# 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.Align import PairwiseAligner from Bio.Seq import Seq from Bio.SeqRecord import SeqRecord import numpy as np 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) 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) motif = motifs.Motif("ACGT", alignment) counts = motif.counts self.assertEqual( counts.calculate_consensus(identity=0.7), "TATACATTAAAGNAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAATATATATATATATATAATATATTTCAAATTNCCTTATATATCCAAATATAAAAATATCTAATAAATTAGATGAATATCAAAGAATCTATTGATTTAGTGTACCAGA", ) self.assertEqual( str(counts), """\ 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 """, ) alignment = msa.alignment motif = motifs.Motif("ACGT", alignment) counts = motif.counts self.assertEqual( str(counts), """\ 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 """, ) with self.assertWarns(BiopythonDeprecationWarning): align_info = AlignInfo.SummaryInfo(msa) self.assertEqual(align_info.get_column(1), "AAAAAAA") self.assertEqual(align_info.get_column(7), "TTTATTT") alignment = msa.alignment motif = motifs.Motif("ACGT", alignment) counts = motif.counts self.assertEqual( str(counts), """\ 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 """, ) value = sum(motif[5:50].relative_entropy) self.assertAlmostEqual(value, 88.42309908538343) # Alignment relative_entropy = motif.relative_entropy value = sum(relative_entropy) self.assertAlmostEqual(value, 306.2080592664532) # Alignment 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) # create a new-style Alignment object del seq_record del align_info del dictionary del value 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) 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), "NTNGCNTNNNNNGNNGGNTGGNTCN" ) class TestFromAlignmentsWithSameReference(unittest.TestCase): def test_pwas_built_with_strings(self): """Test that from_alignments_with_same_reference creates the correct Alignment when PWA inputs were built with strings""" aligner = PairwiseAligner() # Input sequences reference_str = "ACGT" seq1_str = "ACGGT" seq2_str = "AT" # Generate pairwise alignments pwa1 = next(aligner.align(reference_str, seq1_str)) pwa2 = next(aligner.align(reference_str, seq2_str)) # Use the method being tested msa = Alignment.from_alignments_with_same_reference([pwa1, pwa2]) # Check that the output is of correct type self.assertIsInstance(msa, Alignment) # Check the number of sequences in the MSA self.assertEqual(len(msa), 3) # Validate that from_alignments_with_same_reference gives the right msa self.assertEqual(str(msa[0]), "ACG-T") self.assertEqual(str(msa[1]), "ACGGT") self.assertEqual(str(msa[2]), "A---T") def test_pwas_built_with_seqs(self): """Test that from_alignments_with_same_reference works with PWAs built with Seq objects.""" aligner = PairwiseAligner() # Input sequences reference_seq = Seq("ACGT") seq1_seq = Seq("ACGGT") seq2_seq = Seq("AT") # Generate pairwise alignments pwa1 = next(aligner.align(reference_seq, seq1_seq)) pwa2 = next(aligner.align(reference_seq, seq2_seq)) # Use the method being tested msa = Alignment.from_alignments_with_same_reference([pwa1, pwa2]) # Check that the output is of correct type self.assertIsInstance(msa, Alignment) # Validate that from_alignments_with_same_reference gives the right msa self.assertEqual(str(msa[0]), "ACG-T") self.assertEqual(str(msa[1]), "ACGGT") self.assertEqual(str(msa[2]), "A---T") # Works with undefined sequences pwa1_undefined = Alignment([Seq(None, 4), Seq(None, 5)], pwa1.coordinates) pwa2_undefined = Alignment([Seq(None, 4), Seq(None, 2)], pwa2.coordinates) msa_undefined = Alignment.from_alignments_with_same_reference( [pwa1_undefined, pwa2_undefined] ) self.assertTrue((msa_undefined.coordinates == msa.coordinates).all()) def test_metadata_preservation(self): """Test that sequence metadata (IDs and descriptions) are preserved in the Alignment. Sequence metadata may exist if pairwise alignments are built with SeqRecords. This also tests that from_alignments_with_same_reference works with pairwise alignments built with SeqRecord objects. """ aligner = PairwiseAligner() # Input sequences reference_seqr = SeqRecord(Seq("ACGT"), id="reference", description="desc 1") seq1_seqr = SeqRecord(Seq("ACGGT"), id="seq1", description="desc 2") seq2_seqr = SeqRecord(Seq("AT"), id="seq2", description="desc 3") # Generate pairwise alignments pwa1 = next(aligner.align(reference_seqr, seq1_seqr)) pwa2 = next(aligner.align(reference_seqr, seq2_seqr)) # Use the method being tested msa = Alignment.from_alignments_with_same_reference([pwa1, pwa2]) # Validate that from_alignments_with_same_reference gives the right msa self.assertEqual(str(msa[0]), "ACG-T") self.assertEqual(str(msa[1]), "ACGGT") self.assertEqual(str(msa[2]), "A---T") # Check that id and description are retained self.assertEqual(msa.sequences[0].id, "reference") self.assertEqual(msa.sequences[1].id, "seq1") self.assertEqual(msa.sequences[2].id, "seq2") self.assertEqual(msa.sequences[0].description, "desc 1") self.assertEqual(msa.sequences[1].description, "desc 2") def test_mismatched_references(self): """Test that mismatched reference sequences raise a ValueError.""" aligner = PairwiseAligner() pwa1 = next(aligner.align("ACGAAAT", "ACGGT")) pwa2 = next(aligner.align("ACCT", "AT")) with self.assertRaises(ValueError) as context: Alignment.from_alignments_with_same_reference([pwa1, pwa2]) self.assertIn("All reference sequences must", str(context.exception)) # Works with undefined sequences pwa1_undefined = Alignment([Seq(None, 7), Seq(None, 5)], pwa1.coordinates) pwa2_undefined = Alignment([Seq(None, 4), Seq(None, 2)], pwa2.coordinates) with self.assertRaises(ValueError) as context: Alignment.from_alignments_with_same_reference( [pwa1_undefined, pwa2_undefined] ) self.assertIn("All reference sequences must", str(context.exception)) # Works with mix pwa1_undefined = Alignment([Seq(None, 7), Seq(None, 5)], pwa1.coordinates) with self.assertRaises(ValueError) as context: Alignment.from_alignments_with_same_reference([pwa1_undefined, pwa2]) self.assertIn("All reference sequences must", str(context.exception)) def test_empty_input(self): """Test that empty input raises a ValueError.""" with self.assertRaises(ValueError): Alignment.from_alignments_with_same_reference([]) def test_input_with_three_sequences(self): """Test that the method works with input Alignments of three sequences""" # Input sequences reference_str = "ACGT" seq1_str = "ACGGT" seq2_str = "AT" seq3_str = "AGT" seq4_str = "ACT" # Coordinates for each alignment coords1 = np.array([[0, 1, 2, 3, 3, 4], [0, 1, 2, 3, 4, 5], [0, 1, 1, 1, 1, 2]]) coords2 = np.array([[0, 1, 2, 3, 4], [0, 1, 1, 2, 3], [0, 1, 2, 2, 3]]) # Generate input alignments alignment1 = Alignment([reference_str, seq1_str, seq2_str], coords1) alignment2 = Alignment([reference_str, seq3_str, seq4_str], coords2) # Use the method being tested msa = Alignment.from_alignments_with_same_reference([alignment1, alignment2]) # Check that the output is of correct type self.assertIsInstance(msa, Alignment) # Check the number of sequences in the MSA self.assertEqual(len(msa), 5) # Validate that from_alignments_with_same_reference gives the right msa self.assertEqual(str(msa[0]), "ACG-T") self.assertEqual(str(msa[1]), "ACGGT") self.assertEqual(str(msa[2]), "A---T") self.assertEqual(str(msa[3]), "A-G-T") self.assertEqual(str(msa[4]), "AC--T") def test_mixed_input(self): """Test that the method works with input Alignments of mixed number of sequences""" aligner = PairwiseAligner() # Input sequences reference_str = "ACGT" seq1_str = "ACT" seq2_str = "ACGGT" seq3_str = "AT" # Coordinates for an alignment of three sequences coords = np.array([[0, 1, 2, 3, 3, 4], [0, 1, 2, 3, 4, 5], [0, 1, 1, 1, 1, 2]]) # Generate input alignments pwa = next(aligner.align(reference_str, seq1_str)) not_pwa = Alignment([reference_str, seq2_str, seq3_str], coords) # Use the method being tested msa = Alignment.from_alignments_with_same_reference([pwa, not_pwa]) # Check that the output is of correct type self.assertIsInstance(msa, Alignment) # Check the number of sequences in the MSA self.assertEqual(len(msa), 4) # Validate that from_alignments_with_same_reference gives the right msa self.assertEqual(str(msa[0]), "ACG-T") self.assertEqual(str(msa[1]), "AC--T") self.assertEqual(str(msa[2]), "ACGGT") self.assertEqual(str(msa[3]), "A---T") if __name__ == "__main__": runner = unittest.TextTestRunner(verbosity=2) unittest.main(testRunner=runner)