 0.0 0.0 A 7.0 0.0 0.0 0.0 G 0.0 0.0 7.0 0.0 G 0.0 0.0 7.0 0.0 C 0.0 7.0 0.0 0.0 G 0.0 0.0 7.0 0.0 A 7.0 0.0 0.0 0.0 A 7.0 0.0 0.0 0.0 A 7.0 0.0 0.0 0.0 G 0.0 0.0 7.0 0.0 A 7.0 0.0 0.0 0.0 A 7.0 0.0 0.0 0.0 A 7.0 0.0 0.0 0.0 G 0.0 0.0 7.0 0.0 A 7.0 0.0 0.0 0.0 A 7.0 0.0 0.0 0.0 T 0.0 0.0 0.0 7.0 A 7.0 0.0 0.0 0.0 T 0.0 0.0 0.0 7.0 A 7.0 0.0 0.0 0.0 T 0.0 0.0 0.0 7.0 A 7.0 0.0 0.0 0.0 T 0.0 0.0 0.0 4.0 A 4.0 0.0 0.0 0.0 T 0.0 0.0 0.0 3.0 A 3.0 0.0 0.0 0.0 T 0.0 0.0 0.0 1.0 A 1.0 0.0 0.0 0.0 T 0.0 0.0 0.0 1.0 A 1.0 0.0 0.0 0.0 T 0.0 0.0 0.0 1.0 A 1.0 0.0 0.0 0.0 A 7.0 0.0 0.0 0.0 T 0.0 0.0 0.0 7.0 A 7.0 0.0 0.0 0.0 T 0.0 0.0 0.0 7.0 A 7.0 0.0 0.0 0.0 T 0.0 0.0 0.0 7.0 T 0.0 0.0 0.0 7.0 T 0.0 0.0 0.0 7.0 C 1.0 6.0 0.0 0.0 A 6.0 0.0 0.0 1.0 A 7.0 0.0 0.0 0.0 A 7.0 0.0 0.0 0.0 T 0.0 0.0 0.0 7.0 T 0.0 0.0 0.0 7.0 N 0.0 3.0 0.0 4.0 C 0.0 7.0 0.0 0.0 C 0.0 7.0 0.0 0.0 T 0.0 0.0 0.0 7.0 T 0.0 0.0 0.0 7.0 A 7.0 0.0 0.0 0.0 T 0.0 0.0 0.0 7.0 A 7.0 0.0 0.0 0.0 T 0.0 0.0 0.0 7.0 A 7.0 0.0 0.0 0.0 T 0.0 2.0 0.0 5.0 C 0.0 7.0 0.0 0.0 C 0.0 7.0 0.0 0.0 A 7.0 0.0 0.0 0.0 A 7.0 0.0 0.0 0.0 A 7.0 0.0 0.0 0.0 T 0.0 0.0 0.0 7.0 A 7.0 0.0 0.0 0.0 T 0.0 0.0 0.0 7.0 A 7.0 0.0 0.0 0.0 A 7.0 0.0 0.0 0.0 A 7.0 0.0 0.0 0.0 A 7.0 0.0 0.0 0.0 A 7.0 0.0 0.0 0.0 T 0.0 0.0 0.0 7.0 A 7.0 0.0 0.0 0.0 T 0.0 0.0 0.0 7.0 C 0.0 7.0 0.0 0.0 T 0.0 0.0 0.0 7.0 A 7.0 0.0 0.0 0.0 A 7.0 0.0 0.0 0.0 T 0.0 0.0 0.0 7.0 A 7.0 0.0 0.0 0.0 A 7.0 0.0 0.0 0.0 A 7.0 0.0 0.0 0.0 T 0.0 0.0 0.0 7.0 T 0.0 0.0 0.0 7.0 A 7.0 0.0 0.0 0.0 G 0.0 0.0 7.0 0.0 A 7.0 0.0 0.0 0.0 T 0.0 0.0 0.0 7.0 G 0.0 0.0 7.0 0.0 A 7.0 0.0 0.0 0.0 A 7.0 0.0 0.0 0.0 T 0.0 0.0 0.0 7.0 A 7.0 0.0 0.0 0.0 T 0.0 0.0 0.0 7.0 C 0.0 7.0 0.0 0.0 A 7.0 0.0 0.0 0.0 A 7.0 0.0 0.0 0.0 A 7.0 0.0 0.0 0.0 G 0.0 0.0 7.0 0.0 A 7.0 0.0 0.0 0.0 A 7.0 0.0 0.0 0.0 T 0.0 0.0 0.0 7.0 C 0.0 7.0 0.0 0.0 T 0.0 1.0 0.0 6.0 A 7.0 0.0 0.0 0.0 T 0.0 0.0 0.0 7.0 T 0.0 0.0 0.0 7.0 G 0.0 0.0 7.0 0.0 A 7.0 0.0 0.0 0.0 T 0.0 0.0 0.0 7.0 T 0.0 0.0 0.0 7.0 T 0.0 0.0 0.0 7.0 A 7.0 0.0 0.0 0.0 G 0.0 0.0 7.0 0.0 T 0.0 0.0 0.0 7.0 G 1.0 0.0 6.0 0.0 T 0.0 0.0 0.0 7.0 A 7.0 0.0 0.0 0.0 C 0.0 7.0 0.0 0.0 C 0.0 7.0 0.0 0.0 A 7.0 0.0 0.0 0.0 G 0.0 0.0 7.0 0.0 A 7.0 0.0 0.0 0.0 """, ) with self.assertWarns(BiopythonDeprecationWarning): matrix = align_info.pos_specific_score_matrix(chars_to_ignore=["N", "-"]) alignment = msa.alignment motif = motifs.Motif("ACGT", alignment) counts = motif.counts for i in range(alignment.length): for letter in "ACGT": self.assertAlmostEqual(counts[letter][i], matrix[i][letter]) self.assertEqual( str(matrix), """\ A C G T T 0.0 0.0 0.0 7.0 A 7.0 0.0 0.0 0.0 T 0.0 0.0 0.0 7.0 A 7.0 0.0 0.0 0.0 C 0.0 7.0 0.0 0.0 A 7.0 0.0 0.0 0.0 T 0.0 0.0 0.0 7.0 T 1.0 0.0 0.0 6.0 A 7.0 0.0 0.0 0.0 A 7.0 0.0 0.0 0.0 A 7.0 0.0 0.0 0.0 G 0.0 0.0 7.0 0.0 X 4.0 0.0 3.0 0.0 A 7.0 0.0 0.0 0.0 G 0.0 0.0 7.0 0.0 G 0.0 0.0 7.0 0.0 G 0.0 0.0 7.0 0.0 G 0.0 0.0 7.0 0.0 G 0.0 0.0 7.0 0.0 A 7.0 0.0 0.0 0.0 T 0.0 0.0 0.0 7.0 G 0.0 0.0 7.0 0.0 C 0.0 7.0 0.0 0.0 G 0.0 0.0 7.0 0.0 G 0.0 0.0 7.0 0.0 A 7.0 0.0 0.0 0.0 T 0.0 0.0 0.0 7.0 A 7.0 0.0 0.0 0.0 A 7.0 0.0 0.0 0.0 A 7.0 0.0 0.0 0.0 T 0.0 0.0 0.0 7.0 G 0.0 0.0 7.0 0.0 G 0.0 0.0 7.0 0.0 A 7.0 0.0 0.0 0.0 A 7.0 0.0 0.0 0.0 A 7.0 0.0 0.0 0.0 G 0.0 0.0 7.0 0.0 G 0.0 0.0 7.0 0.0 C 0.0 7.0 0.0 0.0 G 0.0 0.0 7.0 0.0 A 7.0 0.0 0.0 0.0 A 7.0 0.0 0.0 0.0 A 7.0 0.0 0.0 0.0 G 0.0 0.0 7.0 0.0 A 7.0 0.0 0.0 0.0 A 7.0 0.0 0.0 0.0 A 7.0 0.0 0.0 0.0 G 0.0 0.0 7.0 0.0 A 7.0 0.0 0.0 0.0 A 7.0 0.0 0.0 0.0 T 0.0 0.0 0.0 7.0 A 7.0 0.0 0.0 0.0 T 0.0 0.0 0.0 7.0 A 7.0 0.0 0.0 0.0 T 0.0 0.0 0.0 7.0 A 7.0 0.0 0.0 0.0 T 0.0 0.0 0.0 4.0 A 4.0 0.0 0.0 0.0 T 0.0 0.0 0.0 3.0 A 3.0 0.0 0.0 0.0 T 0.0 0.0 0.0 1.0 A 1.0 0.0 0.0 0.0 T 0.0 0.0 0.0 1.0 A 1.0 0.0 0.0 0.0 T 0.0 0.0 0.0 1.0 A 1.0 0.0 0.0 0.0 A 7.0 0.0 0.0 0.0 T 0.0 0.0 0.0 7.0 A 7.0 0.0 0.0 0.0 T 0.0 0.0 0.0 7.0 A 7.0 0.0 0.0 0.0 T 0.0 0.0 0.0 7.0 T 0.0 0.0 0.0 7.0 T 0.0 0.0 0.0 7.0 C 1.0 6.0 0.0 0.0 A 6.0 0.0 0.0 1.0 A 7.0 0.0 0.0 0.0 A 7.0 0.0 0.0 0.0 T 0.0 0.0 0.0 7.0 T 0.0 0.0 0.0 7.0 X 0.0 3.0 0.0 4.0 C 0.0 7.0 0.0 0.0 C 0.0 7.0 0.0 0.0 T 0.0 0.0 0.0 7.0 T 0.0 0.0 0.0 7.0 A 7.0 0.0 0.0 0.0 T 0.0 0.0 0.0 7.0 A 7.0 0.0 0.0 0.0 T 0.0 0.0 0.0 7.0 A 7.0 0.0 0.0 0.0 T 0.0 2.0 0.0 5.0 C 0.0 7.0 0.0 0.0 C 0.0 7.0 0.0 0.0 A 7.0 0.0 0.0 0.0 A 7.0 0.0 0.0 0.0 A 7.0 0.0 0.0 0.0 T 0.0 0.0 0.0 7.0 A 7.0 0.0 0.0 0.0 T 0.0 0.0 0.0 7.0 A 7.0 0.0 0.0 0.0 A 7.0 0.0 0.0 0.0 A 7.0 0.0 0.0 0.0 A 7.0 0.0 0.0 0.0 A 7.0 0.0 0.0 0.0 T 0.0 0.0 0.0 7.0 A 7.0 0.0 0.0 0.0 T 0.0 0.0 0.0 7.0 C 0.0 7.0 0.0 0.0 T 0.0 0.0 0.0 7.0 A 7.0 0.0 0.0 0.0 A 7.0 0.0 0.0 0.0 T 0.0 0.0 0.0 7.0 A 7.0 0.0 0.0 0.0 A 7.0 0.0 0.0 0.0 A 7.0 0.0 0.0 0.0 T 0.0 0.0 0.0 7.0 T 0.0 0.0 0.0 7.0 A 7.0 0.0 0.0 0.0 G 0.0 0.0 7.0 0.0 A 7.0 0.0 0.0 0.0 T 0.0 0.0 0.0 7.0 G 0.0 0.0 7.0 0.0 A 7.0 0.0 0.0 0.0 A 7.0 0.0 0.0 0.0 T 0.0 0.0 0.0 7.0 A 7.0 0.0 0.0 0.0 T 0.0 0.0 0.0 7.0 C 0.0 7.0 0.0 0.0 A 7.0 0.0 0.0 0.0 A 7.0 0.0 0.0 0.0 A 7.0 0.0 0.0 0.0 G 0.0 0.0 7.0 0.0 A 7.0 0.0 0.0 0.0 A 7.0 0.0 0.0 0.0 T 0.0 0.0 0.0 7.0 C 0.0 7.0 0.0 0.0 T 0.0 1.0 0.0 6.0 A 7.0 0.0 0.0 0.0 T 0.0 0.0 0.0 7.0 T 0.0 0.0 0.0 7.0 G 0.0 0.0 7.0 0.0 A 7.0 0.0 0.0 0.0 T 0.0 0.0 0.0 7.0 T 0.0 0.0 0.0 7.0 T 0.0 0.0 0.0 7.0 A 7.0 0.0 0.0 0.0 G 0.0 0.0 7.0 0.0 T 0.0 0.0 0.0 7.0 G 1.0 0.0 6.0 0.0 T 0.0 0.0 0.0 7.0 A 7.0 0.0 0.0 0.0 C 0.0 7.0 0.0 0.0 C 0.0 7.0 0.0 0.0 A 7.0 0.0 0.0 0.0 G 0.0 0.0 7.0 0.0 A 7.0 0.0 0.0 0.0 """, ) second_seq = msa[1].seq with self.assertWarns(BiopythonDeprecationWarning): matrix = align_info.pos_specific_score_matrix(second_seq, ["N", "-"]) alignment = msa.alignment motif = motifs.Motif("ACGT", alignment) counts = motif.counts for i in range(alignment.length): for letter in "ACGT": self.assertAlmostEqual(counts[letter][i], matrix[i][letter]) self.assertEqual( str(matrix), """\ A C G T T 0.0 0.0 0.0 7.0 A 7.0 0.0 0.0 0.0 T 0.0 0.0 0.0 7.0 A 7.0 0.0 0.0 0.0 C 0.0 7.0 0.0 0.0 A 7.0 0.0 0.0 0.0 T 0.0 0.0 0.0 7.0 T 1.0 0.0 0.0 6.0 A 7.0 0.0 0.0 0.0 A 7.0 0.0 0.0 0.0 A 7.0 0.0 0.0 0.0 G 0.0 0.0 7.0 0.0 A 4.0 0.0 3.0 0.0 A 7.0 0.0 0.0 0.0 G 0.0 0.0 7.0 0.0 G 0.0 0.0 7.0 0.0 G 0.0 0.0 7.0 0.0 G 0.0 0.0 7.0 0.0 G 0.0 0.0 7.0 0.0 A 7.0 0.0 0.0 0.0 T 0.0 0.0 0.0 7.0 G 0.0 0.0 7.0 0.0 C 0.0 7.0 0.0 0.0 G 0.0 0.0 7.0 0.0 G 0.0 0.0 7.0 0.0 A 7.0 0.0 0.0 0.0 T 0.0 0.0 0.0 7.0 A 7.0 0.0 0.0 0.0 A 7.0 0.0 0.0 0.0 A 7.0 0.0 0.0 0.0 T 0.0 0.0 0.0 7.0 G 0.0 0.0 7.0 0.0 G 0.0 0.0 7.0 0.0 A 7.0 0.0 0.0 0.0 A 7.0 0.0 0.0 0.0 A 7.0 0.0 0.0 0.0 G 0.0 0.0 7.0 0.0 G 0.0 0.0 7.0 0.0 C 0.0 7.0 0.0 0.0 G 0.0 0.0 7.0 0.0 A 7.0 0.0 0.0 0.0 A 7.0 0.0 0.0 0.0 A 7.0 0.0 0.0 0.0 G 0.0 0.0 7.0 0.0 A 7.0 0.0 0.0 0.0 A 7.0 0.0 0.0 0.0 A 7.0 0.0 0.0 0.0 G 0.0 0.0 7.0 0.0 A 7.0 0.0 0.0 0.0 A 7.0 0.0 0.0 0.0 T 0.0 0.0 0.0 7.0 A 7.0 0.0 0.0 0.0 T 0.0 0.0 0.0 7.0 A 7.0 0.0 0.0 0.0 T 0.0 0.0 0.0 7.0 A 7.0 0.0 0.0 0.0 T 0.0 0.0 0.0 4.0 A 4.0 0.0 0.0 0.0 - 0.0 0.0 0.0 3.0 - 3.0 0.0 0.0 0.0 - 0.0 0.0 0.0 1.0 - 1.0 0.0 0.0 0.0 - 0.0 0.0 0.0 1.0 - 1.0 0.0 0.0 0.0 - 0.0 0.0 0.0 1.0 - 1.0 0.0 0.0 0.0 A 7.0 0.0 0.0 0.0 T 0.0 0.0 0.0 7.0 A 7.0 0.0 0.0 0.0 T 0.0 0.0 0.0 7.0 A 7.0 0.0 0.0 0.0 T 0.0 0.0 0.0 7.0 T 0.0 0.0 0.0 7.0 T 0.0 0.0 0.0 7.0 C 1.0 6.0 0.0 0.0 A 6.0 0.0 0.0 1.0 A 7.0 0.0 0.0 0.0 A 7.0 0.0 0.0 0.0 T 0.0 0.0 0.0 7.0 T 0.0 0.0 0.0 7.0 T 0.0 3.0 0.0 4.0 C 0.0 7.0 0.0 0.0 C 0.0 7.0 0.0 0.0 T 0.0 0.0 0.0 7.0 T 0.0 0.0 0.0 7.0 A 7.0 0.0 0.0 0.0 T 0.0 0.0 0.0 7.0 A 7.0 0.0 0.0 0.0 T 0.0 0.0 0.0 7.0 A 7.0 0.0 0.0 0.0 C 0.0 2.0 0.0 5.0 C 0.0 7.0 0.0 0.0 C 0.0 7.0 0.0 0.0 A 7.0 0.0 0.0 0.0 A 7.0 0.0 0.0 0.0 A 7.0 0.0 0.0 0.0 T 0.0 0.0 0.0 7.0 A 7.0 0.0 0.0 0.0 T 0.0 0.0 0.0 7.0 A 7.0 0.0 0.0 0.0 A 7.0 0.0 0.0 0.0 A 7.0 0.0 0.0 0.0 A 7.0 0.0 0.0 0.0 A 7.0 0.0 0.0 0.0 T 0.0 0.0 0.0 7.0 A 7.0 0.0 0.0 0.0 T 0.0 0.0 0.0 7.0 C 0.0 7.0 0.0 0.0 T 0.0 0.0 0.0 7.0 A 7.0 0.0 0.0 0.0 A 7.0 0.0 0.0 0.0 T 0.0 0.0 0.0 7.0 A 7.0 0.0 0.0 0.0 A 7.0 0.0 0.0 0.0 A 7.0 0.0 0.0 0.0 T 0.0 0.0 0.0 7.0 T 0.0 0.0 0.0 7.0 A 7.0 0.0 0.0 0.0 G 0.0 0.0 7.0 0.0 A 7.0 0.0 0.0 0.0 T 0.0 0.0 0.0 7.0 G 0.0 0.0 7.0 0.0 A 7.0 0.0 0.0 0.0 A 7.0 0.0 0.0 0.0 T 0.0 0.0 0.0 7.0 A 7.0 0.0 0.0 0.0 T 0.0 0.0 0.0 7.0 C 0.0 7.0 0.0 0.0 A 7.0 0.0 0.0 0.0 A 7.0 0.0 0.0 0.0 A 7.0 0.0 0.0 0.0 G 0.0 0.0 7.0 0.0 A 7.0 0.0 0.0 0.0 A 7.0 0.0 0.0 0.0 T 0.0 0.0 0.0 7.0 C 0.0 7.0 0.0 0.0 T 0.0 1.0 0.0 6.0 A 7.0 0.0 0.0 0.0 T 0.0 0.0 0.0 7.0 T 0.0 0.0 0.0 7.0 G 0.0 0.0 7.0 0.0 A 7.0 0.0 0.0 0.0 T 0.0 0.0 0.0 7.0 T 0.0 0.0 0.0 7.0 T 0.0 0.0 0.0 7.0 A 7.0 0.0 0.0 0.0 G 0.0 0.0 7.0 0.0 T 0.0 0.0 0.0 7.0 G 1.0 0.0 6.0 0.0 T 0.0 0.0 0.0 7.0 A 7.0 0.0 0.0 0.0 C 0.0 7.0 0.0 0.0 C 0.0 7.0 0.0 0.0 A 7.0 0.0 0.0 0.0 G 0.0 0.0 7.0 0.0 A 7.0 0.0 0.0 0.0 """, ) e_freq_table = {"G": 0.25, "C": 0.25, "A": 0.25, "T": 0.25} with self.assertWarns(BiopythonDeprecationWarning): value = align_info.information_content( 5, 50, chars_to_ignore=["N"], e_freq_table=e_freq_table ) self.assertAlmostEqual(value, 88.42309908538343) # MultipleSeqAlignment value = sum(motif[5:50].relative_entropy) self.assertAlmostEqual(value, 88.42309908538343) # Alignment with self.assertWarns(BiopythonDeprecationWarning): value = align_info.information_content( e_freq_table=e_freq_table, chars_to_ignore=["N", "-"] ) self.assertAlmostEqual(value, 306.2080592664532) # MultipleSeqAlignment relative_entropy = motif.relative_entropy value = sum(relative_entropy) self.assertAlmostEqual(value, 306.2080592664532) # Alignment self.assertEqual(align_info.get_column(1), "AAAAAAA") self.assertAlmostEqual(align_info.ic_vector[1], 2.00) self.assertEqual(align_info.get_column(7), "TTTATTT") self.assertAlmostEqual(align_info.ic_vector[7], 1.4083272214176725) self.assertAlmostEqual(relative_entropy[0], 2.0) self.assertAlmostEqual(relative_entropy[1], 2.0) self.assertAlmostEqual(relative_entropy[2], 2.0) self.assertAlmostEqual(relative_entropy[3], 2.0) self.assertAlmostEqual(relative_entropy[4], 2.0) self.assertAlmostEqual(relative_entropy[5], 2.0) self.assertAlmostEqual(relative_entropy[6], 2.0) self.assertAlmostEqual(relative_entropy[7], 1.4083272214176723) self.assertAlmostEqual(relative_entropy[8], 2.0) self.assertAlmostEqual(relative_entropy[9], 2.0) self.assertAlmostEqual(relative_entropy[10], 2.0) self.assertAlmostEqual(relative_entropy[11], 2.0) self.assertAlmostEqual(relative_entropy[12], 1.0147718639657484) self.assertAlmostEqual(relative_entropy[13], 2.0) self.assertAlmostEqual(relative_entropy[14], 2.0) self.assertAlmostEqual(relative_entropy[15], 2.0) self.assertAlmostEqual(relative_entropy[16], 2.0) self.assertAlmostEqual(relative_entropy[17], 2.0) self.assertAlmostEqual(relative_entropy[18], 2.0) self.assertAlmostEqual(relative_entropy[19], 2.0) self.assertAlmostEqual(relative_entropy[20], 2.0) self.assertAlmostEqual(relative_entropy[21], 2.0) self.assertAlmostEqual(relative_entropy[22], 2.0) self.assertAlmostEqual(relative_entropy[23], 2.0) self.assertAlmostEqual(relative_entropy[24], 2.0) self.assertAlmostEqual(relative_entropy[25], 2.0) self.assertAlmostEqual(relative_entropy[26], 2.0) self.assertAlmostEqual(relative_entropy[27], 2.0) self.assertAlmostEqual(relative_entropy[28], 2.0) self.assertAlmostEqual(relative_entropy[29], 2.0) self.assertAlmostEqual(relative_entropy[30], 2.0) self.assertAlmostEqual(relative_entropy[31], 2.0) self.assertAlmostEqual(relative_entropy[32], 2.0) self.assertAlmostEqual(relative_entropy[33], 2.0) self.assertAlmostEqual(relative_entropy[34], 2.0) self.assertAlmostEqual(relative_entropy[35], 2.0) self.assertAlmostEqual(relative_entropy[36], 2.0) self.assertAlmostEqual(relative_entropy[37], 2.0) self.assertAlmostEqual(relative_entropy[38], 2.0) self.assertAlmostEqual(relative_entropy[39], 2.0) self.assertAlmostEqual(relative_entropy[40], 2.0) self.assertAlmostEqual(relative_entropy[41], 2.0) self.assertAlmostEqual(relative_entropy[42], 2.0) self.assertAlmostEqual(relative_entropy[43], 2.0) self.assertAlmostEqual(relative_entropy[44], 2.0) self.assertAlmostEqual(relative_entropy[45], 2.0) self.assertAlmostEqual(relative_entropy[46], 2.0) self.assertAlmostEqual(relative_entropy[47], 2.0) self.assertAlmostEqual(relative_entropy[48], 2.0) self.assertAlmostEqual(relative_entropy[49], 2.0) self.assertAlmostEqual(relative_entropy[50], 2.0) self.assertAlmostEqual(relative_entropy[51], 2.0) self.assertAlmostEqual(relative_entropy[52], 2.0) self.assertAlmostEqual(relative_entropy[53], 2.0) self.assertAlmostEqual(relative_entropy[54], 2.0) self.assertAlmostEqual(relative_entropy[55], 2.0) self.assertAlmostEqual(relative_entropy[56], 2.0) self.assertAlmostEqual(relative_entropy[57], 2.0) self.assertAlmostEqual(relative_entropy[58], 2.0) self.assertAlmostEqual(relative_entropy[59], 2.0) self.assertAlmostEqual(relative_entropy[60], 2.0) self.assertAlmostEqual(relative_entropy[61], 2.0) self.assertAlmostEqual(relative_entropy[62], 2.0) self.assertAlmostEqual(relative_entropy[63], 2.0) self.assertAlmostEqual(relative_entropy[64], 2.0) self.assertAlmostEqual(relative_entropy[65], 2.0) self.assertAlmostEqual(relative_entropy[66], 2.0) self.assertAlmostEqual(relative_entropy[67], 2.0) self.assertAlmostEqual(relative_entropy[68], 2.0) self.assertAlmostEqual(relative_entropy[69], 2.0) self.assertAlmostEqual(relative_entropy[70], 2.0) self.assertAlmostEqual(relative_entropy[71], 2.0) self.assertAlmostEqual(relative_entropy[72], 2.0) self.assertAlmostEqual(relative_entropy[73], 2.0) self.assertAlmostEqual(relative_entropy[74], 1.4083272214176723) self.assertAlmostEqual(relative_entropy[75], 1.4083272214176723) self.assertAlmostEqual(relative_entropy[76], 2.0) self.assertAlmostEqual(relative_entropy[77], 2.0) self.assertAlmostEqual(relative_entropy[78], 2.0) self.assertAlmostEqual(relative_entropy[79], 2.0) self.assertAlmostEqual(relative_entropy[80], 1.0147718639657484) self.assertAlmostEqual(relative_entropy[81], 2.0) self.assertAlmostEqual(relative_entropy[82], 2.0) self.assertAlmostEqual(relative_entropy[83], 2.0) self.assertAlmostEqual(relative_entropy[84], 2.0) self.assertAlmostEqual(relative_entropy[85], 2.0) self.assertAlmostEqual(relative_entropy[86], 2.0) self.assertAlmostEqual(relative_entropy[87], 2.0) self.assertAlmostEqual(relative_entropy[88], 2.0) self.assertAlmostEqual(relative_entropy[89], 2.0) self.assertAlmostEqual(relative_entropy[90], 1.136879431433369) self.assertAlmostEqual(relative_entropy[91], 2.0) self.assertAlmostEqual(relative_entropy[92], 2.0) self.assertAlmostEqual(relative_entropy[93], 2.0) self.assertAlmostEqual(relative_entropy[94], 2.0) self.assertAlmostEqual(relative_entropy[95], 2.0) self.assertAlmostEqual(relative_entropy[96], 2.0) self.assertAlmostEqual(relative_entropy[97], 2.0) self.assertAlmostEqual(relative_entropy[98], 2.0) self.assertAlmostEqual(relative_entropy[99], 2.0) self.assertAlmostEqual(relative_entropy[100], 2.0) self.assertAlmostEqual(relative_entropy[101], 2.0) self.assertAlmostEqual(relative_entropy[102], 2.0) self.assertAlmostEqual(relative_entropy[103], 2.0) self.assertAlmostEqual(relative_entropy[104], 2.0) self.assertAlmostEqual(relative_entropy[105], 2.0) self.assertAlmostEqual(relative_entropy[106], 2.0) self.assertAlmostEqual(relative_entropy[107], 2.0) self.assertAlmostEqual(relative_entropy[108], 2.0) self.assertAlmostEqual(relative_entropy[109], 2.0) self.assertAlmostEqual(relative_entropy[110], 2.0) self.assertAlmostEqual(relative_entropy[111], 2.0) self.assertAlmostEqual(relative_entropy[112], 2.0) self.assertAlmostEqual(relative_entropy[113], 2.0) self.assertAlmostEqual(relative_entropy[114], 2.0) self.assertAlmostEqual(relative_entropy[115], 2.0) self.assertAlmostEqual(relative_entropy[116], 2.0) self.assertAlmostEqual(relative_entropy[117], 2.0) self.assertAlmostEqual(relative_entropy[118], 2.0) self.assertAlmostEqual(relative_entropy[119], 2.0) self.assertAlmostEqual(relative_entropy[120], 2.0) self.assertAlmostEqual(relative_entropy[121], 2.0) self.assertAlmostEqual(relative_entropy[122], 2.0) self.assertAlmostEqual(relative_entropy[123], 2.0) self.assertAlmostEqual(relative_entropy[124], 2.0) self.assertAlmostEqual(relative_entropy[125], 2.0) self.assertAlmostEqual(relative_entropy[126], 2.0) self.assertAlmostEqual(relative_entropy[127], 2.0) self.assertAlmostEqual(relative_entropy[128], 2.0) self.assertAlmostEqual(relative_entropy[129], 2.0) self.assertAlmostEqual(relative_entropy[130], 2.0) self.assertAlmostEqual(relative_entropy[131], 2.0) self.assertAlmostEqual(relative_entropy[132], 2.0) self.assertAlmostEqual(relative_entropy[133], 2.0) self.assertAlmostEqual(relative_entropy[134], 2.0) self.assertAlmostEqual(relative_entropy[135], 2.0) self.assertAlmostEqual(relative_entropy[136], 1.4083272214176723) self.assertAlmostEqual(relative_entropy[137], 2.0) self.assertAlmostEqual(relative_entropy[138], 2.0) self.assertAlmostEqual(relative_entropy[139], 2.0) self.assertAlmostEqual(relative_entropy[140], 2.0) self.assertAlmostEqual(relative_entropy[141], 2.0) self.assertAlmostEqual(relative_entropy[142], 2.0) self.assertAlmostEqual(relative_entropy[143], 2.0) self.assertAlmostEqual(relative_entropy[144], 2.0) self.assertAlmostEqual(relative_entropy[145], 2.0) self.assertAlmostEqual(relative_entropy[146], 2.0) self.assertAlmostEqual(relative_entropy[147], 2.0) self.assertAlmostEqual(relative_entropy[148], 1.4083272214176723) self.assertAlmostEqual(relative_entropy[149], 2.0) self.assertAlmostEqual(relative_entropy[150], 2.0) self.assertAlmostEqual(relative_entropy[151], 2.0) self.assertAlmostEqual(relative_entropy[152], 2.0) self.assertAlmostEqual(relative_entropy[153], 2.0) self.assertAlmostEqual(relative_entropy[154], 2.0) self.assertAlmostEqual(relative_entropy[155], 2.0) handle = StringIO() with self.assertWarns(BiopythonDeprecationWarning): AlignInfo.print_info_content(align_info, fout=handle) self.assertEqual( handle.getvalue(), """\ 0 T 2.000 1 A 2.000 2 T 2.000 3 A 2.000 4 C 2.000 5 A 2.000 6 T 2.000 7 T 1.408 8 A 2.000 9 A 2.000 10 A 2.000 11 G 2.000 12 A 1.015 13 A 2.000 14 G 2.000 15 G 2.000 16 G 2.000 17 G 2.000 18 G 2.000 19 A 2.000 20 T 2.000 21 G 2.000 22 C 2.000 23 G 2.000 24 G 2.000 25 A 2.000 26 T 2.000 27 A 2.000 28 A 2.000 29 A 2.000 30 T 2.000 31 G 2.000 32 G 2.000 33 A 2.000 34 A 2.000 35 A 2.000 36 G 2.000 37 G 2.000 38 C 2.000 39 G 2.000 40 A 2.000 41 A 2.000 42 A 2.000 43 G 2.000 44 A 2.000 45 A 2.000 46 A 2.000 47 G 2.000 48 A 2.000 49 A 2.000 50 T 2.000 51 A 2.000 52 T 2.000 53 A 2.000 54 T 2.000 55 A 2.000 56 - 2.000 57 - 2.000 58 - 2.000 59 - 2.000 60 - 2.000 61 - 2.000 62 - 2.000 63 - 2.000 64 - 2.000 65 - 2.000 66 A 2.000 67 T 2.000 68 A 2.000 69 T 2.000 70 A 2.000 71 T 2.000 72 T 2.000 73 T 2.000 74 C 1.408 75 A 1.408 76 A 2.000 77 A 2.000 78 T 2.000 79 T 2.000 80 T 1.015 81 C 2.000 82 C 2.000 83 T 2.000 84 T 2.000 85 A 2.000 86 T 2.000 87 A 2.000 88 T 2.000 89 A 2.000 90 C 1.137 91 C 2.000 92 C 2.000 93 A 2.000 94 A 2.000 95 A 2.000 96 T 2.000 97 A 2.000 98 T 2.000 99 A 2.000 100 A 2.000 101 A 2.000 102 A 2.000 103 A 2.000 104 T 2.000 105 A 2.000 106 T 2.000 107 C 2.000 108 T 2.000 109 A 2.000 110 A 2.000 111 T 2.000 112 A 2.000 113 A 2.000 114 A 2.000 115 T 2.000 116 T 2.000 117 A 2.000 118 G 2.000 119 A 2.000 120 T 2.000 121 G 2.000 122 A 2.000 123 A 2.000 124 T 2.000 125 A 2.000 126 T 2.000 127 C 2.000 128 A 2.000 129 A 2.000 130 A 2.000 131 G 2.000 132 A 2.000 133 A 2.000 134 T 2.000 135 C 2.000 136 C 1.408 137 A 2.000 138 T 2.000 139 T 2.000 140 G 2.000 141 A 2.000 142 T 2.000 143 T 2.000 144 T 2.000 145 A 2.000 146 G 2.000 147 T 2.000 148 G 1.408 149 T 2.000 150 A 2.000 151 C 2.000 152 C 2.000 153 A 2.000 154 G 2.000 155 A 2.000 """, ) # create a new-style Alignment object del seq_record del align_info del consensus del dictionary del matrix del second_seq del e_freq_table del value del handle alignment = msa.alignment self.assertEqual(len(alignment), 7) seq_record = alignment.sequences[0] self.assertEqual(seq_record.description, "gi|6273285|gb|AF191659.1|AF191") self.assertEqual( alignment[0], "TATACATTAAAGAAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAATATATA----------ATATATTTCAAATTTCCTTATATACCCAAATATAAAAATATCTAATAAATTAGATGAATATCAAAGAATCCATTGATTTAGTGTACCAGA", ) self.assertEqual( seq_record.seq, Seq( "TATACATTAAAGAAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAATATATAATATATTTCAAATTTCCTTATATACCCAAATATAAAAATATCTAATAAATTAGATGAATATCAAAGAATCCATTGATTTAGTGTACCAGA" ), ) seq_record = alignment.sequences[1] self.assertEqual(seq_record.description, "gi|6273284|gb|AF191658.1|AF191") self.assertEqual( alignment[1], "TATACATTAAAGAAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAATATATATA--------ATATATTTCAAATTTCCTTATATACCCAAATATAAAAATATCTAATAAATTAGATGAATATCAAAGAATCTATTGATTTAGTGTACCAGA", ) self.assertEqual( seq_record.seq, "TATACATTAAAGAAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAATATATATAATATATTTCAAATTTCCTTATATACCCAAATATAAAAATATCTAATAAATTAGATGAATATCAAAGAATCTATTGATTTAGTGTACCAGA", ) seq_record = alignment.sequences[2] self.assertEqual(seq_record.description, "gi|6273287|gb|AF191661.1|AF191") self.assertEqual( alignment[2], "TATACATTAAAGAAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAATATATA----------ATATATTTCAAATTTCCTTATATATCCAAATATAAAAATATCTAATAAATTAGATGAATATCAAAGAATCTATTGATTTAGTGTACCAGA", ) self.assertEqual( seq_record.seq, "TATACATTAAAGAAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAATATATAATATATTTCAAATTTCCTTATATATCCAAATATAAAAATATCTAATAAATTAGATGAATATCAAAGAATCTATTGATTTAGTGTACCAGA", ) seq_record = alignment.sequences[3] self.assertEqual(seq_record.description, "gi|6273286|gb|AF191660.1|AF191") self.assertEqual( alignment[3], "TATACATAAAAGAAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAATATATA----------ATATATTTATAATTTCCTTATATATCCAAATATAAAAATATCTAATAAATTAGATGAATATCAAAGAATCTATTGATTTAGTGTACCAGA", ) self.assertEqual( seq_record.seq, "TATACATAAAAGAAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAATATATAATATATTTATAATTTCCTTATATATCCAAATATAAAAATATCTAATAAATTAGATGAATATCAAAGAATCTATTGATTTAGTGTACCAGA", ) seq_record = alignment.sequences[4] self.assertEqual(seq_record.description, "gi|6273290|gb|AF191664.1|AF191") self.assertEqual( alignment[4], "TATACATTAAAGGAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAATATATATATA------ATATATTTCAAATTCCCTTATATATCCAAATATAAAAATATCTAATAAATTAGATGAATATCAAAGAATCTATTGATTTAGTGTACCAGA", ) self.assertEqual( seq_record.seq, "TATACATTAAAGGAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAATATATATATAATATATTTCAAATTCCCTTATATATCCAAATATAAAAATATCTAATAAATTAGATGAATATCAAAGAATCTATTGATTTAGTGTACCAGA", ) seq_record = alignment.sequences[5] self.assertEqual(seq_record.description, "gi|6273289|gb|AF191663.1|AF191") self.assertEqual( alignment[5], "TATACATTAAAGGAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAATATATATATA------ATATATTTCAAATTCCCTTATATATCCAAATATAAAAATATCTAATAAATTAGATGAATATCAAAGAATCTATTGATTTAGTATACCAGA", ) self.assertEqual( seq_record.seq, "TATACATTAAAGGAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAATATATATATAATATATTTCAAATTCCCTTATATATCCAAATATAAAAATATCTAATAAATTAGATGAATATCAAAGAATCTATTGATTTAGTATACCAGA", ) seq_record = alignment.sequences[6] self.assertEqual(seq_record.description, "gi|6273291|gb|AF191665.1|AF191") self.assertEqual( alignment[6], "TATACATTAAAGGAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAATATATATATATATATAATATATTTCAAATTCCCTTATATATCCAAATATAAAAATATCTAATAAATTAGATGAATATCAAAGAATCTATTGATTTAGTGTACCAGA", ) self.assertEqual( seq_record.seq, "TATACATTAAAGGAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAATATATATATATATATAATATATTTCAAATTCCCTTATATATCCAAATATAAAAATATCTAATAAATTAGATGAATATCAAAGAATCTATTGATTTAGTGTACCAGA", ) self.assertEqual(alignment.shape, (7, 156)) substitutions = alignment.substitutions self.assertEqual(len(substitutions), 4) self.assertEqual(substitutions.shape, (4, 4)) self.assertAlmostEqual(substitutions[("A", "A")], 1395) self.assertAlmostEqual(substitutions[("A", "C")], 3) self.assertAlmostEqual(substitutions[("A", "G")], 13) self.assertAlmostEqual(substitutions[("A", "T")], 6) self.assertAlmostEqual(substitutions[("C", "A")], 3) self.assertAlmostEqual(substitutions[("C", "C")], 271) self.assertAlmostEqual(substitutions[("C", "G")], 0) self.assertAlmostEqual(substitutions[("C", "T")], 16) self.assertAlmostEqual(substitutions[("G", "A")], 5) self.assertAlmostEqual(substitutions[("G", "C")], 0) self.assertAlmostEqual(substitutions[("G", "G")], 480) self.assertAlmostEqual(substitutions[("G", "T")], 0) self.assertAlmostEqual(substitutions[("T", "A")], 6) self.assertAlmostEqual(substitutions[("T", "C")], 12) self.assertAlmostEqual(substitutions[("T", "G")], 0) self.assertAlmostEqual(substitutions[("T", "T")], 874) motif = motifs.Motif(alphabet="ACGT", alignment=alignment) self.assertEqual( motif.consensus, "TATACATTAAAGAAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAATATATATATATATATAATATATTTCAAATTTCCTTATATATCCAAATATAAAAATATCTAATAAATTAGATGAATATCAAAGAATCTATTGATTTAGTGTACCAGA", ) self.assertEqual( motif.degenerate_consensus, "TATACATTAAAGRAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAATATATATATATATATAATATATTTCAAATTYCCTTATATATCCAAATATAAAAATATCTAATAAATTAGATGAATATCAAAGAATCTATTGATTTAGTGTACCAGA", ) matrix = motif.counts self.assertEqual( str(matrix), """\ 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 A: 0.00 7.00 0.00 7.00 0.00 7.00 0.00 1.00 7.00 7.00 7.00 0.00 4.00 7.00 0.00 0.00 0.00 0.00 0.00 7.00 0.00 0.00 0.00 0.00 0.00 7.00 0.00 7.00 7.00 7.00 0.00 0.00 0.00 7.00 7.00 7.00 0.00 0.00 0.00 0.00 7.00 7.00 7.00 0.00 7.00 7.00 7.00 0.00 7.00 7.00 0.00 7.00 0.00 7.00 0.00 7.00 0.00 4.00 0.00 3.00 0.00 1.00 0.00 1.00 0.00 1.00 7.00 0.00 7.00 0.00 7.00 0.00 0.00 0.00 1.00 6.00 7.00 7.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 7.00 0.00 7.00 0.00 7.00 0.00 0.00 0.00 7.00 7.00 7.00 0.00 7.00 0.00 7.00 7.00 7.00 7.00 7.00 0.00 7.00 0.00 0.00 0.00 7.00 7.00 0.00 7.00 7.00 7.00 0.00 0.00 7.00 0.00 7.00 0.00 0.00 7.00 7.00 0.00 7.00 0.00 0.00 7.00 7.00 7.00 0.00 7.00 7.00 0.00 0.00 0.00 7.00 0.00 0.00 0.00 7.00 0.00 0.00 0.00 7.00 0.00 0.00 1.00 0.00 7.00 0.00 0.00 7.00 0.00 7.00 C: 0.00 0.00 0.00 0.00 7.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 7.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 7.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 6.00 0.00 0.00 0.00 0.00 0.00 3.00 7.00 7.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 2.00 7.00 7.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 7.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 7.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 7.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 7.00 7.00 0.00 0.00 0.00 G: 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 7.00 3.00 0.00 7.00 7.00 7.00 7.00 7.00 0.00 0.00 7.00 0.00 7.00 7.00 0.00 0.00 0.00 0.00 0.00 0.00 7.00 7.00 0.00 0.00 0.00 7.00 7.00 0.00 7.00 0.00 0.00 0.00 7.00 0.00 0.00 0.00 7.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 7.00 0.00 0.00 7.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 7.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 7.00 0.00 0.00 0.00 0.00 0.00 7.00 0.00 6.00 0.00 0.00 0.00 0.00 0.00 7.00 0.00 T: 7.00 0.00 7.00 0.00 0.00 0.00 7.00 6.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 7.00 0.00 0.00 0.00 0.00 0.00 7.00 0.00 0.00 0.00 7.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 7.00 0.00 7.00 0.00 7.00 0.00 4.00 0.00 3.00 0.00 1.00 0.00 1.00 0.00 1.00 0.00 0.00 7.00 0.00 7.00 0.00 7.00 7.00 7.00 0.00 1.00 0.00 0.00 7.00 7.00 4.00 0.00 0.00 7.00 7.00 0.00 7.00 0.00 7.00 0.00 5.00 0.00 0.00 0.00 0.00 0.00 7.00 0.00 7.00 0.00 0.00 0.00 0.00 0.00 7.00 0.00 7.00 0.00 7.00 0.00 0.00 7.00 0.00 0.00 0.00 7.00 7.00 0.00 0.00 0.00 7.00 0.00 0.00 0.00 7.00 0.00 7.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 7.00 0.00 6.00 0.00 7.00 7.00 0.00 0.00 7.00 7.00 7.00 0.00 0.00 7.00 0.00 7.00 0.00 0.00 0.00 0.00 0.00 0.00 """, ) self.assertEqual( format(motif, "transfac"), """\ P0 A C G T 01 0 0 0 7 T 02 7 0 0 0 A 03 0 0 0 7 T 04 7 0 0 0 A 05 0 7 0 0 C 06 7 0 0 0 A 07 0 0 0 7 T 08 1 0 0 6 T 09 7 0 0 0 A 10 7 0 0 0 A 11 7 0 0 0 A 12 0 0 7 0 G 13 4 0 3 0 R 14 7 0 0 0 A 15 0 0 7 0 G 16 0 0 7 0 G 17 0 0 7 0 G 18 0 0 7 0 G 19 0 0 7 0 G 20 7 0 0 0 A 21 0 0 0 7 T 22 0 0 7 0 G 23 0 7 0 0 C 24 0 0 7 0 G 25 0 0 7 0 G 26 7 0 0 0 A 27 0 0 0 7 T 28 7 0 0 0 A 29 7 0 0 0 A 30 7 0 0 0 A 31 0 0 0 7 T 32 0 0 7 0 G 33 0 0 7 0 G 34 7 0 0 0 A 35 7 0 0 0 A 36 7 0 0 0 A 37 0 0 7 0 G 38 0 0 7 0 G 39 0 7 0 0 C 40 0 0 7 0 G 41 7 0 0 0 A 42 7 0 0 0 A 43 7 0 0 0 A 44 0 0 7 0 G 45 7 0 0 0 A 46 7 0 0 0 A 47 7 0 0 0 A 48 0 0 7 0 G 49 7 0 0 0 A 50 7 0 0 0 A 51 0 0 0 7 T 52 7 0 0 0 A 53 0 0 0 7 T 54 7 0 0 0 A 55 0 0 0 7 T 56 7 0 0 0 A 57 0 0 0 4 T 58 4 0 0 0 A 59 0 0 0 3 T 60 3 0 0 0 A 61 0 0 0 1 T 62 1 0 0 0 A 63 0 0 0 1 T 64 1 0 0 0 A 65 0 0 0 1 T 66 1 0 0 0 A 67 7 0 0 0 A 68 0 0 0 7 T 69 7 0 0 0 A 70 0 0 0 7 T 71 7 0 0 0 A 72 0 0 0 7 T 73 0 0 0 7 T 74 0 0 0 7 T 75 1 6 0 0 C 76 6 0 0 1 A 77 7 0 0 0 A 78 7 0 0 0 A 79 0 0 0 7 T 80 0 0 0 7 T 81 0 3 0 4 Y 82 0 7 0 0 C 83 0 7 0 0 C 84 0 0 0 7 T 85 0 0 0 7 T 86 7 0 0 0 A 87 0 0 0 7 T 88 7 0 0 0 A 89 0 0 0 7 T 90 7 0 0 0 A 91 0 2 0 5 T 92 0 7 0 0 C 93 0 7 0 0 C 94 7 0 0 0 A 95 7 0 0 0 A 96 7 0 0 0 A 97 0 0 0 7 T 98 7 0 0 0 A 99 0 0 0 7 T 100 7 0 0 0 A 101 7 0 0 0 A 102 7 0 0 0 A 103 7 0 0 0 A 104 7 0 0 0 A 105 0 0 0 7 T 106 7 0 0 0 A 107 0 0 0 7 T 108 0 7 0 0 C 109 0 0 0 7 T 110 7 0 0 0 A 111 7 0 0 0 A 112 0 0 0 7 T 113 7 0 0 0 A 114 7 0 0 0 A 115 7 0 0 0 A 116 0 0 0 7 T 117 0 0 0 7 T 118 7 0 0 0 A 119 0 0 7 0 G 120 7 0 0 0 A 121 0 0 0 7 T 122 0 0 7 0 G 123 7 0 0 0 A 124 7 0 0 0 A 125 0 0 0 7 T 126 7 0 0 0 A 127 0 0 0 7 T 128 0 7 0 0 C 129 7 0 0 0 A 130 7 0 0 0 A 131 7 0 0 0 A 132 0 0 7 0 G 133 7 0 0 0 A 134 7 0 0 0 A 135 0 0 0 7 T 136 0 7 0 0 C 137 0 1 0 6 T 138 7 0 0 0 A 139 0 0 0 7 T 140 0 0 0 7 T 141 0 0 7 0 G 142 7 0 0 0 A 143 0 0 0 7 T 144 0 0 0 7 T 145 0 0 0 7 T 146 7 0 0 0 A 147 0 0 7 0 G 148 0 0 0 7 T 149 1 0 6 0 G 150 0 0 0 7 T 151 7 0 0 0 A 152 0 7 0 0 C 153 0 7 0 0 C 154 7 0 0 0 A 155 0 0 7 0 G 156 7 0 0 0 A XX // """, ) self.assertAlmostEqual(sum(motif[5:50].relative_entropy), 88.42309908538343) relative_entropy = motif.relative_entropy self.assertAlmostEqual(sum(relative_entropy[5:50]), 88.42309908538343) self.assertAlmostEqual(sum(relative_entropy), 306.20805926645323) self.assertEqual(alignment[:, 1], "AAAAAAA") self.assertAlmostEqual(motif.relative_entropy[1], 2.0) self.assertEqual(alignment[:, 7], "TTTATTT") self.assertAlmostEqual(relative_entropy[7], 1.4083272214176723) def test_read_fasta(self): path = os.path.join(os.curdir, "Quality", "example.fasta") msa = AlignIO.read(path, "fasta") self.assertEqual(len(msa), 3) seq_record = msa[0] self.assertEqual(seq_record.description, "EAS54_6_R1_2_1_413_324") self.assertEqual(seq_record.seq, "CCCTTCTTGTCTTCAGCGTTTCTCC") seq_record = msa[1] self.assertEqual(seq_record.description, "EAS54_6_R1_2_1_540_792") self.assertEqual(seq_record.seq, "TTGGCAGGCCAAGGCCGATGGATCA") seq_record = msa[2] self.assertEqual(seq_record.description, "EAS54_6_R1_2_1_443_348") self.assertEqual(seq_record.seq, "GTTGCTTCTGGCGTGGGTGGGGGGG") self.assertEqual(msa.get_alignment_length(), 25) align_info = AlignInfo.SummaryInfo(msa) with self.assertWarns(BiopythonDeprecationWarning): consensus = align_info.dumb_consensus(ambiguous="N", threshold=0.6) self.assertIsInstance(consensus, Seq) self.assertEqual(consensus, "NTNGCNTNNNNNGNNGGNTGGNTCN") self.assertEqual( str(msa), """\ Alignment with 3 rows and 25 columns CCCTTCTTGTCTTCAGCGTTTCTCC EAS54_6_R1_2_1_413_324 TTGGCAGGCCAAGGCCGATGGATCA EAS54_6_R1_2_1_540_792 GTTGCTTCTGGCGTGGGTGGGGGGG EAS54_6_R1_2_1_443_348""", ) alignment = msa.alignment self.assertEqual(len(alignment), 3) seq_record = alignment.sequences[0] self.assertEqual(seq_record.description, "EAS54_6_R1_2_1_413_324") self.assertEqual(seq_record.seq, "CCCTTCTTGTCTTCAGCGTTTCTCC") seq_record = alignment.sequences[1] self.assertEqual(seq_record.description, "EAS54_6_R1_2_1_540_792") self.assertEqual(seq_record.seq, "TTGGCAGGCCAAGGCCGATGGATCA") seq_record = alignment.sequences[2] self.assertEqual(seq_record.description, "EAS54_6_R1_2_1_443_348") self.assertEqual(seq_record.seq, "GTTGCTTCTGGCGTGGGTGGGGGGG") self.assertEqual(alignment.length, 25) motif = motifs.Motif(alphabet="ACGT", alignment=alignment) self.assertEqual(motif.consensus, "CTCGCATCCCAAGCAGGATGGATCA") self.assertEqual(motif.degenerate_consensus, "BYBKYHKBBBVHKBVSSDKKKVKSV") self.assertEqual( str(alignment), """\ EAS54_6_R 0 CCCTTCTTGTCTTCAGCGTTTCTCC 25 EAS54_6_R 0 TTGGCAGGCCAAGGCCGATGGATCA 25 EAS54_6_R 0 GTTGCTTCTGGCGTGGGTGGGGGGG 25 """, ) self.assertEqual(motif.counts.calculate_consensus(identity=0.6), consensus) if __name__ == "__main__": runner = unittest.TextTestRunner(verbosity=2) unittest.main(testRunner=runner)