# Copyright 2008 by Bartek Wilczynski. All rights reserved. # Revisions copyright 2019 by Victor Lin. # Adapted from test_Mymodule.py by Jeff Chang. # This file is part of the Biopython distribution and governed by your # choice of the "Biopython License Agreement" or the "BSD 3-Clause License". # Please see the LICENSE file that should have been included as part of this # package. """Tests for motifs module.""" import os import unittest import math try: import numpy except ImportError: from Bio import MissingExternalDependencyError raise MissingExternalDependencyError( "Install numpy if you want to use Bio.motifs." ) from None from Bio import motifs from Bio.Seq import Seq class MotifTestsBasic(unittest.TestCase): """Basic motif tests.""" def setUp(self): self.PFMin = open("motifs/SRF.pfm") self.SITESin = open("motifs/Arnt.sites") self.CLUSTERBUSTERin = open("motifs/clusterbuster.pfm") self.XMSin = open("motifs/abdb.xms") self.PFMFOURCOLUMNSin = open("motifs/fourcolumns.pfm") self.PFMFOURROWSin = open("motifs/fourrows.pfm") self.TFout = "motifs/tf.out" self.FAout = "motifs/fa.out" self.PFMout = "motifs/fa.out" instance = Seq("ATATA") instances = [instance] self.m = motifs.create(instances) def tearDown(self): self.PFMin.close() self.SITESin.close() if os.path.exists(self.TFout): os.remove(self.TFout) if os.path.exists(self.FAout): os.remove(self.FAout) def test_alignace_parsing(self): """Test if Bio.motifs can parse AlignAce output files.""" with open("motifs/alignace.out") as handle: record = motifs.parse(handle, "AlignAce") self.assertEqual(record.version, "AlignACE 4.0 05/13/04") self.assertEqual(record.command, "./AlignACE -i test.fa") self.assertEqual(len(record.parameters), 7) self.assertEqual(record.parameters["expect"], "10") self.assertEqual(record.parameters["gcback"], "0.38") self.assertEqual(record.parameters["minpass"], "200") self.assertEqual(record.parameters["seed"], "1227623309") self.assertEqual(record.parameters["numcols"], "10") self.assertEqual(record.parameters["undersample"], "1") self.assertEqual(record.parameters["oversample"], "1") self.assertEqual(len(record.sequences), 10) self.assertEqual(record.sequences[0], "SEQ1; M: CTCAATCGTAGA at 52") self.assertEqual(record.sequences[1], "SEQ2; M: CTCAATCGTAGA at 172") self.assertEqual(record.sequences[2], "SEQ3; M: CTCAATCGTAGA at 112") self.assertEqual(record.sequences[3], "SEQ4; M: CTCAATCGTAGA at 173") self.assertEqual(record.sequences[4], "SEQ5; M: CTCAATCGTAGA at 185") self.assertEqual(record.sequences[5], "SEQ6; M: CTCAATCGTAGA at 105") self.assertEqual(record.sequences[6], "SEQ7; M: CTCAATCGTAGA at 177") self.assertEqual(record.sequences[7], "SEQ8; M: CTCAATCGTAGA at 172") self.assertEqual(record.sequences[8], "SEQ9; M: CTCAATCGTAGA at 93") self.assertEqual(record.sequences[9], "SEQ10; M: CTCAATCGTAGA at 3") self.assertEqual(len(record), 16) self.assertEqual(record[0].alphabet, "ACGT") self.assertEqual(len(record[0].instances), 11) self.assertEqual(record[0].instances[0], "TCTACGATTGAG") self.assertEqual(record[0].instances[1], "TCTACGATTGAG") self.assertEqual(record[0].instances[2], "TCTACGATTGAG") self.assertEqual(record[0].instances[3], "TCTACGATTGAG") self.assertEqual(record[0].instances[4], "TCTACGATTGAG") self.assertEqual(record[0].instances[5], "TCTACGATTGAG") self.assertEqual(record[0].instances[6], "TCTACGATTGAG") self.assertEqual(record[0].instances[7], "TCTACGATTGAG") self.assertEqual(record[0].instances[8], "TCTACGATTGAG") self.assertEqual(record[0].instances[9], "TCAAAGATAGAG") self.assertEqual(record[0].instances[10], "TCTACGATTGAG") self.assertEqual(record[0].mask, (1, 1, 0, 1, 1, 1, 1, 1, 0, 1, 1, 1)) self.assertAlmostEqual(record[0].score, 57.9079) self.assertEqual(record[1].alphabet, "ACGT") self.assertEqual(len(record[1].instances), 22) self.assertEqual(record[1].instances[0], "GCGAAGGAAGCAGCGCGTGTG") self.assertEqual(record[1].instances[1], "GGCACCGCCTCTACGATTGAG") self.assertEqual(record[1].instances[2], "CAGAGCTTAGCATTGAACGCG") self.assertEqual(record[1].instances[3], "CTAATGAAAGCAATGAGAGTG") self.assertEqual(record[1].instances[4], "CTTGTGCCCTCTAAGCGTCCG") self.assertEqual(record[1].instances[5], "GAGCACGACGCTTTGTACCTG") self.assertEqual(record[1].instances[6], "CGGCACTTAGCAGCGTATCGT") self.assertEqual(record[1].instances[7], "CTGGTTTCATCTACGATTGAG") self.assertEqual(record[1].instances[8], "GGGCCAATAGCGGCGCCGGAG") self.assertEqual(record[1].instances[9], "GTGGAGTTATCTTAGTGCGCG") self.assertEqual(record[1].instances[10], "GAGAGGTTATCTACGATTGAG") self.assertEqual(record[1].instances[11], "CTGCTCCCCGCATACAGCGCG") self.assertEqual(record[1].instances[12], "CAGAACCGAGGTCCGGTACGG") self.assertEqual(record[1].instances[13], "GTGCCCCAAGCTTACCCAGGG") self.assertEqual(record[1].instances[14], "CGCCTCTGATCTACGATTGAG") self.assertEqual(record[1].instances[15], "GTGCTCATAGGGACGTCGCGG") self.assertEqual(record[1].instances[16], "CTGCCCCCCGCATAGTAGGGG") self.assertEqual(record[1].instances[17], "GTAAAGAAATCGATGTGCCAG") self.assertEqual(record[1].instances[18], "CACCTGCAATTGCTGGCAGCG") self.assertEqual(record[1].instances[19], "GGCGGGCCATCCCTGTATGAA") self.assertEqual(record[1].instances[20], "CTCCAGGTCGCATGGAGAGAG") self.assertEqual(record[1].instances[21], "CCTCGGATCGCTTGGGAAGAG") self.assertEqual( record[1].mask, (1, 0, 1, 1, 0, 1, 0, 0, 1, 1, 1, 0, 0, 0, 1, 0, 0, 0, 1, 0, 1), ) self.assertAlmostEqual(record[1].score, 19.6235) self.assertEqual(record[2].alphabet, "ACGT") self.assertEqual(len(record[2].instances), 18) self.assertEqual(record[2].instances[0], "GTGCGCGAAGGAAGCAGCGCG") self.assertEqual(record[2].instances[1], "CAGAGCTTAGCATTGAACGCG") self.assertEqual(record[2].instances[2], "GTGCCCGATGACCACCCGTCG") self.assertEqual(record[2].instances[3], "GCCCTCTAAGCGTCCGCGGAT") self.assertEqual(record[2].instances[4], "GAGCACGACGCTTTGTACCTG") self.assertEqual(record[2].instances[5], "CGGCACTTAGCAGCGTATCGT") self.assertEqual(record[2].instances[6], "GGGCCAATAGCGGCGCCGGAG") self.assertEqual(record[2].instances[7], "GCGCACTAAGATAACTCCACG") self.assertEqual(record[2].instances[8], "CGGCCCGTTGTCCAGCAGACG") self.assertEqual(record[2].instances[9], "CTGCTCCCCGCATACAGCGCG") self.assertEqual(record[2].instances[10], "GTGCCCCAAGCTTACCCAGGG") self.assertEqual(record[2].instances[11], "GTGCTCATAGGGACGTCGCGG") self.assertEqual(record[2].instances[12], "CTGCCCCCCGCATAGTAGGGG") self.assertEqual(record[2].instances[13], "CGCCGCCATGCGACGCAGAGG") self.assertEqual(record[2].instances[14], "AACCTCTAAGCATACTCTACG") self.assertEqual(record[2].instances[15], "GACCTGGAGGCTTAGACTTGG") self.assertEqual(record[2].instances[16], "GCGCTCTTCCCAAGCGATCCG") self.assertEqual(record[2].instances[17], "GGGCCGTCAGCTCTCAAGTCT") self.assertEqual( record[2].mask, (1, 0, 1, 1, 0, 1, 0, 0, 0, 1, 1, 0, 0, 0, 1, 0, 1, 0, 0, 1, 1), ) self.assertAlmostEqual(record[2].score, 19.1804) self.assertEqual(record[3].alphabet, "ACGT") self.assertEqual(len(record[3].instances), 16) self.assertEqual(record[3].instances[0], "GCCCCAAGCTTACCCAGGGAC") self.assertEqual(record[3].instances[1], "GCCGTCTGCTGGACAACGGGC") self.assertEqual(record[3].instances[2], "GCCGACGGGTGGTCATCGGGC") self.assertEqual(record[3].instances[3], "GCCAATAGCGGCGCCGGAGTC") self.assertEqual(record[3].instances[4], "GCCCCCCGCATAGTAGGGGGA") self.assertEqual(record[3].instances[5], "GCCCGTACCGGACCTCGGTTC") self.assertEqual(record[3].instances[6], "GCCTCATGTACCGGAAGGGAC") self.assertEqual(record[3].instances[7], "GACACGCGCCTGGGAGGGTTC") self.assertEqual(record[3].instances[8], "GCCTTTGGCCTTGGATGAGAA") self.assertEqual(record[3].instances[9], "GGCCCTCGGATCGCTTGGGAA") self.assertEqual(record[3].instances[10], "GCATGTTGGGAATCCGCGGAC") self.assertEqual(record[3].instances[11], "GACACGCGCTGTATGCGGGGA") self.assertEqual(record[3].instances[12], "GCCAGGTACAAAGCGTCGTGC") self.assertEqual(record[3].instances[13], "GCGATCAGCTTGTGGGCGTGC") self.assertEqual(record[3].instances[14], "GACAAATCGGATACTGGGGCA") self.assertEqual(record[3].instances[15], "GCACTTAGCAGCGTATCGTTA") self.assertEqual( record[3].mask, (1, 1, 1, 0, 0, 0, 0, 1, 1, 0, 0, 0, 0, 1, 0, 0, 1, 1, 1, 0, 1), ) self.assertAlmostEqual(record[3].score, 18.0097) self.assertEqual(record[4].alphabet, "ACGT") self.assertEqual(len(record[4].instances), 15) self.assertEqual(record[4].instances[0], "CGGCACAGAGCTT") self.assertEqual(record[4].instances[1], "ATCCGCGGACGCT") self.assertEqual(record[4].instances[2], "CGCCTGGGAGGGT") self.assertEqual(record[4].instances[3], "CGGAAGGGACGTT") self.assertEqual(record[4].instances[4], "ACACACAGACGGT") self.assertEqual(record[4].instances[5], "TGCCAGAGAGGTT") self.assertEqual(record[4].instances[6], "AGACTGAGACGTT") self.assertEqual(record[4].instances[7], "AATCGTAGAGGAT") self.assertEqual(record[4].instances[8], "CGTCTCGTAGGGT") self.assertEqual(record[4].instances[9], "CGTCGCGGAGGAT") self.assertEqual(record[4].instances[10], "CTTCTTAGACGCT") self.assertEqual(record[4].instances[11], "CGACGCAGAGGAT") self.assertEqual(record[4].instances[12], "ATGCTTAGAGGTT") self.assertEqual(record[4].instances[13], "AGACTTGGGCGAT") self.assertEqual(record[4].instances[14], "CGACCTGGAGGCT") self.assertEqual(record[4].mask, (1, 1, 0, 1, 0, 1, 1, 1, 1, 1, 1, 0, 1)) self.assertAlmostEqual(record[4].score, 16.8287) self.assertEqual(record[5].alphabet, "ACGT") self.assertEqual(len(record[5].instances), 18) self.assertEqual(record[5].instances[0], "GTGCGCGAAGGAAGCAGCGCGTG") self.assertEqual(record[5].instances[1], "TTGAGCCGAGTAAAGGGCTGGTG") self.assertEqual(record[5].instances[2], "CAATGCTAAGCTCTGTGCCGACG") self.assertEqual(record[5].instances[3], "CAACTCTCTATGTAGTGCCCGAG") self.assertEqual(record[5].instances[4], "CGACGCTTTGTACCTGGCTTGCG") self.assertEqual(record[5].instances[5], "CGAGTCAATGACACGCGCCTGGG") self.assertEqual(record[5].instances[6], "CGATACGCTGCTAAGTGCCGTCC") self.assertEqual(record[5].instances[7], "CCGGGCCAATAGCGGCGCCGGAG") self.assertEqual(record[5].instances[8], "CCACGCTTCGACACGTGGTATAG") self.assertEqual(record[5].instances[9], "CCGAGCCTCATGTACCGGAAGGG") self.assertEqual(record[5].instances[10], "CTGCTCCCCGCATACAGCGCGTG") self.assertEqual(record[5].instances[11], "CCGAGGTCCGGTACGGGCAAGCC") self.assertEqual(record[5].instances[12], "GTGCTCATAGGGACGTCGCGGAG") self.assertEqual(record[5].instances[13], "CCCTACTATGCGGGGGGCAGGTC") self.assertEqual(record[5].instances[14], "GCCAGCAATTGCAGGTGGTCGTG") self.assertEqual(record[5].instances[15], "CTCTGCGTCGCATGGCGGCGTGG") self.assertEqual(record[5].instances[16], "GGAGGCTTAGACTTGGGCGATAC") self.assertEqual(record[5].instances[17], "GCATGGAGAGAGATCCGGAGGAG") self.assertEqual( record[5].mask, (1, 0, 1, 0, 1, 1, 0, 0, 0, 1, 0, 0, 0, 0, 1, 0, 1, 1, 0, 0, 1, 0, 1), ) self.assertAlmostEqual(record[5].score, 15.0441) self.assertEqual(record[6].alphabet, "ACGT") self.assertEqual(len(record[6].instances), 20) self.assertEqual(record[6].instances[0], "GCGCGTGTGTGTAAC") self.assertEqual(record[6].instances[1], "GCACAGAGCTTAGCA") self.assertEqual(record[6].instances[2], "GGTGGTCATCGGGCA") self.assertEqual(record[6].instances[3], "GCGCGTGTCATTGAC") self.assertEqual(record[6].instances[4], "GGACGGCACTTAGCA") self.assertEqual(record[6].instances[5], "GCGCGTCCCGGGCCA") self.assertEqual(record[6].instances[6], "GCTCGGCCCGTTGTC") self.assertEqual(record[6].instances[7], "GCGCGTGTCCTTTAA") self.assertEqual(record[6].instances[8], "GCTGATCGCTGCTCC") self.assertEqual(record[6].instances[9], "GCCCGTACCGGACCT") self.assertEqual(record[6].instances[10], "GGACGTCGCGGAGGA") self.assertEqual(record[6].instances[11], "GCGGGGGGCAGGTCA") self.assertEqual(record[6].instances[12], "GGACGTACTGGCACA") self.assertEqual(record[6].instances[13], "GCAGGTGGTCGTGCA") self.assertEqual(record[6].instances[14], "GCGCATACCTTAACA") self.assertEqual(record[6].instances[15], "GCACGGGACTTCAAC") self.assertEqual(record[6].instances[16], "GCACGTAGCTGGTAA") self.assertEqual(record[6].instances[17], "GCTCGTCTATGGTCA") self.assertEqual(record[6].instances[18], "GCGCATGCTGGATCC") self.assertEqual(record[6].instances[19], "GGCCGTCAGCTCTCA") self.assertEqual(record[6].mask, (1, 1, 0, 1, 1, 1, 1, 0, 1, 0, 1, 0, 0, 1, 1)) self.assertAlmostEqual(record[6].score, 13.3145) self.assertEqual(record[7].alphabet, "ACGT") self.assertEqual(len(record[7].instances), 20) self.assertEqual(record[7].instances[0], "GAACCGAGGTCCGGTACGGGC") self.assertEqual(record[7].instances[1], "GCCCCCCGCATAGTAGGGGGA") self.assertEqual(record[7].instances[2], "GTCCCTGGGTAAGCTTGGGGC") self.assertEqual(record[7].instances[3], "ACTCCACGCTTCGACACGTGG") self.assertEqual(record[7].instances[4], "ATCCTCTGCGTCGCATGGCGG") self.assertEqual(record[7].instances[5], "GTTCAATGCTAAGCTCTGTGC") self.assertEqual(record[7].instances[6], "GCTCATAGGGACGTCGCGGAG") self.assertEqual(record[7].instances[7], "GTCCCGGGCCAATAGCGGCGC") self.assertEqual(record[7].instances[8], "GCACTTAGCAGCGTATCGTTA") self.assertEqual(record[7].instances[9], "GGCCCTCGGATCGCTTGGGAA") self.assertEqual(record[7].instances[10], "CTGCTGGACAACGGGCCGAGC") self.assertEqual(record[7].instances[11], "GGGCACTACATAGAGAGTTGC") self.assertEqual(record[7].instances[12], "AGCCTCCAGGTCGCATGGAGA") self.assertEqual(record[7].instances[13], "AATCGTAGATCAGAGGCGAGA") self.assertEqual(record[7].instances[14], "GAACTCCACTAAGACTTGAGA") self.assertEqual(record[7].instances[15], "GAGCAGCGATCAGCTTGTGGG") self.assertEqual(record[7].instances[16], "GCCAGGTACAAAGCGTCGTGC") self.assertEqual(record[7].instances[17], "AGTCAATGACACGCGCCTGGG") self.assertEqual(record[7].instances[18], "GGTCATGGAATCTTATGTAGC") self.assertEqual(record[7].instances[19], "GTAGATAACAGAGGTCGGGGG") self.assertEqual( record[7].mask, (1, 0, 0, 1, 0, 0, 0, 1, 1, 0, 0, 1, 1, 0, 0, 0, 1, 1, 0, 1, 1), ) self.assertAlmostEqual(record[7].score, 11.6098) self.assertEqual(record[8].alphabet, "ACGT") self.assertEqual(len(record[8].instances), 14) self.assertEqual(record[8].instances[0], "CCGAGTAAAGGGCTG") self.assertEqual(record[8].instances[1], "GTGGTCATCGGGCAC") self.assertEqual(record[8].instances[2], "GATAACAGAGGTCGG") self.assertEqual(record[8].instances[3], "CGGCGCCGGAGTCTG") self.assertEqual(record[8].instances[4], "GCGCGTCCCGGGCCA") self.assertEqual(record[8].instances[5], "CTGGACAACGGGCCG") self.assertEqual(record[8].instances[6], "CGGATACTGGGGCAG") self.assertEqual(record[8].instances[7], "GGGAGCAGCGATCAG") self.assertEqual(record[8].instances[8], "CAGAACCGAGGTCCG") self.assertEqual(record[8].instances[9], "GGGTCCCTGGGTAAG") self.assertEqual(record[8].instances[10], "GTGCTCATAGGGACG") self.assertEqual(record[8].instances[11], "GAGATCCGGAGGAGG") self.assertEqual(record[8].instances[12], "GCGATCCGAGGGCCG") self.assertEqual(record[8].instances[13], "GAGTTCACATGGCTG") self.assertEqual(record[8].mask, (1, 0, 1, 0, 0, 1, 1, 0, 1, 1, 1, 1, 1, 0, 1)) self.assertAlmostEqual(record[8].score, 11.2943) self.assertEqual(record[9].alphabet, "ACGT") self.assertEqual(len(record[9].instances), 18) self.assertEqual(record[9].instances[0], "TAGAGGCGGTG") self.assertEqual(record[9].instances[1], "GCTAAGCTCTG") self.assertEqual(record[9].instances[2], "TGGAAGCAGTG") self.assertEqual(record[9].instances[3], "GCGAGGCTGTG") self.assertEqual(record[9].instances[4], "ACGACGCTTTG") self.assertEqual(record[9].instances[5], "GGGACGCGCAC") self.assertEqual(record[9].instances[6], "TCGAAGCGTGG") self.assertEqual(record[9].instances[7], "TGTATGCGGGG") self.assertEqual(record[9].instances[8], "GGTAAGCTTGG") self.assertEqual(record[9].instances[9], "TGTACGCTGGG") self.assertEqual(record[9].instances[10], "ACTATGCGGGG") self.assertEqual(record[9].instances[11], "GGTATGCGCTG") self.assertEqual(record[9].instances[12], "GGTACCCGGAG") self.assertEqual(record[9].instances[13], "GCGACGCAGAG") self.assertEqual(record[9].instances[14], "TGGCGGCGTGG") self.assertEqual(record[9].instances[15], "TCTAGGCGGGC") self.assertEqual(record[9].instances[16], "AGTATGCTTAG") self.assertEqual(record[9].instances[17], "TGGAGGCTTAG") self.assertEqual(record[9].mask, (1, 1, 1, 1, 0, 1, 1, 1, 1, 1, 1)) self.assertAlmostEqual(record[9].score, 9.7924) self.assertEqual(record[10].alphabet, "ACGT") self.assertEqual(len(record[10].instances), 13) self.assertEqual(record[10].instances[0], "GCACAGAGCTTAGCATTGAAC") self.assertEqual(record[10].instances[1], "GTCCGCGGATTCCCAACATGC") self.assertEqual(record[10].instances[2], "ATACACAGCCTCGCAAGCCAG") self.assertEqual(record[10].instances[3], "GGCCCGGGACGCGCACTAAGA") self.assertEqual(record[10].instances[4], "GCCCGTTGTCCAGCAGACGGC") self.assertEqual(record[10].instances[5], "GAGCAGCGATCAGCTTGTGGG") self.assertEqual(record[10].instances[6], "GAACCGAGGTCCGGTACGGGC") self.assertEqual(record[10].instances[7], "GTCCCTGGGTAAGCTTGGGGC") self.assertEqual(record[10].instances[8], "GACCTGCCCCCCGCATAGTAG") self.assertEqual(record[10].instances[9], "AACCAGCGCATACCTTAACAG") self.assertEqual(record[10].instances[10], "ATCCTCTGCGTCGCATGGCGG") self.assertEqual(record[10].instances[11], "GACCATAGACGAGCATCAAAG") self.assertEqual(record[10].instances[12], "GGCCCTCGGATCGCTTGGGAA") self.assertEqual( record[10].mask, (1, 0, 1, 1, 0, 0, 0, 1, 0, 0, 0, 1, 1, 1, 1, 0, 0, 0, 0, 1, 1), ) self.assertAlmostEqual(record[10].score, 9.01393) self.assertEqual(record[11].alphabet, "ACGT") self.assertEqual(len(record[11].instances), 16) self.assertEqual(record[11].instances[0], "GCCGTCCGTC") self.assertEqual(record[11].instances[1], "GGCGTGCGCG") self.assertEqual(record[11].instances[2], "GGCGCGTGTC") self.assertEqual(record[11].instances[3], "AGCGCGTGTG") self.assertEqual(record[11].instances[4], "GCGGTGCGTG") self.assertEqual(record[11].instances[5], "AGCGCGTGTC") self.assertEqual(record[11].instances[6], "AGCGTCCGCG") self.assertEqual(record[11].instances[7], "ACCGTCTGTG") self.assertEqual(record[11].instances[8], "GCCATGCGAC") self.assertEqual(record[11].instances[9], "ACCACCCGTC") self.assertEqual(record[11].instances[10], "GGCGCCGGAG") self.assertEqual(record[11].instances[11], "ACCACGTGTC") self.assertEqual(record[11].instances[12], "GGCTTGCGAG") self.assertEqual(record[11].instances[13], "GCGATCCGAG") self.assertEqual(record[11].instances[14], "AGTGCGCGTC") self.assertEqual(record[11].instances[15], "AGTGCCCGAG") self.assertEqual(record[11].mask, (1, 1, 1, 1, 1, 1, 1, 1, 1, 1)) self.assertAlmostEqual(record[11].score, 7.51121) self.assertEqual(record[12].alphabet, "ACGT") self.assertEqual(len(record[12].instances), 16) self.assertEqual(record[12].instances[0], "GCCGACGGGTGGTCATCGGG") self.assertEqual(record[12].instances[1], "GCACGACGCTTTGTACCTGG") self.assertEqual(record[12].instances[2], "CCTGGGAGGGTTCAATAACG") self.assertEqual(record[12].instances[3], "GCGCGTCCCGGGCCAATAGC") self.assertEqual(record[12].instances[4], "GCCGTCTGCTGGACAACGGG") self.assertEqual(record[12].instances[5], "GTCCCTTCCGGTACATGAGG") self.assertEqual(record[12].instances[6], "GCTGCTCCCCGCATACAGCG") self.assertEqual(record[12].instances[7], "GCCCCAAGCTTACCCAGGGA") self.assertEqual(record[12].instances[8], "ACCGGCTGACGCTAATACGG") self.assertEqual(record[12].instances[9], "GCGGGGGGCAGGTCATTACA") self.assertEqual(record[12].instances[10], "GCTGGCAGCGTCTAAGAAGG") self.assertEqual(record[12].instances[11], "GCAGGTGGTCGTGCAATACG") self.assertEqual(record[12].instances[12], "GCTGGTTGAAGTCCCGTGCG") self.assertEqual(record[12].instances[13], "GCACGTAGCTGGTAAATAGG") self.assertEqual(record[12].instances[14], "GCGGCGTGGATTTCATACAG") self.assertEqual(record[12].instances[15], "CCTGGAGGCTTAGACTTGGG") self.assertEqual( record[12].mask, (1, 1, 0, 1, 1, 0, 0, 1, 1, 0, 1, 0, 0, 0, 1, 0, 0, 0, 1, 1), ) self.assertAlmostEqual(record[12].score, 5.63667) self.assertEqual(record[13].alphabet, "ACGT") self.assertEqual(len(record[13].instances), 15) self.assertEqual(record[13].instances[0], "GCCGACGGGTGGTCATCGGG") self.assertEqual(record[13].instances[1], "ATCCGCGGACGCTTAGAGGG") self.assertEqual(record[13].instances[2], "ACGCTTTGTACCTGGCTTGC") self.assertEqual(record[13].instances[3], "ACGGACGGCACTTAGCAGCG") self.assertEqual(record[13].instances[4], "GCCGTCTGCTGGACAACGGG") self.assertEqual(record[13].instances[5], "ACACACAGACGGTTGAAAGG") self.assertEqual(record[13].instances[6], "GCCGATAGTGCTTAAGTTCG") self.assertEqual(record[13].instances[7], "CTTGCCCGTACCGGACCTCG") self.assertEqual(record[13].instances[8], "ACCGGCTGACGCTAATACGG") self.assertEqual(record[13].instances[9], "GCCCCCCGCATAGTAGGGGG") self.assertEqual(record[13].instances[10], "GCTGGCAGCGTCTAAGAAGG") self.assertEqual(record[13].instances[11], "GCAGGTGGTCGTGCAATACG") self.assertEqual(record[13].instances[12], "ACGCACGGGACTTCAACCAG") self.assertEqual(record[13].instances[13], "GCACGTAGCTGGTAAATAGG") self.assertEqual(record[13].instances[14], "ATCCTCTGCGTCGCATGGCG") self.assertEqual( record[13].mask, (1, 1, 0, 1, 0, 1, 0, 1, 0, 0, 1, 0, 1, 0, 1, 0, 0, 0, 1, 1), ) self.assertAlmostEqual(record[13].score, 3.89842) self.assertEqual(record[14].alphabet, "ACGT") self.assertEqual(len(record[14].instances), 14) self.assertEqual(record[14].instances[0], "GAGGCTGTGTAT") self.assertEqual(record[14].instances[1], "GAGGTCGGGGGT") self.assertEqual(record[14].instances[2], "GACGGACGGCAC") self.assertEqual(record[14].instances[3], "TTGGCCCGGGAC") self.assertEqual(record[14].instances[4], "GAGGCTCGGCCC") self.assertEqual(record[14].instances[5], "CACGCGCTGTAT") self.assertEqual(record[14].instances[6], "TAGGCCAGGTAT") self.assertEqual(record[14].instances[7], "GAGGTCCGGTAC") self.assertEqual(record[14].instances[8], "TACGCTGGGGAT") self.assertEqual(record[14].instances[9], "GTCGCGGAGGAT") self.assertEqual(record[14].instances[10], "TACGCACGGGAC") self.assertEqual(record[14].instances[11], "TACTCCGGGTAC") self.assertEqual(record[14].instances[12], "GACGCAGAGGAT") self.assertEqual(record[14].instances[13], "TAGGCGGGCCAT") self.assertEqual(record[14].mask, (1, 1, 1, 1, 1, 0, 1, 1, 1, 0, 1, 1)) self.assertAlmostEqual(record[14].score, 3.33444) self.assertEqual(record[15].alphabet, "ACGT") self.assertEqual(len(record[15].instances), 21) self.assertEqual(record[15].instances[0], "CGGCTCAATCGTAGAGGC") self.assertEqual(record[15].instances[1], "CGACGGGTGGTCATCGGG") self.assertEqual(record[15].instances[2], "CGCTTAGAGGGCACAAGC") self.assertEqual(record[15].instances[3], "TGACACGCGCCTGGGAGG") self.assertEqual(record[15].instances[4], "CGATACGCTGCTAAGTGC") self.assertEqual(record[15].instances[5], "CGTCCCGGGCCAATAGCG") self.assertEqual(record[15].instances[6], "CCACGCTTCGACACGTGG") self.assertEqual(record[15].instances[7], "CGTCTGCTGGACAACGGG") self.assertEqual(record[15].instances[8], "ACACAGACGGTTGAAAGG") self.assertEqual(record[15].instances[9], "TGCTCCCCGCATACAGCG") self.assertEqual(record[15].instances[10], "TGAGGCTTGCCCGTACCG") self.assertEqual(record[15].instances[11], "TGCCCCAAGCTTACCCAG") self.assertEqual(record[15].instances[12], "CGGCTGACGCTAATACGG") self.assertEqual(record[15].instances[13], "CGCGACGTCCCTATGAGC") self.assertEqual(record[15].instances[14], "TGCCCCCCGCATAGTAGG") self.assertEqual(record[15].instances[15], "CGTTGCCTTCTTAGACGC") self.assertEqual(record[15].instances[16], "TGACTCAATCGTAGACCC") self.assertEqual(record[15].instances[17], "AGTCCCGTGCGTATGTGG") self.assertEqual(record[15].instances[18], "AGGCTCGCACGTAGCTGG") self.assertEqual(record[15].instances[19], "CCACGCCGCCATGCGACG") self.assertEqual(record[15].instances[20], "AGCCTCCAGGTCGCATGG") self.assertEqual( record[15].mask, (1, 1, 0, 1, 0, 1, 0, 0, 1, 1, 0, 1, 1, 0, 0, 0, 1, 1) ) self.assertAlmostEqual(record[15].score, 1.0395) def test_clusterbuster_parsing_and_output(self): """Test if Bio.motifs can parse and output Cluster Buster PFM files.""" record = motifs.parse(self.CLUSTERBUSTERin, "clusterbuster") self.assertEqual(len(record), 3) self.assertEqual(record[0].name, "MA0004.1") self.assertEqual(record[1].name, "MA0006.1") self.assertEqual(record[2].name, "MA0008.1") self.assertEqual(record[0].degenerate_consensus, "CACGTG") self.assertEqual(record[1].degenerate_consensus, "YGCGTG") self.assertEqual(record[2].degenerate_consensus, "CAATTATT") self.CLUSTERBUSTERin.seek(0) self.assertEqual( motifs.write(record, "clusterbuster").split(), self.CLUSTERBUSTERin.read().split(), ) def test_xms_parsing(self): """Test if Bio.motifs can parse and output xms PFM files.""" record = motifs.parse(self.XMSin, "xms") self.assertEqual(len(record), 1) self.assertEqual(record[0].name, "Abd-B") self.assertEqual(record[0].length, 14) def test_pfm_parsing(self): """Test if Bio.motifs can parse JASPAR-style pfm files.""" m = motifs.read(self.PFMin, "pfm") self.assertEqual(m.length, 12) def test_pfm_four_columns_parsing(self): """Test if Bio.motifs.pfm can parse motifs in position frequency matrix format (4 columns).""" record = motifs.parse(self.PFMFOURCOLUMNSin, "pfm-four-columns") self.assertEqual(len(record), 8) self.assertEqual(record[0].length, 8) self.assertEqual(record[1].length, 20) self.assertEqual(record[2].name, "M1734_0.90") self.assertEqual(record[2].length, 11) self.assertEqual(record[3].name, "AbdA_Cell_FBgn0000014") self.assertEqual(record[3].length, 7) self.assertEqual(record[4].length, 10) self.assertEqual(record[5].name, "AHR_si") self.assertEqual(record[5].length, 9) self.assertEqual(record[6].length, 8) self.assertEqual(record[7].length, 11) def test_pfm_four_rows_parsing(self): """Test if Bio.motifs.pfm can parse motifs in position frequency matrix format (4 rows).""" record = motifs.parse(self.PFMFOURROWSin, "pfm-four-rows") self.assertEqual(len(record), 8) self.assertEqual(record[0].length, 6) self.assertEqual(record[1].length, 15) self.assertEqual(record[2].length, 15) self.assertEqual(record[3].length, 6) self.assertEqual(record[4].length, 6) self.assertEqual(record[5].name, "abd-A") self.assertEqual(record[5].length, 8) self.assertEqual(record[6].name, "MA0001.1 AGL3") self.assertEqual(record[6].length, 10) self.assertEqual(record[7].name, "MA0001.1 AGL3") self.assertEqual(record[7].length, 10) def test_sites_parsing(self): """Test if Bio.motifs can parse JASPAR-style sites files.""" m = motifs.read(self.SITESin, "sites") self.assertEqual(m.length, 6) def test_TFoutput(self): """Ensure that we can write proper TransFac output files.""" with open(self.TFout, "w") as output_handle: output_handle.write(self.m.format("transfac")) def test_format(self): self.m.name = "Foo" s1 = self.m.format("pfm") expected_pfm = """ 1.00 0.00 1.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00 1.00 0.00 """ s2 = self.m.format("jaspar") expected_jaspar = """>None Foo A [ 1.00 0.00 1.00 0.00 1.00] C [ 0.00 0.00 0.00 0.00 0.00] G [ 0.00 0.00 0.00 0.00 0.00] T [ 0.00 1.00 0.00 1.00 0.00] """ self.assertEqual(s2, expected_jaspar) s3 = self.m.format("transfac") expected_transfac = """P0 A C G T 01 1 0 0 0 A 02 0 0 0 1 T 03 1 0 0 0 A 04 0 0 0 1 T 05 1 0 0 0 A XX // """ self.assertEqual(s3, expected_transfac) self.assertRaises(ValueError, self.m.format, "foo_bar") def test_reverse_complement(self): """Test if motifs can be reverse-complemented.""" background = {"A": 0.3, "C": 0.2, "G": 0.2, "T": 0.3} pseudocounts = 0.5 m = self.m m.background = background m.pseudocounts = pseudocounts received_forward = self.m.format("transfac") expected_forward = """\ P0 A C G T 01 1 0 0 0 A 02 0 0 0 1 T 03 1 0 0 0 A 04 0 0 0 1 T 05 1 0 0 0 A XX // """ self.assertEqual(received_forward, expected_forward) expected_forward_pwm = """\ 0 1 2 3 4 A: 0.50 0.17 0.50 0.17 0.50 C: 0.17 0.17 0.17 0.17 0.17 G: 0.17 0.17 0.17 0.17 0.17 T: 0.17 0.50 0.17 0.50 0.17 """ self.assertEqual(str(m.pwm), expected_forward_pwm) m = m.reverse_complement() received_reverse = m.format("transfac") expected_reverse = """\ P0 A C G T 01 0 0 0 1 T 02 1 0 0 0 A 03 0 0 0 1 T 04 1 0 0 0 A 05 0 0 0 1 T XX // """ self.assertEqual(received_reverse, expected_reverse) expected_reverse_pwm = """\ 0 1 2 3 4 A: 0.17 0.50 0.17 0.50 0.17 C: 0.17 0.17 0.17 0.17 0.17 G: 0.17 0.17 0.17 0.17 0.17 T: 0.50 0.17 0.50 0.17 0.50 """ self.assertEqual(str(m.pwm), expected_reverse_pwm) # Same thing, but now start with a motif calculated from a count matrix counts = self.m.counts m = motifs.Motif(counts=counts) m.background = background m.pseudocounts = pseudocounts received_forward = m.format("transfac") self.assertEqual(received_forward, expected_forward) self.assertEqual(str(m.pwm), expected_forward_pwm) m = m.reverse_complement() received_reverse = m.format("transfac") self.assertEqual(received_reverse, expected_reverse) self.assertEqual(str(m.pwm), expected_reverse_pwm) class TestMEME(unittest.TestCase): def test_meme_parser_1(self): """Parse motifs/meme.INO_up800.classic.oops.xml file.""" with open("motifs/meme.INO_up800.classic.oops.xml") as handle: record = motifs.parse(handle, "meme") self.assertEqual(record.version, "5.0.1") self.assertEqual(record.datafile, "common/INO_up800.s") self.assertEqual(record.alphabet, "ACGT") self.assertEqual(len(record.sequences), 7) self.assertEqual(record.sequences[0], "sequence_0") self.assertEqual(record.sequences[1], "sequence_1") self.assertEqual(record.sequences[2], "sequence_2") self.assertEqual(record.sequences[3], "sequence_3") self.assertEqual(record.sequences[4], "sequence_4") self.assertEqual(record.sequences[5], "sequence_5") self.assertEqual(record.sequences[6], "sequence_6") self.assertEqual( record.command, "meme common/INO_up800.s -oc results/meme10 -mod oops -dna -revcomp -bfile common/yeast.nc.6.freq -nmotifs 2 -objfun classic -minw 8 -nostatus ", ) self.assertEqual(len(record), 2) motif = record[0] self.assertEqual(motif.name, "GSKGCATGTGAAA") self.assertEqual(record["GSKGCATGTGAAA"], motif) self.assertEqual(motif.num_occurrences, 7) self.assertAlmostEqual(motif.evalue, 0.19) self.assertEqual(motif.alphabet, "ACGT") self.assertEqual(len(motif.instances), 7) self.assertAlmostEqual(motif.instances[0].pvalue, 1.21e-08) self.assertAlmostEqual(motif.instances[1].pvalue, 1.87e-08) self.assertAlmostEqual(motif.instances[2].pvalue, 6.62e-08) self.assertAlmostEqual(motif.instances[3].pvalue, 1.05e-07) self.assertAlmostEqual(motif.instances[4].pvalue, 1.69e-07) self.assertAlmostEqual(motif.instances[5].pvalue, 5.62e-07) self.assertAlmostEqual(motif.instances[6].pvalue, 1.08e-06) self.assertEqual(motif.instances[0].sequence_name, "INO1") self.assertEqual(motif.instances[1].sequence_name, "FAS1") self.assertEqual(motif.instances[2].sequence_name, "ACC1") self.assertEqual(motif.instances[3].sequence_name, "CHO2") self.assertEqual(motif.instances[4].sequence_name, "CHO1") self.assertEqual(motif.instances[5].sequence_name, "FAS2") self.assertEqual(motif.instances[6].sequence_name, "OPI3") self.assertEqual(motif.instances[0].sequence_id, "sequence_5") self.assertEqual(motif.instances[1].sequence_id, "sequence_2") self.assertEqual(motif.instances[2].sequence_id, "sequence_4") self.assertEqual(motif.instances[3].sequence_id, "sequence_1") self.assertEqual(motif.instances[4].sequence_id, "sequence_0") self.assertEqual(motif.instances[5].sequence_id, "sequence_3") self.assertEqual(motif.instances[6].sequence_id, "sequence_6") self.assertEqual(motif.instances[0].strand, "+") self.assertEqual(motif.instances[1].strand, "-") self.assertEqual(motif.instances[2].strand, "-") self.assertEqual(motif.instances[3].strand, "-") self.assertEqual(motif.instances[4].strand, "-") self.assertEqual(motif.instances[5].strand, "-") self.assertEqual(motif.instances[6].strand, "+") self.assertEqual(motif.instances[0].length, 13) self.assertEqual(motif.instances[1].length, 13) self.assertEqual(motif.instances[2].length, 13) self.assertEqual(motif.instances[3].length, 13) self.assertEqual(motif.instances[4].length, 13) self.assertEqual(motif.instances[5].length, 13) self.assertEqual(motif.instances[6].length, 13) self.assertEqual(motif.instances[0].start, 620) self.assertEqual(motif.instances[1].start, 94) self.assertEqual(motif.instances[2].start, 82) self.assertEqual(motif.instances[3].start, 353) self.assertEqual(motif.instances[4].start, 639) self.assertEqual(motif.instances[5].start, 566) self.assertEqual(motif.instances[6].start, 585) self.assertEqual(motif.instances[0], "GCGGCATGTGAAA") self.assertEqual(motif.instances[1], "GCGGCATGTGAAG") self.assertEqual(motif.instances[2], "GGGCCATGTGAAG") self.assertEqual(motif.instances[3], "GCGGCATGAGAAA") self.assertEqual(motif.instances[4], "GGTCCATGTGAAA") self.assertEqual(motif.instances[5], "GTAGCATGTGAAA") self.assertEqual(motif.instances[6], "AGTGCATGTGGAA") motif = record[1] self.assertEqual(motif.name, "TTGACWCYTGCYCWG") self.assertEqual(record["TTGACWCYTGCYCWG"], motif) self.assertEqual(motif.num_occurrences, 7) self.assertAlmostEqual(motif.evalue, 54) self.assertEqual(motif.alphabet, "ACGT") self.assertEqual(len(motif.instances), 7) self.assertAlmostEqual(motif.instances[0].pvalue, 7.2e-10) self.assertAlmostEqual(motif.instances[1].pvalue, 2.56e-08) self.assertAlmostEqual(motif.instances[2].pvalue, 1.59e-07) self.assertAlmostEqual(motif.instances[3].pvalue, 2.05e-07) self.assertAlmostEqual(motif.instances[4].pvalue, 3.85e-07) self.assertAlmostEqual(motif.instances[5].pvalue, 5.11e-07) self.assertAlmostEqual(motif.instances[6].pvalue, 8.01e-07) self.assertEqual(motif.instances[0].sequence_id, "sequence_1") self.assertEqual(motif.instances[1].sequence_id, "sequence_6") self.assertEqual(motif.instances[2].sequence_id, "sequence_4") self.assertEqual(motif.instances[3].sequence_id, "sequence_0") self.assertEqual(motif.instances[4].sequence_id, "sequence_2") self.assertEqual(motif.instances[5].sequence_id, "sequence_3") self.assertEqual(motif.instances[6].sequence_id, "sequence_5") self.assertEqual(motif.instances[0].strand, "+") self.assertEqual(motif.instances[1].strand, "-") self.assertEqual(motif.instances[2].strand, "-") self.assertEqual(motif.instances[3].strand, "+") self.assertEqual(motif.instances[4].strand, "+") self.assertEqual(motif.instances[5].strand, "-") self.assertEqual(motif.instances[6].strand, "+") self.assertEqual(motif.instances[0].length, 15) self.assertEqual(motif.instances[1].length, 15) self.assertEqual(motif.instances[2].length, 15) self.assertEqual(motif.instances[3].length, 15) self.assertEqual(motif.instances[4].length, 15) self.assertEqual(motif.instances[5].length, 15) self.assertEqual(motif.instances[6].length, 15) self.assertEqual(motif.instances[0].start, 104) self.assertEqual(motif.instances[1].start, 566) self.assertEqual(motif.instances[2].start, 585) self.assertEqual(motif.instances[3].start, 30) self.assertEqual(motif.instances[4].start, 54) self.assertEqual(motif.instances[5].start, 272) self.assertEqual(motif.instances[6].start, 214) self.assertEqual(motif.instances[0], "TTGACACCTGCCCAG") self.assertEqual(motif.instances[1], "TTGACACCTACCCTG") self.assertEqual(motif.instances[2], "TTGTCTCTTGCTCTG") self.assertEqual(motif.instances[3], "TTGACACTTGATCAG") self.assertEqual(motif.instances[4], "TTCACTACTCCCCTG") self.assertEqual(motif.instances[5], "TTGACAACGGCTGGG") self.assertEqual(motif.instances[6], "TTCACGCTTGCTACG") def test_meme_parser_2(self): """Parsing motifs/meme.adh.classic.oops.xml file.""" with open("motifs/meme.adh.classic.oops.xml") as handle: record = motifs.parse(handle, "meme") self.assertEqual(record.version, "5.0.1") self.assertEqual(record.datafile, "common/adh.s") self.assertEqual(record.alphabet, "ACDEFGHIKLMNPQRSTVWY") self.assertEqual(len(record.sequences), 33) self.assertEqual(record.sequences[0], "sequence_0") self.assertEqual(record.sequences[1], "sequence_1") self.assertEqual(record.sequences[2], "sequence_2") self.assertEqual(record.sequences[3], "sequence_3") self.assertEqual(record.sequences[4], "sequence_4") self.assertEqual(record.sequences[5], "sequence_5") self.assertEqual(record.sequences[6], "sequence_6") self.assertEqual(record.sequences[7], "sequence_7") self.assertEqual(record.sequences[8], "sequence_8") self.assertEqual(record.sequences[9], "sequence_9") self.assertEqual(record.sequences[10], "sequence_10") self.assertEqual(record.sequences[11], "sequence_11") self.assertEqual(record.sequences[12], "sequence_12") self.assertEqual(record.sequences[13], "sequence_13") self.assertEqual(record.sequences[14], "sequence_14") self.assertEqual(record.sequences[15], "sequence_15") self.assertEqual(record.sequences[16], "sequence_16") self.assertEqual(record.sequences[17], "sequence_17") self.assertEqual(record.sequences[18], "sequence_18") self.assertEqual(record.sequences[19], "sequence_19") self.assertEqual(record.sequences[20], "sequence_20") self.assertEqual(record.sequences[21], "sequence_21") self.assertEqual(record.sequences[22], "sequence_22") self.assertEqual(record.sequences[23], "sequence_23") self.assertEqual(record.sequences[24], "sequence_24") self.assertEqual(record.sequences[25], "sequence_25") self.assertEqual(record.sequences[26], "sequence_26") self.assertEqual(record.sequences[27], "sequence_27") self.assertEqual(record.sequences[28], "sequence_28") self.assertEqual(record.sequences[29], "sequence_29") self.assertEqual(record.sequences[30], "sequence_30") self.assertEqual(record.sequences[31], "sequence_31") self.assertEqual(record.sequences[32], "sequence_32") self.assertEqual( record.command, "meme common/adh.s -oc results/meme4 -mod oops -protein -nmotifs 2 -objfun classic -minw 8 -nostatus ", ) self.assertEqual(len(record), 2) motif = record[0] self.assertEqual(motif.id, "motif_1") self.assertEqual(motif.name, "GKVALVTGAASGJGKATAKAL") self.assertEqual(motif.alt_id, "MEME-1") self.assertEqual(record["GKVALVTGAASGJGKATAKAL"], motif) self.assertEqual(motif.num_occurrences, 33) self.assertAlmostEqual(motif.evalue, 3.6e-165) self.assertEqual(motif.alphabet, "ACDEFGHIKLMNPQRSTVWY") self.assertEqual(len(motif.instances), 33) self.assertAlmostEqual(motif.instances[0].pvalue, 8.78e-18) self.assertAlmostEqual(motif.instances[1].pvalue, 1.41e-17) self.assertAlmostEqual(motif.instances[2].pvalue, 1.42e-16) self.assertAlmostEqual(motif.instances[3].pvalue, 2.75e-16) self.assertAlmostEqual(motif.instances[4].pvalue, 3.55e-16) self.assertAlmostEqual(motif.instances[5].pvalue, 3.55e-16) self.assertAlmostEqual(motif.instances[6].pvalue, 1.74e-15) self.assertAlmostEqual(motif.instances[7].pvalue, 3.87e-15) self.assertAlmostEqual(motif.instances[8].pvalue, 4.84e-15) self.assertAlmostEqual(motif.instances[9].pvalue, 1.04e-14) self.assertAlmostEqual(motif.instances[10].pvalue, 1.58e-14) self.assertAlmostEqual(motif.instances[11].pvalue, 1.76e-14) self.assertAlmostEqual(motif.instances[12].pvalue, 2.16e-14) self.assertAlmostEqual(motif.instances[13].pvalue, 2.94e-14) self.assertAlmostEqual(motif.instances[14].pvalue, 3.25e-14) self.assertAlmostEqual(motif.instances[15].pvalue, 3.98e-14) self.assertAlmostEqual(motif.instances[16].pvalue, 4.39e-14) self.assertAlmostEqual(motif.instances[17].pvalue, 4.39e-14) self.assertAlmostEqual(motif.instances[18].pvalue, 4.85e-14) self.assertAlmostEqual(motif.instances[19].pvalue, 6.52e-14) self.assertAlmostEqual(motif.instances[20].pvalue, 1.41e-13) self.assertAlmostEqual(motif.instances[21].pvalue, 1.55e-13) self.assertAlmostEqual(motif.instances[22].pvalue, 3.07e-12) self.assertAlmostEqual(motif.instances[23].pvalue, 5.43e-12) self.assertAlmostEqual(motif.instances[24].pvalue, 6.91e-12) self.assertAlmostEqual(motif.instances[25].pvalue, 8.76e-12) self.assertAlmostEqual(motif.instances[26].pvalue, 9.48e-12) self.assertAlmostEqual(motif.instances[27].pvalue, 1.2e-11) self.assertAlmostEqual(motif.instances[28].pvalue, 1.19e-09) self.assertAlmostEqual(motif.instances[29].pvalue, 1.54e-09) self.assertAlmostEqual(motif.instances[30].pvalue, 1.99e-09) self.assertAlmostEqual(motif.instances[31].pvalue, 1.42e-06) self.assertAlmostEqual(motif.instances[32].pvalue, 3.43e-06) self.assertEqual(motif.instances[0].sequence_name, "BUDC_KLETE") self.assertEqual(motif.instances[1].sequence_name, "YINL_LISMO") self.assertEqual(motif.instances[2].sequence_name, "DHII_HUMAN") self.assertEqual(motif.instances[3].sequence_name, "HDE_CANTR") self.assertEqual(motif.instances[4].sequence_name, "YRTP_BACSU") self.assertEqual(motif.instances[5].sequence_name, "ENTA_ECOLI") self.assertEqual(motif.instances[6].sequence_name, "HDHA_ECOLI") self.assertEqual(motif.instances[7].sequence_name, "RIDH_KLEAE") self.assertEqual(motif.instances[8].sequence_name, "DHB2_HUMAN") self.assertEqual(motif.instances[9].sequence_name, "FIXR_BRAJA") self.assertEqual(motif.instances[10].sequence_name, "PCR_PEA") self.assertEqual(motif.instances[11].sequence_name, "DHCA_HUMAN") self.assertEqual(motif.instances[12].sequence_name, "BDH_HUMAN") self.assertEqual(motif.instances[13].sequence_name, "3BHD_COMTE") self.assertEqual(motif.instances[14].sequence_name, "DHGB_BACME") self.assertEqual(motif.instances[15].sequence_name, "DHMA_FLAS1") self.assertEqual(motif.instances[16].sequence_name, "FVT1_HUMAN") self.assertEqual(motif.instances[17].sequence_name, "BA72_EUBSP") self.assertEqual(motif.instances[18].sequence_name, "BPHB_PSEPS") self.assertEqual(motif.instances[19].sequence_name, "DHB3_HUMAN") self.assertEqual(motif.instances[20].sequence_name, "DHES_HUMAN") self.assertEqual(motif.instances[21].sequence_name, "AP27_MOUSE") self.assertEqual(motif.instances[22].sequence_name, "2BHD_STREX") self.assertEqual(motif.instances[23].sequence_name, "NODG_RHIME") self.assertEqual(motif.instances[24].sequence_name, "HMTR_LEIMA") self.assertEqual(motif.instances[25].sequence_name, "LIGD_PSEPA") self.assertEqual(motif.instances[26].sequence_name, "MAS1_AGRRA") self.assertEqual(motif.instances[27].sequence_name, "RFBB_NEIGO") self.assertEqual(motif.instances[28].sequence_name, "GUTD_ECOLI") self.assertEqual(motif.instances[29].sequence_name, "ADH_DROME") self.assertEqual(motif.instances[30].sequence_name, "FABI_ECOLI") self.assertEqual(motif.instances[31].sequence_name, "CSGA_MYXXA") self.assertEqual(motif.instances[32].sequence_name, "YURA_MYXXA") self.assertEqual(motif.instances[0].sequence_id, "sequence_7") self.assertEqual(motif.instances[1].sequence_id, "sequence_20") self.assertEqual(motif.instances[2].sequence_id, "sequence_10") self.assertEqual(motif.instances[3].sequence_id, "sequence_15") self.assertEqual(motif.instances[4].sequence_id, "sequence_21") self.assertEqual(motif.instances[5].sequence_id, "sequence_12") self.assertEqual(motif.instances[6].sequence_id, "sequence_16") self.assertEqual(motif.instances[7].sequence_id, "sequence_19") self.assertEqual(motif.instances[8].sequence_id, "sequence_23") self.assertEqual(motif.instances[9].sequence_id, "sequence_13") self.assertEqual(motif.instances[10].sequence_id, "sequence_30") self.assertEqual(motif.instances[11].sequence_id, "sequence_25") self.assertEqual(motif.instances[12].sequence_id, "sequence_5") self.assertEqual(motif.instances[13].sequence_id, "sequence_1") self.assertEqual(motif.instances[14].sequence_id, "sequence_9") self.assertEqual(motif.instances[15].sequence_id, "sequence_11") self.assertEqual(motif.instances[16].sequence_id, "sequence_27") self.assertEqual(motif.instances[17].sequence_id, "sequence_4") self.assertEqual(motif.instances[18].sequence_id, "sequence_6") self.assertEqual(motif.instances[19].sequence_id, "sequence_24") self.assertEqual(motif.instances[20].sequence_id, "sequence_8") self.assertEqual(motif.instances[21].sequence_id, "sequence_3") self.assertEqual(motif.instances[22].sequence_id, "sequence_0") self.assertEqual(motif.instances[23].sequence_id, "sequence_18") self.assertEqual(motif.instances[24].sequence_id, "sequence_28") self.assertEqual(motif.instances[25].sequence_id, "sequence_17") self.assertEqual(motif.instances[26].sequence_id, "sequence_29") self.assertEqual(motif.instances[27].sequence_id, "sequence_31") self.assertEqual(motif.instances[28].sequence_id, "sequence_14") self.assertEqual(motif.instances[29].sequence_id, "sequence_2") self.assertEqual(motif.instances[30].sequence_id, "sequence_26") self.assertEqual(motif.instances[31].sequence_id, "sequence_22") self.assertEqual(motif.instances[32].sequence_id, "sequence_32") self.assertEqual(motif.instances[0].strand, "+") self.assertEqual(motif.instances[1].strand, "+") self.assertEqual(motif.instances[2].strand, "+") self.assertEqual(motif.instances[3].strand, "+") self.assertEqual(motif.instances[4].strand, "+") self.assertEqual(motif.instances[5].strand, "+") self.assertEqual(motif.instances[6].strand, "+") self.assertEqual(motif.instances[7].strand, "+") self.assertEqual(motif.instances[8].strand, "+") self.assertEqual(motif.instances[9].strand, "+") self.assertEqual(motif.instances[10].strand, "+") self.assertEqual(motif.instances[11].strand, "+") self.assertEqual(motif.instances[12].strand, "+") self.assertEqual(motif.instances[13].strand, "+") self.assertEqual(motif.instances[14].strand, "+") self.assertEqual(motif.instances[15].strand, "+") self.assertEqual(motif.instances[16].strand, "+") self.assertEqual(motif.instances[17].strand, "+") self.assertEqual(motif.instances[18].strand, "+") self.assertEqual(motif.instances[19].strand, "+") self.assertEqual(motif.instances[20].strand, "+") self.assertEqual(motif.instances[21].strand, "+") self.assertEqual(motif.instances[22].strand, "+") self.assertEqual(motif.instances[23].strand, "+") self.assertEqual(motif.instances[24].strand, "+") self.assertEqual(motif.instances[25].strand, "+") self.assertEqual(motif.instances[26].strand, "+") self.assertEqual(motif.instances[27].strand, "+") self.assertEqual(motif.instances[28].strand, "+") self.assertEqual(motif.instances[29].strand, "+") self.assertEqual(motif.instances[30].strand, "+") self.assertEqual(motif.instances[31].strand, "+") self.assertEqual(motif.instances[32].strand, "+") self.assertEqual(motif.instances[0].length, 21) self.assertEqual(motif.instances[1].length, 21) self.assertEqual(motif.instances[2].length, 21) self.assertEqual(motif.instances[3].length, 21) self.assertEqual(motif.instances[4].length, 21) self.assertEqual(motif.instances[5].length, 21) self.assertEqual(motif.instances[6].length, 21) self.assertEqual(motif.instances[7].length, 21) self.assertEqual(motif.instances[8].length, 21) self.assertEqual(motif.instances[9].length, 21) self.assertEqual(motif.instances[10].length, 21) self.assertEqual(motif.instances[11].length, 21) self.assertEqual(motif.instances[12].length, 21) self.assertEqual(motif.instances[13].length, 21) self.assertEqual(motif.instances[14].length, 21) self.assertEqual(motif.instances[15].length, 21) self.assertEqual(motif.instances[16].length, 21) self.assertEqual(motif.instances[17].length, 21) self.assertEqual(motif.instances[18].length, 21) self.assertEqual(motif.instances[19].length, 21) self.assertEqual(motif.instances[20].length, 21) self.assertEqual(motif.instances[21].length, 21) self.assertEqual(motif.instances[22].length, 21) self.assertEqual(motif.instances[23].length, 21) self.assertEqual(motif.instances[24].length, 21) self.assertEqual(motif.instances[25].length, 21) self.assertEqual(motif.instances[26].length, 21) self.assertEqual(motif.instances[27].length, 21) self.assertEqual(motif.instances[28].length, 21) self.assertEqual(motif.instances[29].length, 21) self.assertEqual(motif.instances[30].length, 21) self.assertEqual(motif.instances[31].length, 21) self.assertEqual(motif.instances[32].length, 21) self.assertEqual(motif.instances[0].start, 2) self.assertEqual(motif.instances[1].start, 5) self.assertEqual(motif.instances[2].start, 34) self.assertEqual(motif.instances[3].start, 322) self.assertEqual(motif.instances[4].start, 6) self.assertEqual(motif.instances[5].start, 5) self.assertEqual(motif.instances[6].start, 11) self.assertEqual(motif.instances[7].start, 14) self.assertEqual(motif.instances[8].start, 82) self.assertEqual(motif.instances[9].start, 36) self.assertEqual(motif.instances[10].start, 86) self.assertEqual(motif.instances[11].start, 4) self.assertEqual(motif.instances[12].start, 55) self.assertEqual(motif.instances[13].start, 6) self.assertEqual(motif.instances[14].start, 7) self.assertEqual(motif.instances[15].start, 14) self.assertEqual(motif.instances[16].start, 32) self.assertEqual(motif.instances[17].start, 6) self.assertEqual(motif.instances[18].start, 5) self.assertEqual(motif.instances[19].start, 48) self.assertEqual(motif.instances[20].start, 2) self.assertEqual(motif.instances[21].start, 7) self.assertEqual(motif.instances[22].start, 6) self.assertEqual(motif.instances[23].start, 6) self.assertEqual(motif.instances[24].start, 6) self.assertEqual(motif.instances[25].start, 6) self.assertEqual(motif.instances[26].start, 245) self.assertEqual(motif.instances[27].start, 6) self.assertEqual(motif.instances[28].start, 2) self.assertEqual(motif.instances[29].start, 6) self.assertEqual(motif.instances[30].start, 6) self.assertEqual(motif.instances[31].start, 13) self.assertEqual(motif.instances[32].start, 116) self.assertEqual(motif.instances[0], "QKVALVTGAGQGIGKAIALRL") self.assertEqual(motif.instances[1], "NKVIIITGASSGIGKATALLL") self.assertEqual(motif.instances[2], "GKKVIVTGASKGIGREMAYHL") self.assertEqual(motif.instances[3], "DKVVLITGAGAGLGKEYAKWF") self.assertEqual(motif.instances[4], "HKTALITGGGRGIGRATALAL") self.assertEqual(motif.instances[5], "GKNVWVTGAGKGIGYATALAF") self.assertEqual(motif.instances[6], "GKCAIITGAGAGIGKEIAITF") self.assertEqual(motif.instances[7], "GKVAAITGAASGIGLECARTL") self.assertEqual(motif.instances[8], "QKAVLVTGGDCGLGHALCKYL") self.assertEqual(motif.instances[9], "PKVMLLTGASRGIGHATAKLF") self.assertEqual(motif.instances[10], "KGNVVITGASSGLGLATAKAL") self.assertEqual(motif.instances[11], "IHVALVTGGNKGIGLAIVRDL") self.assertEqual(motif.instances[12], "SKAVLVTGCDSGFGFSLAKHL") self.assertEqual(motif.instances[13], "GKVALVTGGASGVGLEVVKLL") self.assertEqual(motif.instances[14], "GKVVVITGSSTGLGKSMAIRF") self.assertEqual(motif.instances[15], "GKAAIVTGAAGGIGRATVEAY") self.assertEqual(motif.instances[16], "GAHVVVTGGSSGIGKCIAIEC") self.assertEqual(motif.instances[17], "DKVTIITGGTRGIGFAAAKIF") self.assertEqual(motif.instances[18], "GEAVLITGGASGLGRALVDRF") self.assertEqual(motif.instances[19], "GQWAVITGAGDGIGKAYSFEL") self.assertEqual(motif.instances[20], "RTVVLITGCSSGIGLHLAVRL") self.assertEqual(motif.instances[21], "GLRALVTGAGKGIGRDTVKAL") self.assertEqual(motif.instances[22], "GKTVIITGGARGLGAEAARQA") self.assertEqual(motif.instances[23], "GRKALVTGASGAIGGAIARVL") self.assertEqual(motif.instances[24], "VPVALVTGAAKRLGRSIAEGL") self.assertEqual(motif.instances[25], "DQVAFITGGASGAGFGQAKVF") self.assertEqual(motif.instances[26], "SPVILVSGSNRGVGKAIAEDL") self.assertEqual(motif.instances[27], "KKNILVTGGAGFIGSAVVRHI") self.assertEqual(motif.instances[28], "NQVAVVIGGGQTLGAFLCHGL") self.assertEqual(motif.instances[29], "NKNVIFVAGLGGIGLDTSKEL") self.assertEqual(motif.instances[30], "GKRILVTGVASKLSIAYGIAQ") self.assertEqual(motif.instances[31], "VDVLINNAGVSGLWCALGDVD") self.assertEqual(motif.instances[32], "IIDTNVTGAAATLSAVLPQMV") motif = record[1] self.assertEqual(motif.name, "VGNPGASAYSASKAAVRGLTESLALELAP") self.assertEqual(motif.alt_id, "MEME-2") self.assertEqual(record["VGNPGASAYSASKAAVRGLTESLALELAP"], motif) self.assertEqual(motif.num_occurrences, 33) self.assertAlmostEqual(motif.evalue, 3.1e-130) self.assertEqual(motif.alphabet, "ACDEFGHIKLMNPQRSTVWY") self.assertEqual(len(motif.instances), 33) self.assertAlmostEqual(motif.instances[0].pvalue, 2.09e-21) self.assertAlmostEqual(motif.instances[1].pvalue, 7.63e-20) self.assertAlmostEqual(motif.instances[2].pvalue, 6.49e-19) self.assertAlmostEqual(motif.instances[3].pvalue, 1.92e-18) self.assertAlmostEqual(motif.instances[4].pvalue, 5.46e-18) self.assertAlmostEqual(motif.instances[5].pvalue, 6.21e-18) self.assertAlmostEqual(motif.instances[6].pvalue, 4.52e-17) self.assertAlmostEqual(motif.instances[7].pvalue, 4.52e-17) self.assertAlmostEqual(motif.instances[8].pvalue, 9.21e-17) self.assertAlmostEqual(motif.instances[9].pvalue, 1.65e-16) self.assertAlmostEqual(motif.instances[10].pvalue, 2.07e-16) self.assertAlmostEqual(motif.instances[11].pvalue, 3.65e-16) self.assertAlmostEqual(motif.instances[12].pvalue, 5.7e-16) self.assertAlmostEqual(motif.instances[13].pvalue, 5.7e-16) self.assertAlmostEqual(motif.instances[14].pvalue, 7.93e-16) self.assertAlmostEqual(motif.instances[15].pvalue, 8.85e-16) self.assertAlmostEqual(motif.instances[16].pvalue, 1.1e-15) self.assertAlmostEqual(motif.instances[17].pvalue, 1.69e-15) self.assertAlmostEqual(motif.instances[18].pvalue, 3.54e-15) self.assertAlmostEqual(motif.instances[19].pvalue, 4.83e-15) self.assertAlmostEqual(motif.instances[20].pvalue, 7.27e-15) self.assertAlmostEqual(motif.instances[21].pvalue, 9.85e-15) self.assertAlmostEqual(motif.instances[22].pvalue, 2.41e-14) self.assertAlmostEqual(motif.instances[23].pvalue, 2.66e-14) self.assertAlmostEqual(motif.instances[24].pvalue, 1.22e-13) self.assertAlmostEqual(motif.instances[25].pvalue, 5.18e-13) self.assertAlmostEqual(motif.instances[26].pvalue, 1.24e-12) self.assertAlmostEqual(motif.instances[27].pvalue, 1.35e-12) self.assertAlmostEqual(motif.instances[28].pvalue, 5.59e-12) self.assertAlmostEqual(motif.instances[29].pvalue, 1.44e-10) self.assertAlmostEqual(motif.instances[30].pvalue, 1.61e-08) self.assertAlmostEqual(motif.instances[31].pvalue, 4.26e-08) self.assertAlmostEqual(motif.instances[32].pvalue, 1.16e-07) self.assertEqual(motif.instances[0].sequence_name, "BUDC_KLETE") self.assertEqual(motif.instances[1].sequence_name, "NODG_RHIME") self.assertEqual(motif.instances[2].sequence_name, "FVT1_HUMAN") self.assertEqual(motif.instances[3].sequence_name, "DHES_HUMAN") self.assertEqual(motif.instances[4].sequence_name, "DHB3_HUMAN") self.assertEqual(motif.instances[5].sequence_name, "YRTP_BACSU") self.assertEqual(motif.instances[6].sequence_name, "HMTR_LEIMA") self.assertEqual(motif.instances[7].sequence_name, "HDE_CANTR") self.assertEqual(motif.instances[8].sequence_name, "DHGB_BACME") self.assertEqual(motif.instances[9].sequence_name, "GUTD_ECOLI") self.assertEqual(motif.instances[10].sequence_name, "3BHD_COMTE") self.assertEqual(motif.instances[11].sequence_name, "DHII_HUMAN") self.assertEqual(motif.instances[12].sequence_name, "BPHB_PSEPS") self.assertEqual(motif.instances[13].sequence_name, "AP27_MOUSE") self.assertEqual(motif.instances[14].sequence_name, "BDH_HUMAN") self.assertEqual(motif.instances[15].sequence_name, "YINL_LISMO") self.assertEqual(motif.instances[16].sequence_name, "FIXR_BRAJA") self.assertEqual(motif.instances[17].sequence_name, "2BHD_STREX") self.assertEqual(motif.instances[18].sequence_name, "RFBB_NEIGO") self.assertEqual(motif.instances[19].sequence_name, "YURA_MYXXA") self.assertEqual(motif.instances[20].sequence_name, "RIDH_KLEAE") self.assertEqual(motif.instances[21].sequence_name, "DHMA_FLAS1") self.assertEqual(motif.instances[22].sequence_name, "DHB2_HUMAN") self.assertEqual(motif.instances[23].sequence_name, "HDHA_ECOLI") self.assertEqual(motif.instances[24].sequence_name, "ENTA_ECOLI") self.assertEqual(motif.instances[25].sequence_name, "LIGD_PSEPA") self.assertEqual(motif.instances[26].sequence_name, "CSGA_MYXXA") self.assertEqual(motif.instances[27].sequence_name, "BA72_EUBSP") self.assertEqual(motif.instances[28].sequence_name, "ADH_DROME") self.assertEqual(motif.instances[29].sequence_name, "MAS1_AGRRA") self.assertEqual(motif.instances[30].sequence_name, "PCR_PEA") self.assertEqual(motif.instances[31].sequence_name, "FABI_ECOLI") self.assertEqual(motif.instances[32].sequence_name, "DHCA_HUMAN") self.assertEqual(motif.instances[0].sequence_id, "sequence_7") self.assertEqual(motif.instances[1].sequence_id, "sequence_18") self.assertEqual(motif.instances[2].sequence_id, "sequence_27") self.assertEqual(motif.instances[3].sequence_id, "sequence_8") self.assertEqual(motif.instances[4].sequence_id, "sequence_24") self.assertEqual(motif.instances[5].sequence_id, "sequence_21") self.assertEqual(motif.instances[6].sequence_id, "sequence_28") self.assertEqual(motif.instances[7].sequence_id, "sequence_15") self.assertEqual(motif.instances[8].sequence_id, "sequence_9") self.assertEqual(motif.instances[9].sequence_id, "sequence_14") self.assertEqual(motif.instances[10].sequence_id, "sequence_1") self.assertEqual(motif.instances[11].sequence_id, "sequence_10") self.assertEqual(motif.instances[12].sequence_id, "sequence_6") self.assertEqual(motif.instances[13].sequence_id, "sequence_3") self.assertEqual(motif.instances[14].sequence_id, "sequence_5") self.assertEqual(motif.instances[15].sequence_id, "sequence_20") self.assertEqual(motif.instances[16].sequence_id, "sequence_13") self.assertEqual(motif.instances[17].sequence_id, "sequence_0") self.assertEqual(motif.instances[18].sequence_id, "sequence_31") self.assertEqual(motif.instances[19].sequence_id, "sequence_32") self.assertEqual(motif.instances[20].sequence_id, "sequence_19") self.assertEqual(motif.instances[21].sequence_id, "sequence_11") self.assertEqual(motif.instances[22].sequence_id, "sequence_23") self.assertEqual(motif.instances[23].sequence_id, "sequence_16") self.assertEqual(motif.instances[24].sequence_id, "sequence_12") self.assertEqual(motif.instances[25].sequence_id, "sequence_17") self.assertEqual(motif.instances[26].sequence_id, "sequence_22") self.assertEqual(motif.instances[27].sequence_id, "sequence_4") self.assertEqual(motif.instances[28].sequence_id, "sequence_2") self.assertEqual(motif.instances[29].sequence_id, "sequence_29") self.assertEqual(motif.instances[30].sequence_id, "sequence_30") self.assertEqual(motif.instances[31].sequence_id, "sequence_26") self.assertEqual(motif.instances[32].sequence_id, "sequence_25") self.assertEqual(motif.instances[0].start, 144) self.assertEqual(motif.instances[1].start, 144) self.assertEqual(motif.instances[2].start, 178) self.assertEqual(motif.instances[3].start, 147) self.assertEqual(motif.instances[4].start, 190) self.assertEqual(motif.instances[5].start, 147) self.assertEqual(motif.instances[6].start, 185) self.assertEqual(motif.instances[7].start, 459) self.assertEqual(motif.instances[8].start, 152) self.assertEqual(motif.instances[9].start, 146) self.assertEqual(motif.instances[10].start, 143) self.assertEqual(motif.instances[11].start, 175) self.assertEqual(motif.instances[12].start, 145) self.assertEqual(motif.instances[13].start, 141) self.assertEqual(motif.instances[14].start, 200) self.assertEqual(motif.instances[15].start, 146) self.assertEqual(motif.instances[16].start, 181) self.assertEqual(motif.instances[17].start, 144) self.assertEqual(motif.instances[18].start, 157) self.assertEqual(motif.instances[19].start, 152) self.assertEqual(motif.instances[20].start, 152) self.assertEqual(motif.instances[21].start, 157) self.assertEqual(motif.instances[22].start, 224) self.assertEqual(motif.instances[23].start, 151) self.assertEqual(motif.instances[24].start, 136) self.assertEqual(motif.instances[25].start, 149) self.assertEqual(motif.instances[26].start, 80) self.assertEqual(motif.instances[27].start, 149) self.assertEqual(motif.instances[28].start, 144) self.assertEqual(motif.instances[29].start, 384) self.assertEqual(motif.instances[30].start, 18) self.assertEqual(motif.instances[31].start, 177) self.assertEqual(motif.instances[32].start, 144) self.assertEqual(motif.instances[0], "VGNPELAVYSSSKFAVRGLTQTAARDLAP") self.assertEqual(motif.instances[1], "IGNPGQTNYCASKAGMIGFSKSLAQEIAT") self.assertEqual(motif.instances[2], "LGLFGFTAYSASKFAIRGLAEALQMEVKP") self.assertEqual(motif.instances[3], "MGLPFNDVYCASKFALEGLCESLAVLLLP") self.assertEqual(motif.instances[4], "FPWPLYSMYSASKAFVCAFSKALQEEYKA") self.assertEqual(motif.instances[5], "RGAAVTSAYSASKFAVLGLTESLMQEVRK") self.assertEqual(motif.instances[6], "QPLLGYTIYTMAKGALEGLTRSAALELAP") self.assertEqual(motif.instances[7], "YGNFGQANYSSSKAGILGLSKTMAIEGAK") self.assertEqual(motif.instances[8], "IPWPLFVHYAASKGGMKLMTETLALEYAP") self.assertEqual(motif.instances[9], "VGSKHNSGYSAAKFGGVGLTQSLALDLAE") self.assertEqual(motif.instances[10], "LPIEQYAGYSASKAAVSALTRAAALSCRK") self.assertEqual(motif.instances[11], "VAYPMVAAYSASKFALDGFFSSIRKEYSV") self.assertEqual(motif.instances[12], "YPNGGGPLYTAAKQAIVGLVRELAFELAP") self.assertEqual(motif.instances[13], "VTFPNLITYSSTKGAMTMLTKAMAMELGP") self.assertEqual(motif.instances[14], "MANPARSPYCITKFGVEAFSDCLRYEMYP") self.assertEqual(motif.instances[15], "KAYPGGAVYGATKWAVRDLMEVLRMESAQ") self.assertEqual(motif.instances[16], "VHPFAGSAYATSKAALASLTRELAHDYAP") self.assertEqual(motif.instances[17], "MGLALTSSYGASKWGVRGLSKLAAVELGT") self.assertEqual(motif.instances[18], "TPYAPSSPYSASKAAADHLVRAWQRTYRL") self.assertEqual(motif.instances[19], "FRGLPATRYSASKAFLSTFMESLRVDLRG") self.assertEqual(motif.instances[20], "VPVIWEPVYTASKFAVQAFVHTTRRQVAQ") self.assertEqual(motif.instances[21], "MAEPEAAAYVAAKGGVAMLTRAMAVDLAR") self.assertEqual(motif.instances[22], "APMERLASYGSSKAAVTMFSSVMRLELSK") self.assertEqual(motif.instances[23], "NKNINMTSYASSKAAASHLVRNMAFDLGE") self.assertEqual(motif.instances[24], "TPRIGMSAYGASKAALKSLALSVGLELAG") self.assertEqual(motif.instances[25], "MGSALAGPYSAAKAASINLMEGYRQGLEK") self.assertEqual(motif.instances[26], "NTDGGAYAYRMSKAALNMAVRSMSTDLRP") self.assertEqual(motif.instances[27], "FGSLSGVGYPASKASVIGLTHGLGREIIR") self.assertEqual(motif.instances[28], "NAIYQVPVYSGTKAAVVNFTSSLAKLAPI") self.assertEqual(motif.instances[29], "RVLNPLVGYNMTKHALGGLTKTTQHVGWD") self.assertEqual(motif.instances[30], "EGKIGASLKDSTLFGVSSLSDSLKGDFTS") self.assertEqual(motif.instances[31], "MGPEGVRVNAISAGPIRTLAASGIKDFRK") self.assertEqual(motif.instances[32], "RALKSCSPELQQKFRSETITEEELVGLMN") def test_meme_parser_3(self): """Parse motifs/meme.farntrans5.classic.anr.xml file.""" with open("motifs/meme.farntrans5.classic.anr.xml") as handle: record = motifs.parse(handle, "meme") self.assertEqual(record.version, "5.0.1") self.assertEqual(record.datafile, "common/farntrans5.s") self.assertEqual(record.alphabet, "ACDEFGHIKLMNPQRSTVWY") self.assertEqual(len(record.sequences), 5) self.assertEqual(record.sequences[0], "sequence_0") self.assertEqual(record.sequences[1], "sequence_1") self.assertEqual(record.sequences[2], "sequence_2") self.assertEqual(record.sequences[3], "sequence_3") self.assertEqual(record.sequences[4], "sequence_4") self.assertEqual( record.command, "meme common/farntrans5.s -oc results/meme15 -mod anr -protein -nmotifs 2 -objfun classic -minw 8 -nostatus ", ) self.assertEqual(len(record), 2) motif = record[0] self.assertEqual(motif.name, "GGFGGRPGKEVDLCYTYCALAALAJLGSLD") self.assertEqual(record["GGFGGRPGKEVDLCYTYCALAALAJLGSLD"], motif) self.assertEqual(motif.num_occurrences, 24) self.assertAlmostEqual(motif.evalue, 2.2e-94) self.assertEqual(motif.alphabet, "ACDEFGHIKLMNPQRSTVWY") self.assertEqual(len(motif.instances), 24) self.assertAlmostEqual(motif.instances[0].pvalue, 6.98e-22) self.assertAlmostEqual(motif.instances[1].pvalue, 4.67e-21) self.assertAlmostEqual(motif.instances[2].pvalue, 1.25e-19) self.assertAlmostEqual(motif.instances[3].pvalue, 1.56e-19) self.assertAlmostEqual(motif.instances[4].pvalue, 2.44e-19) self.assertAlmostEqual(motif.instances[5].pvalue, 6.47e-19) self.assertAlmostEqual(motif.instances[6].pvalue, 8.9e-19) self.assertAlmostEqual(motif.instances[7].pvalue, 2.53e-18) self.assertAlmostEqual(motif.instances[8].pvalue, 1.27e-17) self.assertAlmostEqual(motif.instances[9].pvalue, 2.77e-17) self.assertAlmostEqual(motif.instances[10].pvalue, 4.93e-17) self.assertAlmostEqual(motif.instances[11].pvalue, 7.19e-17) self.assertAlmostEqual(motif.instances[12].pvalue, 8.68e-17) self.assertAlmostEqual(motif.instances[13].pvalue, 2.62e-16) self.assertAlmostEqual(motif.instances[14].pvalue, 2.87e-16) self.assertAlmostEqual(motif.instances[15].pvalue, 7.66e-15) self.assertAlmostEqual(motif.instances[16].pvalue, 2.21e-14) self.assertAlmostEqual(motif.instances[17].pvalue, 3.29e-14) self.assertAlmostEqual(motif.instances[18].pvalue, 7.21e-14) self.assertAlmostEqual(motif.instances[19].pvalue, 1.14e-13) self.assertAlmostEqual(motif.instances[20].pvalue, 1.67e-13) self.assertAlmostEqual(motif.instances[21].pvalue, 4.42e-13) self.assertAlmostEqual(motif.instances[22].pvalue, 5.11e-13) self.assertAlmostEqual(motif.instances[23].pvalue, 2.82e-10) self.assertEqual(motif.instances[0].sequence_name, "BET2_YEAST") self.assertEqual(motif.instances[1].sequence_name, "RATRABGERB") self.assertEqual(motif.instances[2].sequence_name, "CAL1_YEAST") self.assertEqual(motif.instances[3].sequence_name, "PFTB_RAT") self.assertEqual(motif.instances[4].sequence_name, "PFTB_RAT") self.assertEqual(motif.instances[5].sequence_name, "RATRABGERB") self.assertEqual(motif.instances[6].sequence_name, "RATRABGERB") self.assertEqual(motif.instances[7].sequence_name, "BET2_YEAST") self.assertEqual(motif.instances[8].sequence_name, "RATRABGERB") self.assertEqual(motif.instances[9].sequence_name, "BET2_YEAST") self.assertEqual(motif.instances[10].sequence_name, "RAM1_YEAST") self.assertEqual(motif.instances[11].sequence_name, "BET2_YEAST") self.assertEqual(motif.instances[12].sequence_name, "RAM1_YEAST") self.assertEqual(motif.instances[13].sequence_name, "PFTB_RAT") self.assertEqual(motif.instances[14].sequence_name, "RAM1_YEAST") self.assertEqual(motif.instances[15].sequence_name, "PFTB_RAT") self.assertEqual(motif.instances[16].sequence_name, "RATRABGERB") self.assertEqual(motif.instances[17].sequence_name, "PFTB_RAT") self.assertEqual(motif.instances[18].sequence_name, "BET2_YEAST") self.assertEqual(motif.instances[19].sequence_name, "CAL1_YEAST") self.assertEqual(motif.instances[20].sequence_name, "RAM1_YEAST") self.assertEqual(motif.instances[21].sequence_name, "CAL1_YEAST") self.assertEqual(motif.instances[22].sequence_name, "RAM1_YEAST") self.assertEqual(motif.instances[23].sequence_name, "BET2_YEAST") self.assertEqual(motif.instances[0].sequence_id, "sequence_2") self.assertEqual(motif.instances[1].sequence_id, "sequence_3") self.assertEqual(motif.instances[2].sequence_id, "sequence_4") self.assertEqual(motif.instances[3].sequence_id, "sequence_1") self.assertEqual(motif.instances[4].sequence_id, "sequence_1") self.assertEqual(motif.instances[5].sequence_id, "sequence_3") self.assertEqual(motif.instances[6].sequence_id, "sequence_3") self.assertEqual(motif.instances[7].sequence_id, "sequence_2") self.assertEqual(motif.instances[8].sequence_id, "sequence_3") self.assertEqual(motif.instances[9].sequence_id, "sequence_2") self.assertEqual(motif.instances[10].sequence_id, "sequence_0") self.assertEqual(motif.instances[11].sequence_id, "sequence_2") self.assertEqual(motif.instances[12].sequence_id, "sequence_0") self.assertEqual(motif.instances[13].sequence_id, "sequence_1") self.assertEqual(motif.instances[14].sequence_id, "sequence_0") self.assertEqual(motif.instances[15].sequence_id, "sequence_1") self.assertEqual(motif.instances[16].sequence_id, "sequence_3") self.assertEqual(motif.instances[17].sequence_id, "sequence_1") self.assertEqual(motif.instances[18].sequence_id, "sequence_2") self.assertEqual(motif.instances[19].sequence_id, "sequence_4") self.assertEqual(motif.instances[20].sequence_id, "sequence_0") self.assertEqual(motif.instances[21].sequence_id, "sequence_4") self.assertEqual(motif.instances[22].sequence_id, "sequence_0") self.assertEqual(motif.instances[23].sequence_id, "sequence_2") self.assertEqual(motif.instances[0].strand, "+") self.assertEqual(motif.instances[1].strand, "+") self.assertEqual(motif.instances[2].strand, "+") self.assertEqual(motif.instances[3].strand, "+") self.assertEqual(motif.instances[4].strand, "+") self.assertEqual(motif.instances[5].strand, "+") self.assertEqual(motif.instances[6].strand, "+") self.assertEqual(motif.instances[7].strand, "+") self.assertEqual(motif.instances[8].strand, "+") self.assertEqual(motif.instances[9].strand, "+") self.assertEqual(motif.instances[10].strand, "+") self.assertEqual(motif.instances[11].strand, "+") self.assertEqual(motif.instances[12].strand, "+") self.assertEqual(motif.instances[13].strand, "+") self.assertEqual(motif.instances[14].strand, "+") self.assertEqual(motif.instances[15].strand, "+") self.assertEqual(motif.instances[16].strand, "+") self.assertEqual(motif.instances[17].strand, "+") self.assertEqual(motif.instances[18].strand, "+") self.assertEqual(motif.instances[19].strand, "+") self.assertEqual(motif.instances[20].strand, "+") self.assertEqual(motif.instances[21].strand, "+") self.assertEqual(motif.instances[22].strand, "+") self.assertEqual(motif.instances[23].strand, "+") self.assertEqual(motif.instances[0].length, 30) self.assertEqual(motif.instances[1].length, 30) self.assertEqual(motif.instances[2].length, 30) self.assertEqual(motif.instances[3].length, 30) self.assertEqual(motif.instances[4].length, 30) self.assertEqual(motif.instances[5].length, 30) self.assertEqual(motif.instances[6].length, 30) self.assertEqual(motif.instances[7].length, 30) self.assertEqual(motif.instances[8].length, 30) self.assertEqual(motif.instances[9].length, 30) self.assertEqual(motif.instances[10].length, 30) self.assertEqual(motif.instances[11].length, 30) self.assertEqual(motif.instances[12].length, 30) self.assertEqual(motif.instances[13].length, 30) self.assertEqual(motif.instances[14].length, 30) self.assertEqual(motif.instances[15].length, 30) self.assertEqual(motif.instances[16].length, 30) self.assertEqual(motif.instances[17].length, 30) self.assertEqual(motif.instances[18].length, 30) self.assertEqual(motif.instances[19].length, 30) self.assertEqual(motif.instances[20].length, 30) self.assertEqual(motif.instances[21].length, 30) self.assertEqual(motif.instances[22].length, 30) self.assertEqual(motif.instances[23].length, 30) self.assertEqual(motif.instances[0].start, 223) self.assertEqual(motif.instances[1].start, 227) self.assertEqual(motif.instances[2].start, 275) self.assertEqual(motif.instances[3].start, 237) self.assertEqual(motif.instances[4].start, 138) self.assertEqual(motif.instances[5].start, 179) self.assertEqual(motif.instances[6].start, 131) self.assertEqual(motif.instances[7].start, 172) self.assertEqual(motif.instances[8].start, 276) self.assertEqual(motif.instances[9].start, 124) self.assertEqual(motif.instances[10].start, 247) self.assertEqual(motif.instances[11].start, 272) self.assertEqual(motif.instances[12].start, 145) self.assertEqual(motif.instances[13].start, 286) self.assertEqual(motif.instances[14].start, 296) self.assertEqual(motif.instances[15].start, 348) self.assertEqual(motif.instances[16].start, 83) self.assertEqual(motif.instances[17].start, 189) self.assertEqual(motif.instances[18].start, 73) self.assertEqual(motif.instances[19].start, 205) self.assertEqual(motif.instances[20].start, 198) self.assertEqual(motif.instances[21].start, 327) self.assertEqual(motif.instances[22].start, 349) self.assertEqual(motif.instances[23].start, 24) self.assertEqual(motif.instances[0], "GGLNGRPSKLPDVCYSWWVLSSLAIIGRLD") self.assertEqual(motif.instances[1], "GGLNGRPEKLPDVCYSWWVLASLKIIGRLH") self.assertEqual(motif.instances[2], "GGFQGRENKFADTCYAFWCLNSLHLLTKDW") self.assertEqual(motif.instances[3], "GGIGGVPGMEAHGGYTFCGLAALVILKKER") self.assertEqual(motif.instances[4], "GGFGGGPGQYPHLAPTYAAVNALCIIGTEE") self.assertEqual(motif.instances[5], "GGFGCRPGSESHAGQIYCCTGFLAITSQLH") self.assertEqual(motif.instances[6], "GSFAGDIWGEIDTRFSFCAVATLALLGKLD") self.assertEqual(motif.instances[7], "GGFGLCPNAESHAAQAFTCLGALAIANKLD") self.assertEqual(motif.instances[8], "GGFADRPGDMVDPFHTLFGIAGLSLLGEEQ") self.assertEqual(motif.instances[9], "GSFQGDRFGEVDTRFVYTALSALSILGELT") self.assertEqual(motif.instances[10], "GFGSCPHVDEAHGGYTFCATASLAILRSMD") self.assertEqual(motif.instances[11], "GGISDRPENEVDVFHTVFGVAGLSLMGYDN") self.assertEqual(motif.instances[12], "GPFGGGPGQLSHLASTYAAINALSLCDNID") self.assertEqual(motif.instances[13], "GGFQGRCNKLVDGCYSFWQAGLLPLLHRAL") self.assertEqual(motif.instances[14], "RGFCGRSNKLVDGCYSFWVGGSAAILEAFG") self.assertEqual(motif.instances[15], "GGLLDKPGKSRDFYHTCYCLSGLSIAQHFG") self.assertEqual(motif.instances[16], "GGVSASIGHDPHLLYTLSAVQILTLYDSIH") self.assertEqual(motif.instances[17], "GSFLMHVGGEVDVRSAYCAASVASLTNIIT") self.assertEqual(motif.instances[18], "GAFAPFPRHDAHLLTTLSAVQILATYDALD") self.assertEqual(motif.instances[19], "YNGAFGAHNEPHSGYTSCALSTLALLSSLE") self.assertEqual(motif.instances[20], "GFKTCLEVGEVDTRGIYCALSIATLLNILT") self.assertEqual(motif.instances[21], "GGFSKNDEEDADLYHSCLGSAALALIEGKF") self.assertEqual(motif.instances[22], "PGLRDKPGAHSDFYHTNYCLLGLAVAESSY") self.assertEqual(motif.instances[23], "HNFEYWLTEHLRLNGIYWGLTALCVLDSPE") motif = record[1] self.assertEqual(motif.name, "JNKEKLLEYILSCQ") self.assertEqual(record["JNKEKLLEYILSCQ"], motif) self.assertEqual(motif.num_occurrences, 21) self.assertAlmostEqual(motif.evalue, 3.1e-19) self.assertEqual(motif.alphabet, "ACDEFGHIKLMNPQRSTVWY") self.assertEqual(len(motif.instances), 21) self.assertAlmostEqual(motif.instances[0].pvalue, 2.71e-12) self.assertAlmostEqual(motif.instances[1].pvalue, 5.7e-12) self.assertAlmostEqual(motif.instances[2].pvalue, 6.43e-12) self.assertAlmostEqual(motif.instances[3].pvalue, 2.61e-11) self.assertAlmostEqual(motif.instances[4].pvalue, 6.3e-11) self.assertAlmostEqual(motif.instances[5].pvalue, 2.7e-10) self.assertAlmostEqual(motif.instances[6].pvalue, 4.03e-10) self.assertAlmostEqual(motif.instances[7].pvalue, 1.27e-09) self.assertAlmostEqual(motif.instances[8].pvalue, 3.17e-09) self.assertAlmostEqual(motif.instances[9].pvalue, 6.39e-09) self.assertAlmostEqual(motif.instances[10].pvalue, 6.96e-09) self.assertAlmostEqual(motif.instances[11].pvalue, 1.06e-08) self.assertAlmostEqual(motif.instances[12].pvalue, 1.26e-08) self.assertAlmostEqual(motif.instances[13].pvalue, 1.37e-08) self.assertAlmostEqual(motif.instances[14].pvalue, 2.07e-08) self.assertAlmostEqual(motif.instances[15].pvalue, 4.96e-08) self.assertAlmostEqual(motif.instances[16].pvalue, 1.15e-07) self.assertAlmostEqual(motif.instances[17].pvalue, 1.44e-07) self.assertAlmostEqual(motif.instances[18].pvalue, 1.55e-07) self.assertAlmostEqual(motif.instances[19].pvalue, 1.93e-07) self.assertAlmostEqual(motif.instances[20].pvalue, 5.2e-07) self.assertEqual(motif.instances[0].sequence_name, "RATRABGERB") self.assertEqual(motif.instances[1].sequence_name, "BET2_YEAST") self.assertEqual(motif.instances[2].sequence_name, "RATRABGERB") self.assertEqual(motif.instances[3].sequence_name, "RATRABGERB") self.assertEqual(motif.instances[4].sequence_name, "CAL1_YEAST") self.assertEqual(motif.instances[5].sequence_name, "RAM1_YEAST") self.assertEqual(motif.instances[6].sequence_name, "PFTB_RAT") self.assertEqual(motif.instances[7].sequence_name, "RATRABGERB") self.assertEqual(motif.instances[8].sequence_name, "BET2_YEAST") self.assertEqual(motif.instances[9].sequence_name, "PFTB_RAT") self.assertEqual(motif.instances[10].sequence_name, "RAM1_YEAST") self.assertEqual(motif.instances[11].sequence_name, "CAL1_YEAST") self.assertEqual(motif.instances[12].sequence_name, "PFTB_RAT") self.assertEqual(motif.instances[13].sequence_name, "BET2_YEAST") self.assertEqual(motif.instances[14].sequence_name, "RAM1_YEAST") self.assertEqual(motif.instances[15].sequence_name, "RAM1_YEAST") self.assertEqual(motif.instances[16].sequence_name, "RATRABGERB") self.assertEqual(motif.instances[17].sequence_name, "RAM1_YEAST") self.assertEqual(motif.instances[18].sequence_name, "PFTB_RAT") self.assertEqual(motif.instances[19].sequence_name, "BET2_YEAST") self.assertEqual(motif.instances[20].sequence_name, "CAL1_YEAST") self.assertEqual(motif.instances[0].sequence_id, "sequence_3") self.assertEqual(motif.instances[1].sequence_id, "sequence_2") self.assertEqual(motif.instances[2].sequence_id, "sequence_3") self.assertEqual(motif.instances[3].sequence_id, "sequence_3") self.assertEqual(motif.instances[4].sequence_id, "sequence_4") self.assertEqual(motif.instances[5].sequence_id, "sequence_0") self.assertEqual(motif.instances[6].sequence_id, "sequence_1") self.assertEqual(motif.instances[7].sequence_id, "sequence_3") self.assertEqual(motif.instances[8].sequence_id, "sequence_2") self.assertEqual(motif.instances[9].sequence_id, "sequence_1") self.assertEqual(motif.instances[10].sequence_id, "sequence_0") self.assertEqual(motif.instances[11].sequence_id, "sequence_4") self.assertEqual(motif.instances[12].sequence_id, "sequence_1") self.assertEqual(motif.instances[13].sequence_id, "sequence_2") self.assertEqual(motif.instances[14].sequence_id, "sequence_0") self.assertEqual(motif.instances[15].sequence_id, "sequence_0") self.assertEqual(motif.instances[16].sequence_id, "sequence_3") self.assertEqual(motif.instances[17].sequence_id, "sequence_0") self.assertEqual(motif.instances[18].sequence_id, "sequence_1") self.assertEqual(motif.instances[19].sequence_id, "sequence_2") self.assertEqual(motif.instances[20].sequence_id, "sequence_4") self.assertEqual(motif.instances[0].strand, "+") self.assertEqual(motif.instances[1].strand, "+") self.assertEqual(motif.instances[2].strand, "+") self.assertEqual(motif.instances[3].strand, "+") self.assertEqual(motif.instances[4].strand, "+") self.assertEqual(motif.instances[5].strand, "+") self.assertEqual(motif.instances[6].strand, "+") self.assertEqual(motif.instances[7].strand, "+") self.assertEqual(motif.instances[8].strand, "+") self.assertEqual(motif.instances[9].strand, "+") self.assertEqual(motif.instances[10].strand, "+") self.assertEqual(motif.instances[11].strand, "+") self.assertEqual(motif.instances[12].strand, "+") self.assertEqual(motif.instances[13].strand, "+") self.assertEqual(motif.instances[14].strand, "+") self.assertEqual(motif.instances[15].strand, "+") self.assertEqual(motif.instances[16].strand, "+") self.assertEqual(motif.instances[17].strand, "+") self.assertEqual(motif.instances[18].strand, "+") self.assertEqual(motif.instances[19].strand, "+") self.assertEqual(motif.instances[20].strand, "+") self.assertEqual(motif.instances[0].length, 14) self.assertEqual(motif.instances[1].length, 14) self.assertEqual(motif.instances[2].length, 14) self.assertEqual(motif.instances[3].length, 14) self.assertEqual(motif.instances[4].length, 14) self.assertEqual(motif.instances[5].length, 14) self.assertEqual(motif.instances[6].length, 14) self.assertEqual(motif.instances[7].length, 14) self.assertEqual(motif.instances[8].length, 14) self.assertEqual(motif.instances[9].length, 14) self.assertEqual(motif.instances[10].length, 14) self.assertEqual(motif.instances[11].length, 14) self.assertEqual(motif.instances[12].length, 14) self.assertEqual(motif.instances[13].length, 14) self.assertEqual(motif.instances[14].length, 14) self.assertEqual(motif.instances[15].length, 14) self.assertEqual(motif.instances[16].length, 14) self.assertEqual(motif.instances[17].length, 14) self.assertEqual(motif.instances[18].length, 14) self.assertEqual(motif.instances[19].length, 14) self.assertEqual(motif.instances[20].length, 14) self.assertEqual(motif.instances[0].start, 66) self.assertEqual(motif.instances[1].start, 254) self.assertEqual(motif.instances[2].start, 258) self.assertEqual(motif.instances[3].start, 162) self.assertEqual(motif.instances[4].start, 190) self.assertEqual(motif.instances[5].start, 278) self.assertEqual(motif.instances[6].start, 172) self.assertEqual(motif.instances[7].start, 114) self.assertEqual(motif.instances[8].start, 7) self.assertEqual(motif.instances[9].start, 268) self.assertEqual(motif.instances[10].start, 414) self.assertEqual(motif.instances[11].start, 126) self.assertEqual(motif.instances[12].start, 220) self.assertEqual(motif.instances[13].start, 55) self.assertEqual(motif.instances[14].start, 229) self.assertEqual(motif.instances[15].start, 330) self.assertEqual(motif.instances[16].start, 18) self.assertEqual(motif.instances[17].start, 180) self.assertEqual(motif.instances[18].start, 73) self.assertEqual(motif.instances[19].start, 107) self.assertEqual(motif.instances[20].start, 36) self.assertEqual(motif.instances[0], "MNKEEILVFIKSCQ") self.assertEqual(motif.instances[1], "INYEKLTEFILKCQ") self.assertEqual(motif.instances[2], "IDREKLRSFILACQ") self.assertEqual(motif.instances[3], "INVEKAIEFVLSCM") self.assertEqual(motif.instances[4], "IDTEKLLGYIMSQQ") self.assertEqual(motif.instances[5], "INVEKLLEWSSARQ") self.assertEqual(motif.instances[6], "INREKLLQYLYSLK") self.assertEqual(motif.instances[7], "INVDKVVAYVQSLQ") self.assertEqual(motif.instances[8], "LLKEKHIRYIESLD") self.assertEqual(motif.instances[9], "LNLKSLLQWVTSRQ") self.assertEqual(motif.instances[10], "ENVRKIIHYFKSNL") self.assertEqual(motif.instances[11], "LDKRSLARFVSKCQ") self.assertEqual(motif.instances[12], "DLFEGTAEWIARCQ") self.assertEqual(motif.instances[13], "FVKEEVISFVLSCW") self.assertEqual(motif.instances[14], "ELTEGVLNYLKNCQ") self.assertEqual(motif.instances[15], "FNKHALRDYILYCC") self.assertEqual(motif.instances[16], "LLLEKHADYIASYG") self.assertEqual(motif.instances[17], "IDRKGIYQWLISLK") self.assertEqual(motif.instances[18], "LQREKHFHYLKRGL") self.assertEqual(motif.instances[19], "DRKVRLISFIRGNQ") self.assertEqual(motif.instances[20], "VNRMAIIFYSISGL") def test_minimal_meme_parser(self): """Parse motifs/minimal_test.meme file.""" with open("motifs/minimal_test.meme") as handle: record = motifs.parse(handle, "minimal") self.assertEqual(record.version, "4") self.assertEqual(record.alphabet, "ACGT") self.assertEqual(len(record.sequences), 0) self.assertEqual(record.command, "") self.assertEqual(len(record), 2) motif = record[0] self.assertEqual(motif.name, "KRP") self.assertEqual(record["KRP"], motif) self.assertEqual(motif.num_occurrences, 17) self.assertEqual(motif.length, 19) self.assertEqual(motif.consensus, "TGTGATCGAGGTCACACTT") self.assertAlmostEqual(motif.background["A"], 0.30269730269730266) self.assertAlmostEqual(motif.background["C"], 0.1828171828171828) self.assertAlmostEqual(motif.background["G"], 0.20879120879120877) self.assertAlmostEqual(motif.background["T"], 0.30569430569430567) self.assertAlmostEqual(motif.evalue, 4.1e-09) self.assertEqual(motif.alphabet, "ACGT") self.assertIsNone(motif.instances) def test_meme_parser_rna(self): """Test if Bio.motifs can parse MEME output files using RNA.""" pass class TestMAST(unittest.TestCase): """MAST format tests.""" def test_mast_parser_1(self): """Parse motifs/mast.crp0.de.oops.txt.xml file.""" with open("motifs/mast.crp0.de.oops.txt.xml") as handle: record = motifs.parse(handle, "MAST") self.assertEqual(record.version, "5.0.1") self.assertEqual(record.database, "common/crp0.s") self.assertEqual(record.alphabet, "DNA") self.assertEqual(len(record), 2) self.assertEqual(record["1"].name, "1") self.assertEqual(record["2"].name, "2") self.assertEqual(record[0].alphabet, "DNA") self.assertEqual(record[0].length, 12) self.assertEqual(record[0].name, "1") self.assertEqual(record[1].alphabet, "DNA") self.assertEqual(record[1].length, 12) self.assertEqual(record[1].name, "2") self.assertEqual(len(record.sequences), 18) self.assertEqual(record.sequences[0], "lac") self.assertEqual(record.sequences[1], "bglr1") self.assertEqual(record.sequences[2], "tdc") self.assertEqual(record.sequences[3], "deop2") self.assertEqual(record.sequences[4], "pbr322") self.assertEqual(record.sequences[5], "malk") self.assertEqual(record.sequences[6], "tnaa") self.assertEqual(record.sequences[7], "male") self.assertEqual(record.sequences[8], "ara") self.assertEqual(record.sequences[9], "cya") self.assertEqual(record.sequences[10], "ompa") self.assertEqual(record.sequences[11], "ilv") self.assertEqual(record.sequences[12], "gale") self.assertEqual(record.sequences[13], "malt") self.assertEqual(record.sequences[14], "crp") self.assertEqual(record.sequences[15], "ce1cg") self.assertEqual(record.sequences[16], "trn9cat") self.assertEqual(record.sequences[17], "uxu1") self.assertEqual(record.diagrams["lac"], "[+1]-2-[-2]-79") self.assertEqual(record.diagrams["bglr1"], "79-[+2]-14") self.assertEqual(record.diagrams["tdc"], "30-[+1]-39-[+2]-12") self.assertEqual(record.diagrams["deop2"], "19-[+1]-74") self.assertEqual(record.diagrams["pbr322"], "58-[-2]-35") self.assertEqual(record.diagrams["malk"], "32-[+2]-61") self.assertEqual(record.diagrams["tnaa"], "105") self.assertEqual(record.diagrams["male"], "105") self.assertEqual(record.diagrams["ara"], "105") self.assertEqual(record.diagrams["cya"], "105") self.assertEqual(record.diagrams["ompa"], "105") self.assertEqual(record.diagrams["ilv"], "105") self.assertEqual(record.diagrams["gale"], "105") self.assertEqual(record.diagrams["malt"], "105") self.assertEqual(record.diagrams["crp"], "105") self.assertEqual(record.diagrams["ce1cg"], "105") self.assertEqual(record.diagrams["trn9cat"], "105") self.assertEqual(record.diagrams["uxu1"], "105") def test_mast_parser_2(self): """Parse motifs/mast.adh.de.oops.html.xml file.""" with open("motifs/mast.adh.de.oops.html.xml") as handle: record = motifs.parse(handle, "MAST") self.assertEqual(record.version, "5.0.1") self.assertEqual(record.database, "common/adh.s") self.assertEqual(record.alphabet, "Protein") self.assertEqual(len(record), 2) self.assertEqual(record["1"].name, "1") self.assertEqual(record["2"].name, "2") self.assertEqual(record[0].alphabet, "Protein") self.assertEqual(record[0].length, 12) self.assertEqual(record[0].name, "1") self.assertEqual(record[1].alphabet, "Protein") self.assertEqual(record[1].length, 12) self.assertEqual(record[1].name, "2") self.assertEqual(len(record.sequences), 33) self.assertEqual(record.sequences[0], "ENTA_ECOLI") self.assertEqual(record.sequences[1], "DHII_HUMAN") self.assertEqual(record.sequences[2], "YINL_LISMO") self.assertEqual(record.sequences[3], "FIXR_BRAJA") self.assertEqual(record.sequences[4], "HDHA_ECOLI") self.assertEqual(record.sequences[5], "BUDC_KLETE") self.assertEqual(record.sequences[6], "AP27_MOUSE") self.assertEqual(record.sequences[7], "FVT1_HUMAN") self.assertEqual(record.sequences[8], "YRTP_BACSU") self.assertEqual(record.sequences[9], "DHMA_FLAS1") self.assertEqual(record.sequences[10], "HDE_CANTR") self.assertEqual(record.sequences[11], "3BHD_COMTE") self.assertEqual(record.sequences[12], "BDH_HUMAN") self.assertEqual(record.sequences[13], "2BHD_STREX") self.assertEqual(record.sequences[14], "BA72_EUBSP") self.assertEqual(record.sequences[15], "RIDH_KLEAE") self.assertEqual(record.sequences[16], "DHGB_BACME") self.assertEqual(record.sequences[17], "PCR_PEA") self.assertEqual(record.sequences[18], "RFBB_NEIGO") self.assertEqual(record.sequences[19], "BPHB_PSEPS") self.assertEqual(record.sequences[20], "DHB2_HUMAN") self.assertEqual(record.sequences[21], "NODG_RHIME") self.assertEqual(record.sequences[22], "MAS1_AGRRA") self.assertEqual(record.sequences[23], "DHCA_HUMAN") self.assertEqual(record.sequences[24], "DHES_HUMAN") self.assertEqual(record.sequences[25], "DHB3_HUMAN") self.assertEqual(record.sequences[26], "HMTR_LEIMA") self.assertEqual(record.sequences[27], "ADH_DROME") self.assertEqual(record.sequences[28], "YURA_MYXXA") self.assertEqual(record.sequences[29], "LIGD_PSEPA") self.assertEqual(record.sequences[30], "FABI_ECOLI") self.assertEqual(record.sequences[31], "GUTD_ECOLI") self.assertEqual(record.sequences[32], "CSGA_MYXXA") self.assertEqual(record.diagrams["ENTA_ECOLI"], "[1]-[2]-224") self.assertEqual(record.diagrams["DHII_HUMAN"], "29-[1]-[2]-239") self.assertEqual(record.diagrams["YINL_LISMO"], "[1]-[2]-224") self.assertEqual(record.diagrams["FIXR_BRAJA"], "43-[2]-149-[1]-62") self.assertEqual(record.diagrams["HDHA_ECOLI"], "6-[1]-[2]-144-[1]-69") self.assertEqual(record.diagrams["BUDC_KLETE"], "9-[2]-53-[1]-81-[1]-62") self.assertEqual(record.diagrams["AP27_MOUSE"], "2-[1]-[2]-138-[1]-68") self.assertEqual(record.diagrams["FVT1_HUMAN"], "39-[2]-150-[1]-119") self.assertEqual(record.diagrams["YRTP_BACSU"], "1-[1]-[2]-145-[1]-56") self.assertEqual(record.diagrams["DHMA_FLAS1"], "9-[1]-[2]-147-[1]-78") self.assertEqual(record.diagrams["HDE_CANTR"], "3-[1]-[2]-290-[1]-[2]-565") self.assertEqual(record.diagrams["3BHD_COMTE"], "1-[1]-[2]-50-[1]-166") self.assertEqual(record.diagrams["BDH_HUMAN"], "50-[1]-[2]-269") self.assertEqual(record.diagrams["2BHD_STREX"], "1-[1]-[2]-142-[1]-76") self.assertEqual(record.diagrams["BA72_EUBSP"], "1-[1]-[2]-125-[2]-10-[1]-65") self.assertEqual(record.diagrams["RIDH_KLEAE"], "9-[1]-[2]-216") self.assertEqual(record.diagrams["DHGB_BACME"], "2-[1]-[2]-149-[1]-75") self.assertEqual(record.diagrams["PCR_PEA"], "81-[1]-[2]-108-[1]-174") self.assertEqual(record.diagrams["RFBB_NEIGO"], "1-[1]-[2]-321") self.assertEqual(record.diagrams["BPHB_PSEPS"], "[1]-[2]-251") self.assertEqual(record.diagrams["DHB2_HUMAN"], "77-[1]-[2]-286") self.assertEqual(record.diagrams["NODG_RHIME"], "1-[1]-[2]-142-[1]-66") self.assertEqual(record.diagrams["MAS1_AGRRA"], "252-[2]-36-[1]-164") self.assertEqual(record.diagrams["DHCA_HUMAN"], "11-[2]-54-[1]-101-[1]-74") self.assertEqual(record.diagrams["DHES_HUMAN"], "9-[2]-108-[1]-186") self.assertEqual(record.diagrams["DHB3_HUMAN"], "55-[2]-146-[1]-85") self.assertEqual(record.diagrams["HMTR_LEIMA"], "24-[2]-172-[1]-67") self.assertEqual(record.diagrams["ADH_DROME"], "13-[2]-217-[1]-1") self.assertEqual(record.diagrams["YURA_MYXXA"], "94-[2]-69-[1]-71") self.assertEqual(record.diagrams["LIGD_PSEPA"], "1-[1]-[2]-280") self.assertEqual(record.diagrams["FABI_ECOLI"], "1-[1]-161-[1]-76") self.assertEqual(record.diagrams["GUTD_ECOLI"], "147-[2]-10-[1]-78") self.assertEqual(record.diagrams["CSGA_MYXXA"], "12-[1]-53-[2]-77") def test_mast_parser_3(self): """Parse motifs/mast.Klf1-200.cd.oops.xml.xml file.""" with open("motifs/mast.Klf1-200.cd.oops.xml.xml") as handle: record = motifs.parse(handle, "MAST") self.assertEqual(record.version, "5.0.1") self.assertEqual(record.database, "common/Klf1-200.fa") self.assertEqual(record.alphabet, "DNA") self.assertEqual(len(record), 2) self.assertEqual(record["1"].name, "1") self.assertEqual(record["2"].name, "2") self.assertEqual(record[0].alphabet, "DNA") self.assertEqual(record[0].length, 20) self.assertEqual(record[0].name, "1") self.assertEqual(record[1].alphabet, "DNA") self.assertEqual(record[1].length, 30) self.assertEqual(record[1].name, "2") self.assertEqual(len(record.sequences), 113) self.assertEqual(record.sequences[0], "chr3:104843905-104844405") self.assertEqual(record.sequences[1], "chr12:114390660-114391160") self.assertEqual(record.sequences[2], "chr12:27135944-27136444") self.assertEqual(record.sequences[3], "chr10:59256089-59256589") self.assertEqual(record.sequences[4], "chr4:135733850-135734350") self.assertEqual(record.sequences[5], "chr1:137838164-137838664") self.assertEqual(record.sequences[6], "chr17:47735006-47735506") self.assertEqual(record.sequences[7], "chr6:72223026-72223526") self.assertEqual(record.sequences[8], "chr13:3866266-3866766") self.assertEqual(record.sequences[9], "chr1:133343883-133344383") self.assertEqual(record.sequences[10], "chr11:117187372-117187872") self.assertEqual(record.sequences[11], "chr13:76003199-76003699") self.assertEqual(record.sequences[12], "chr5:65202593-65203093") self.assertEqual(record.sequences[13], "chr14:79702844-79703344") self.assertEqual(record.sequences[14], "chr12:112796794-112797294") self.assertEqual(record.sequences[15], "chr13:112863645-112864145") self.assertEqual(record.sequences[16], "chr7:111007530-111008030") self.assertEqual(record.sequences[17], "chr1:43307690-43308190") self.assertEqual(record.sequences[18], "chr14:47973722-47974222") self.assertEqual(record.sequences[19], "chr9:120025371-120025871") self.assertEqual(record.sequences[20], "chr7:105490727-105491227") self.assertEqual(record.sequences[21], "chr5:37127175-37127675") self.assertEqual(record.sequences[22], "chr5:45951565-45952065") self.assertEqual(record.sequences[23], "chr7:91033422-91033922") self.assertEqual(record.sequences[24], "chr4:154285745-154286245") self.assertEqual(record.sequences[25], "chr13:100518008-100518508") self.assertEqual(record.sequences[26], "chr1:36977019-36977519") self.assertEqual(record.sequences[27], "chr7:151917814-151918314") self.assertEqual(record.sequences[28], "chr7:110976195-110976695") self.assertEqual(record.sequences[29], "chr15:58719281-58719781") self.assertEqual(record.sequences[30], "chr11:57590460-57590960") self.assertEqual(record.sequences[31], "chr8:83025150-83025650") self.assertEqual(record.sequences[32], "chr13:54345922-54346422") self.assertEqual(record.sequences[33], "chr12:82044358-82044858") self.assertEqual(record.sequences[34], "chr11:105013714-105014214") self.assertEqual(record.sequences[35], "chr10:93585404-93585904") self.assertEqual(record.sequences[36], "chr7:19832207-19832707") self.assertEqual(record.sequences[37], "chr8:97323995-97324495") self.assertEqual(record.sequences[38], "chr10:126642277-126642777") self.assertEqual(record.sequences[39], "chr1:156887119-156887619") self.assertEqual(record.sequences[40], "chr15:81700367-81700867") self.assertEqual(record.sequences[41], "chr6:121187425-121187925") self.assertEqual(record.sequences[42], "chr4:43977111-43977611") self.assertEqual(record.sequences[43], "chr11:102236405-102236905") self.assertEqual(record.sequences[44], "chr17:5112057-5112557") self.assertEqual(record.sequences[45], "chr10:110604369-110604869") self.assertEqual(record.sequences[46], "chr1:169314208-169314708") self.assertEqual(record.sequences[47], "chr9:57618594-57619094") self.assertEqual(record.sequences[48], "chr10:128184604-128185104") self.assertEqual(record.sequences[49], "chr4:109112541-109113041") self.assertEqual(record.sequences[50], "chr3:97461668-97462168") self.assertEqual(record.sequences[51], "chr9:102674395-102674895") self.assertEqual(record.sequences[52], "chr17:24289205-24289705") self.assertEqual(record.sequences[53], "chr17:28960252-28960752") self.assertEqual(record.sequences[54], "chr2:73323093-73323593") self.assertEqual(record.sequences[55], "chr11:32150818-32151318") self.assertEqual(record.sequences[56], "chr7:103853792-103854292") self.assertEqual(record.sequences[57], "chr16:49839621-49840121") self.assertEqual(record.sequences[58], "chr6:135115628-135116128") self.assertEqual(record.sequences[59], "chr3:88305500-88306000") self.assertEqual(record.sequences[60], "chr18:57137388-57137888") self.assertEqual(record.sequences[61], "chr5:97380648-97381148") self.assertEqual(record.sequences[62], "chr15:91082416-91082916") self.assertEqual(record.sequences[63], "chr14:61272713-61273213") self.assertEqual(record.sequences[64], "chr5:33616214-33616714") self.assertEqual(record.sequences[65], "chr18:23982470-23982970") self.assertEqual(record.sequences[66], "chr9:24715045-24715545") self.assertEqual(record.sequences[67], "chr10:116195445-116195945") self.assertEqual(record.sequences[68], "chr11:77795184-77795684") self.assertEqual(record.sequences[69], "chr16:32508975-32509475") self.assertEqual(record.sequences[70], "chr18:80416880-80417380") self.assertEqual(record.sequences[71], "chr10:57252236-57252736") self.assertEqual(record.sequences[72], "chr5:34915767-34916267") self.assertEqual(record.sequences[73], "chr9:98389943-98390443") self.assertEqual(record.sequences[74], "chr19:5845899-5846399") self.assertEqual(record.sequences[75], "chr3:151777796-151778296") self.assertEqual(record.sequences[76], "chr4:76585120-76585620") self.assertEqual(record.sequences[77], "chr7:104332488-104332988") self.assertEqual(record.sequences[78], "chr5:138127197-138127697") self.assertEqual(record.sequences[79], "chr11:60988820-60989320") self.assertEqual(record.sequences[80], "chr8:19984030-19984530") self.assertEqual(record.sequences[81], "chr11:31712262-31712762") self.assertEqual(record.sequences[82], "chr15:41338514-41339014") self.assertEqual(record.sequences[83], "chr9:21362671-21363171") self.assertEqual(record.sequences[84], "chr18:58822702-58823202") self.assertEqual(record.sequences[85], "chr1:173447614-173448114") self.assertEqual(record.sequences[86], "chr6:81915769-81916269") self.assertEqual(record.sequences[87], "chr1:169322898-169323398") self.assertEqual(record.sequences[88], "chr12:70860461-70860961") self.assertEqual(record.sequences[89], "chr9:59598186-59598686") self.assertEqual(record.sequences[90], "chr3:19550495-19550995") self.assertEqual(record.sequences[91], "chr7:36132953-36133453") self.assertEqual(record.sequences[92], "chr7:38970375-38970875") self.assertEqual(record.sequences[93], "chr15:78243390-78243890") self.assertEqual(record.sequences[94], "chr7:87847381-87847881") self.assertEqual(record.sequences[95], "chr1:33631214-33631714") self.assertEqual(record.sequences[96], "chr4:135407873-135408373") self.assertEqual(record.sequences[97], "chr7:101244829-101245329") self.assertEqual(record.sequences[98], "chr10:60612190-60612690") self.assertEqual(record.sequences[99], "chr19:56465963-56466463") self.assertEqual(record.sequences[100], "chr4:41334759-41335259") self.assertEqual(record.sequences[101], "chr8:92969521-92970021") self.assertEqual(record.sequences[102], "chr6:145703215-145703715") self.assertEqual(record.sequences[103], "chr13:57679178-57679678") self.assertEqual(record.sequences[104], "chr19:45121628-45122128") self.assertEqual(record.sequences[105], "chr15:79757891-79758391") self.assertEqual(record.sequences[106], "chr1:134264178-134264678") self.assertEqual(record.sequences[107], "chr13:81067500-81068000") self.assertEqual(record.sequences[108], "chr11:69714224-69714724") self.assertEqual(record.sequences[109], "chr2:103728071-103728571") self.assertEqual(record.sequences[110], "chr5:105994747-105995247") self.assertEqual(record.sequences[111], "chr17:84209565-84210065") self.assertEqual(record.sequences[112], "chr7:16507689-16508189") self.assertEqual( record.diagrams["chr3:104843905-104844405"], "115-[-1]-209-[-2]-126" ) self.assertEqual( record.diagrams["chr12:114390660-114391160"], "3-[+2]-[+2]-3-[+1]-173-[+1]-3-[-2]-188", ) self.assertEqual( record.diagrams["chr12:27135944-27136444"], "275-[-1]-89-[+2]-4-[+2]-52" ) self.assertEqual( record.diagrams["chr10:59256089-59256589"], "247-[+2]-17-[-1]-186" ) self.assertEqual( record.diagrams["chr4:135733850-135734350"], "183-[-1]-263-[+2]-4" ) self.assertEqual( record.diagrams["chr1:137838164-137838664"], "192-[-2]-1-[+1]-44-[-1]-193" ) self.assertEqual( record.diagrams["chr17:47735006-47735506"], "203-[+2]-15-[+1]-97-[-1]-115" ) self.assertEqual( record.diagrams["chr6:72223026-72223526"], "52-[-2]-7-[+2]-162-[-1]-42-[-1]-137", ) self.assertEqual( record.diagrams["chr13:3866266-3866766"], "241-[+1]-2-[-1]-217" ) self.assertEqual( record.diagrams["chr1:133343883-133344383"], "190-[+2]-15-[+1]-245" ) self.assertEqual( record.diagrams["chr11:117187372-117187872"], "242-[+1]-46-[-2]-71-[+1]-71" ) self.assertEqual( record.diagrams["chr13:76003199-76003699"], "230-[+2]-15-[+2]-60-[-1]-115" ) self.assertEqual( record.diagrams["chr5:65202593-65203093"], "24-[-2]-36-[+2]-193-[-1]-11-[+1]-10-[+1]-106", ) self.assertEqual( record.diagrams["chr14:79702844-79703344"], "247-[-1]-46-[-2]-157" ) self.assertEqual( record.diagrams["chr12:112796794-112797294"], "232-[+1]-41-[+1]-187" ) self.assertEqual( record.diagrams["chr13:112863645-112864145"], "228-[+1]-20-[-1]-212" ) self.assertEqual( record.diagrams["chr7:111007530-111008030"], "217-[+1]-83-[+2]-150" ) self.assertEqual( record.diagrams["chr1:43307690-43308190"], "164-[-2]-52-[-2]-224" ) self.assertEqual( record.diagrams["chr14:47973722-47974222"], "21-[+1]-181-[+1]-20-[-2]-208" ) self.assertEqual( record.diagrams["chr9:120025371-120025871"], "110-[-2]-58-[+1]-282" ) self.assertEqual( record.diagrams["chr7:105490727-105491227"], "100-[-2]-111-[-1]-239" ) self.assertEqual( record.diagrams["chr5:37127175-37127675"], "234-[-2]-24-[+1]-192" ) self.assertEqual(record.diagrams["chr5:45951565-45952065"], "261-[-1]-219") self.assertEqual(record.diagrams["chr7:91033422-91033922"], "465-[-1]-15") self.assertEqual( record.diagrams["chr4:154285745-154286245"], "235-[+1]-20-[-2]-195" ) self.assertEqual( record.diagrams["chr13:100518008-100518508"], "226-[-2]-18-[-1]-206" ) self.assertEqual( record.diagrams["chr1:36977019-36977519"], "88-[+1]-187-[+2]-60-[-1]-95" ) self.assertEqual( record.diagrams["chr7:151917814-151918314"], "219-[+1]-80-[+2]-151" ) self.assertEqual( record.diagrams["chr7:110976195-110976695"], "287-[+2]-12-[+1]-151" ) self.assertEqual(record.diagrams["chr15:58719281-58719781"], "212-[-2]-258") self.assertEqual( record.diagrams["chr11:57590460-57590960"], "56-[-1]-271-[-1]-75-[+2]-28" ) self.assertEqual( record.diagrams["chr8:83025150-83025650"], "219-[+1]-87-[+2]-144" ) self.assertEqual( record.diagrams["chr13:54345922-54346422"], "283-[-2]-161-[+1]-6" ) self.assertEqual( record.diagrams["chr12:82044358-82044858"], "50-[+2]-160-[+1]-39-[+2]-171" ) self.assertEqual( record.diagrams["chr11:105013714-105014214"], "115-[-2]-160-[+1]-26-[-1]-129", ) self.assertEqual( record.diagrams["chr10:93585404-93585904"], "141-[+2]-48-[+1]-261" ) self.assertEqual(record.diagrams["chr7:19832207-19832707"], "229-[-1]-251") self.assertEqual( record.diagrams["chr8:97323995-97324495"], "177-[-1]-40-[-2]-139-[+1]-74" ) self.assertEqual( record.diagrams["chr10:126642277-126642777"], "252-[-1]-92-[-2]-106" ) self.assertEqual( record.diagrams["chr1:156887119-156887619"], "189-[-2]-78-[-1]-183" ) self.assertEqual( record.diagrams["chr15:81700367-81700867"], "109-[-1]-99-[-1]-252" ) self.assertEqual( record.diagrams["chr6:121187425-121187925"], "29-[+2]-313-[-1]-108" ) self.assertEqual( record.diagrams["chr4:43977111-43977611"], "60-[+1]-148-[+1]-252" ) self.assertEqual( record.diagrams["chr11:102236405-102236905"], "10-[+2]-145-[-1]-3-[-1]-6-[+2]-60-[+1]-156", ) self.assertEqual(record.diagrams["chr17:5112057-5112557"], "249-[+1]-231") self.assertEqual(record.diagrams["chr10:110604369-110604869"], "232-[+1]-248") self.assertEqual( record.diagrams["chr1:169314208-169314708"], "192-[-1]-[-1]-11-[-2]-227" ) self.assertEqual( record.diagrams["chr9:57618594-57619094"], "125-[+2]-151-[-1]-4-[-1]-150" ) self.assertEqual( record.diagrams["chr10:128184604-128185104"], "30-[-2]-128-[+1]-292" ) self.assertEqual( record.diagrams["chr4:109112541-109113041"], "21-[-1]-13-[+1]-94-[+2]-302" ) self.assertEqual( record.diagrams["chr3:97461668-97462168"], "18-[+2]-256-[-1]-81-[+1]-21-[+1]-34", ) self.assertEqual(record.diagrams["chr9:102674395-102674895"], "372-[+2]-98") self.assertEqual(record.diagrams["chr17:24289205-24289705"], "262-[-1]-218") self.assertEqual( record.diagrams["chr17:28960252-28960752"], "221-[+1]-81-[+1]-158" ) self.assertEqual(record.diagrams["chr2:73323093-73323593"], "49-[-2]-421") self.assertEqual( record.diagrams["chr11:32150818-32151318"], "151-[-1]-27-[-1]-118-[-2]-134" ) self.assertEqual( record.diagrams["chr7:103853792-103854292"], "212-[-2]-42-[+1]-196" ) self.assertEqual( record.diagrams["chr16:49839621-49840121"], "192-[+2]-47-[-1]-17-[+2]-164" ) self.assertEqual(record.diagrams["chr6:135115628-135116128"], "231-[-1]-249") self.assertEqual(record.diagrams["chr3:88305500-88306000"], "229-[+1]-251") self.assertEqual(record.diagrams["chr18:57137388-57137888"], "296-[+2]-174") self.assertEqual(record.diagrams["chr5:97380648-97381148"], "188-[-2]-282") self.assertEqual( record.diagrams["chr15:91082416-91082916"], "239-[-1]-104-[-1]-73-[+2]-14" ) self.assertEqual( record.diagrams["chr14:61272713-61273213"], "216-[+2]-104-[+1]-130" ) self.assertEqual(record.diagrams["chr5:33616214-33616714"], "247-[-1]-233") self.assertEqual(record.diagrams["chr18:23982470-23982970"], "285-[-1]-195") self.assertEqual( record.diagrams["chr9:24715045-24715545"], "214-[-1]-153-[+1]-93" ) self.assertEqual(record.diagrams["chr10:116195445-116195945"], "400-[+2]-70") self.assertEqual( record.diagrams["chr11:77795184-77795684"], "247-[+1]-42-[-2]-67-[-2]-64" ) self.assertEqual( record.diagrams["chr16:32508975-32509475"], "213-[+2]-29-[-1]-208" ) self.assertEqual(record.diagrams["chr18:80416880-80417380"], "239-[-1]-241") self.assertEqual( record.diagrams["chr10:57252236-57252736"], "155-[+1]-158-[+2]-137" ) self.assertEqual( record.diagrams["chr5:34915767-34916267"], "179-[+2]-29-[-1]-242" ) self.assertEqual(record.diagrams["chr9:98389943-98390443"], "252-[-1]-228") self.assertEqual( record.diagrams["chr19:5845899-5846399"], "136-[+1]-193-[+1]-131" ) self.assertEqual( record.diagrams["chr3:151777796-151778296"], "30-[-2]-58-[-1]-362" ) self.assertEqual(record.diagrams["chr4:76585120-76585620"], "329-[+2]-141") self.assertEqual( record.diagrams["chr7:104332488-104332988"], "164-[+2]-23-[-1]-222-[+1]-21" ) self.assertEqual(record.diagrams["chr5:138127197-138127697"], "238-[+1]-242") self.assertEqual( record.diagrams["chr11:60988820-60989320"], "115-[+1]-68-[+1]-47-[+1]-210" ) self.assertEqual( record.diagrams["chr8:19984030-19984530"], "103-[-1]-81-[+2]-266" ) self.assertEqual( record.diagrams["chr11:31712262-31712762"], "118-[+2]-53-[+2]-269" ) self.assertEqual( record.diagrams["chr15:41338514-41339014"], "173-[+2]-75-[+2]-192" ) self.assertEqual( record.diagrams["chr9:21362671-21363171"], "105-[+1]-131-[+1]-224" ) self.assertEqual(record.diagrams["chr18:58822702-58823202"], "467-[-2]-3") self.assertEqual(record.diagrams["chr1:173447614-173448114"], "369-[-1]-111") self.assertEqual(record.diagrams["chr6:81915769-81916269"], "197-[+1]-283") self.assertEqual(record.diagrams["chr1:169322898-169323398"], "253-[-1]-227") self.assertEqual( record.diagrams["chr12:70860461-70860961"], "197-[+2]-22-[-1]-231" ) self.assertEqual( record.diagrams["chr9:59598186-59598686"], "163-[-2]-10-[-1]-277" ) self.assertEqual(record.diagrams["chr3:19550495-19550995"], "452-[-2]-18") self.assertEqual(record.diagrams["chr7:36132953-36133453"], "157-[-1]-323") self.assertEqual( record.diagrams["chr7:38970375-38970875"], "49-[+1]-114-[+1]-297" ) self.assertEqual(record.diagrams["chr15:78243390-78243890"], "234-[+1]-246") self.assertEqual( record.diagrams["chr7:87847381-87847881"], "99-[+2]-2-[-1]-230-[-1]-99" ) self.assertEqual(record.diagrams["chr1:33631214-33631714"], "358-[-1]-122") self.assertEqual( record.diagrams["chr4:135407873-135408373"], "116-[-1]-64-[+2]-270" ) self.assertEqual(record.diagrams["chr7:101244829-101245329"], "311-[-2]-159") self.assertEqual(record.diagrams["chr10:60612190-60612690"], "215-[+1]-265") self.assertEqual( record.diagrams["chr19:56465963-56466463"], "306-[+1]-36-[+1]-18-[+1]-80" ) self.assertEqual(record.diagrams["chr4:41334759-41335259"], "204-[+1]-276") self.assertEqual(record.diagrams["chr8:92969521-92970021"], "453-[+2]-17") self.assertEqual( record.diagrams["chr6:145703215-145703715"], "154-[-2]-58-[+2]-228" ) self.assertEqual(record.diagrams["chr13:57679178-57679678"], "217-[-1]-263") self.assertEqual(record.diagrams["chr19:45121628-45122128"], "35-[-2]-435") self.assertEqual(record.diagrams["chr15:79757891-79758391"], "310-[+1]-170") self.assertEqual(record.diagrams["chr1:134264178-134264678"], "23-[+2]-447") self.assertEqual(record.diagrams["chr13:81067500-81068000"], "252-[+1]-228") self.assertEqual(record.diagrams["chr11:69714224-69714724"], "145-[+2]-325") self.assertEqual(record.diagrams["chr2:103728071-103728571"], "369-[+1]-111") self.assertEqual( record.diagrams["chr5:105994747-105995247"], "93-[+2]-153-[-2]-194" ) self.assertEqual(record.diagrams["chr17:84209565-84210065"], "64-[-2]-406") self.assertEqual(record.diagrams["chr7:16507689-16508189"], "231-[+2]-239") class TestTransfac(unittest.TestCase): """Transfac format tests.""" def test_transfac_parser(self): """Parse motifs/transfac.dat file.""" with open("motifs/transfac.dat") as handle: record = motifs.parse(handle, "TRANSFAC") motif = record[0] self.assertEqual(motif["ID"], "motif1") self.assertEqual(len(motif.counts), 4) self.assertEqual(motif.counts.length, 12) self.assertEqual(motif.counts["A", 0], 1) self.assertEqual(motif.counts["A", 1], 2) self.assertEqual(motif.counts["A", 2], 3) self.assertEqual(motif.counts["A", 3], 0) self.assertEqual(motif.counts["A", 4], 5) self.assertEqual(motif.counts["A", 5], 0) self.assertEqual(motif.counts["A", 6], 0) self.assertEqual(motif.counts["A", 7], 0) self.assertEqual(motif.counts["A", 8], 0) self.assertEqual(motif.counts["A", 9], 0) self.assertEqual(motif.counts["A", 10], 0) self.assertEqual(motif.counts["A", 11], 1) self.assertEqual(motif.counts["C", 0], 2) self.assertEqual(motif.counts["C", 1], 1) self.assertEqual(motif.counts["C", 2], 0) self.assertEqual(motif.counts["C", 3], 5) self.assertEqual(motif.counts["C", 4], 0) self.assertEqual(motif.counts["C", 5], 0) self.assertEqual(motif.counts["C", 6], 1) self.assertEqual(motif.counts["C", 7], 0) self.assertEqual(motif.counts["C", 8], 0) self.assertEqual(motif.counts["C", 9], 1) self.assertEqual(motif.counts["C", 10], 2) self.assertEqual(motif.counts["C", 11], 0) self.assertEqual(motif.counts["G", 0], 2) self.assertEqual(motif.counts["G", 1], 2) self.assertEqual(motif.counts["G", 2], 1) self.assertEqual(motif.counts["G", 3], 0) self.assertEqual(motif.counts["G", 4], 0) self.assertEqual(motif.counts["G", 5], 4) self.assertEqual(motif.counts["G", 6], 4) self.assertEqual(motif.counts["G", 7], 0) self.assertEqual(motif.counts["G", 8], 5) self.assertEqual(motif.counts["G", 9], 2) self.assertEqual(motif.counts["G", 10], 0) self.assertEqual(motif.counts["G", 11], 3) self.assertEqual(motif.counts["T", 0], 0) self.assertEqual(motif.counts["T", 1], 0) self.assertEqual(motif.counts["T", 2], 1) self.assertEqual(motif.counts["T", 3], 0) self.assertEqual(motif.counts["T", 4], 0) self.assertEqual(motif.counts["T", 5], 1) self.assertEqual(motif.counts["T", 6], 0) self.assertEqual(motif.counts["T", 7], 5) self.assertEqual(motif.counts["T", 8], 0) self.assertEqual(motif.counts["T", 9], 2) self.assertEqual(motif.counts["T", 10], 3) self.assertEqual(motif.counts["T", 11], 1) self.assertEqual(motif.counts.degenerate_consensus, "SRACAGGTGKYG") motif = record[1] self.assertEqual(motif["ID"], "motif2") self.assertEqual(len(motif.counts), 4) self.assertEqual(motif.counts.length, 10) self.assertEqual(motif.counts["A", 0], 2) self.assertEqual(motif.counts["A", 1], 1) self.assertEqual(motif.counts["A", 2], 0) self.assertEqual(motif.counts["A", 3], 3) self.assertEqual(motif.counts["A", 4], 0) self.assertEqual(motif.counts["A", 5], 5) self.assertEqual(motif.counts["A", 6], 0) self.assertEqual(motif.counts["A", 7], 0) self.assertEqual(motif.counts["A", 8], 0) self.assertEqual(motif.counts["A", 9], 0) self.assertEqual(motif.counts["C", 0], 1) self.assertEqual(motif.counts["C", 1], 2) self.assertEqual(motif.counts["C", 2], 5) self.assertEqual(motif.counts["C", 3], 0) self.assertEqual(motif.counts["C", 4], 0) self.assertEqual(motif.counts["C", 5], 0) self.assertEqual(motif.counts["C", 6], 1) self.assertEqual(motif.counts["C", 7], 0) self.assertEqual(motif.counts["C", 8], 0) self.assertEqual(motif.counts["C", 9], 2) self.assertEqual(motif.counts["G", 0], 2) self.assertEqual(motif.counts["G", 1], 2) self.assertEqual(motif.counts["G", 2], 0) self.assertEqual(motif.counts["G", 3], 1) self.assertEqual(motif.counts["G", 4], 4) self.assertEqual(motif.counts["G", 5], 0) self.assertEqual(motif.counts["G", 6], 4) self.assertEqual(motif.counts["G", 7], 5) self.assertEqual(motif.counts["G", 8], 0) self.assertEqual(motif.counts["G", 9], 0) self.assertEqual(motif.counts["T", 0], 0) self.assertEqual(motif.counts["T", 1], 0) self.assertEqual(motif.counts["T", 2], 0) self.assertEqual(motif.counts["T", 3], 1) self.assertEqual(motif.counts["T", 4], 1) self.assertEqual(motif.counts["T", 5], 0) self.assertEqual(motif.counts["T", 6], 0) self.assertEqual(motif.counts["T", 7], 0) self.assertEqual(motif.counts["T", 8], 5) self.assertEqual(motif.counts["T", 9], 3) self.assertEqual(motif.counts.degenerate_consensus, "RSCAGAGGTY") def test_permissive_transfac_parser(self): """Parse the TRANSFAC-like file motifs/MA0056.1.transfac.""" # The test file MA0056.1.transfac was obtained from the JASPAR database # in a TRANSFAC-like format. # Khan, A. et al. JASPAR 2018: update of the open-access database of # transcription factor binding profiles and its web framework. # Nucleic Acids Res. 2018; 46:D260-D266, path = "motifs/MA0056.1.transfac" with open(path) as handle: self.assertRaises(ValueError, motifs.parse, handle, "TRANSFAC") with open(path) as handle: records = motifs.parse(handle, "TRANSFAC", strict=False) motif = records[0] self.assertEqual(sorted(motif.keys()), ["AC", "DE", "ID"]) self.assertEqual(motif["AC"], "MA0056.1") self.assertEqual(motif["DE"], "MA0056.1 MZF1 ; From JASPAR 2018") self.assertEqual(motif["ID"], "MZF1") self.assertEqual(motif.counts.length, 6) self.assertEqual(len(motif.counts), 4) self.assertEqual(motif.counts["A", 0], 3.0) self.assertEqual(motif.counts["A", 1], 0.0) self.assertEqual(motif.counts["A", 2], 2.0) self.assertEqual(motif.counts["A", 3], 0.0) self.assertEqual(motif.counts["A", 4], 0.0) self.assertEqual(motif.counts["A", 5], 18.0) self.assertEqual(motif.counts["C", 0], 5.0) self.assertEqual(motif.counts["C", 1], 0.0) self.assertEqual(motif.counts["C", 2], 0.0) self.assertEqual(motif.counts["C", 3], 0.0) self.assertEqual(motif.counts["C", 4], 0.0) self.assertEqual(motif.counts["C", 5], 0.0) self.assertEqual(motif.counts["G", 0], 4.0) self.assertEqual(motif.counts["G", 1], 19.0) self.assertEqual(motif.counts["G", 2], 18.0) self.assertEqual(motif.counts["G", 3], 19.0) self.assertEqual(motif.counts["G", 4], 20.0) self.assertEqual(motif.counts["G", 5], 2.0) self.assertEqual(motif.counts["T", 0], 8.0) self.assertEqual(motif.counts["T", 1], 1.0) self.assertEqual(motif.counts["T", 2], 0.0) self.assertEqual(motif.counts["T", 3], 1.0) self.assertEqual(motif.counts["T", 4], 0.0) self.assertEqual(motif.counts["T", 5], 0.0) class MotifTestPWM(unittest.TestCase): """PWM motif tests.""" def setUp(self): """Define motif and sequence for tests.""" with open("motifs/SRF.pfm") as handle: self.m = motifs.read(handle, "pfm") self.s = Seq("ACGTGTGCGTAGTGCGT") def test_getitem(self): counts = self.m.counts python_integers = range(13) numpy_integers = numpy.array(python_integers) integers = {"python": python_integers, "numpy": numpy_integers} for int_type in ("python", "numpy"): i0, i1, i2, i3, i4, i5, i6, i7, i8, i9, i10, i11, i12 = integers[int_type] msg = f"using {int_type} integers as indices" # slice, slice d = counts[i1::i2, i2:i12:i3] self.assertIsInstance(d, dict, msg=msg) self.assertEqual(len(d), 2, msg=msg) self.assertEqual(len(d["C"]), 4, msg=msg) self.assertEqual(len(d["T"]), 4, msg=msg) self.assertAlmostEqual(d["C"][i0], 45.0, msg=msg) self.assertAlmostEqual(d["C"][i1], 1.0, msg=msg) self.assertAlmostEqual(d["C"][i2], 0.0, msg=msg) self.assertAlmostEqual(d["C"][i3], 1.0, msg=msg) self.assertAlmostEqual(d["T"][i0], 0.0, msg=msg) self.assertAlmostEqual(d["T"][i1], 42.0, msg=msg) self.assertAlmostEqual(d["T"][i2], 3.0, msg=msg) self.assertAlmostEqual(d["T"][i3], 0.0, msg=msg) # slice, int d = counts[i1::i2, i4] self.assertIsInstance(d, dict, msg=msg) self.assertEqual(len(d), 2, msg=msg) self.assertAlmostEqual(d["C"], 1.0, msg=msg) self.assertAlmostEqual(d["T"], 13.0, msg=msg) # int, slice t = counts[i2, i3:i12:i2] self.assertIsInstance(t, tuple, msg=msg) self.assertAlmostEqual(t[i0], 0.0, msg=msg) self.assertAlmostEqual(t[i1], 0.0, msg=msg) self.assertAlmostEqual(t[i2], 0.0, msg=msg) self.assertAlmostEqual(t[i3], 0.0, msg=msg) self.assertAlmostEqual(t[i4], 43.0, msg=msg) # int, int v = counts[i1, i5] self.assertAlmostEqual(v, 1.0, msg=msg) # tuple, slice d = counts[(i0, i3), i3:i12:i2] self.assertIsInstance(d, dict, msg=msg) self.assertEqual(len(d), 2, msg=msg) self.assertEqual(len(d["A"]), 5, msg=msg) self.assertEqual(len(d["T"]), 5, msg=msg) self.assertAlmostEqual(d["A"][i0], 1.0, msg=msg) self.assertAlmostEqual(d["A"][i1], 3.0, msg=msg) self.assertAlmostEqual(d["A"][i2], 1.0, msg=msg) self.assertAlmostEqual(d["A"][i3], 15.0, msg=msg) self.assertAlmostEqual(d["A"][i4], 2.0, msg=msg) self.assertAlmostEqual(d["T"][i0], 0.0, msg=msg) self.assertAlmostEqual(d["T"][i1], 42.0, msg=msg) self.assertAlmostEqual(d["T"][i2], 45.0, msg=msg) self.assertAlmostEqual(d["T"][i3], 30.0, msg=msg) self.assertAlmostEqual(d["T"][i4], 0.0, msg=msg) # tuple, int d = counts[(i0, i3), i5] self.assertIsInstance(d, dict, msg=msg) self.assertEqual(len(d), 2, msg=msg) self.assertAlmostEqual(d["A"], 3.0, msg=msg) self.assertAlmostEqual(d["T"], 42.0, msg=msg) # str, slice t = counts["C", i2:i12:i4] self.assertIsInstance(t, tuple, msg=msg) self.assertAlmostEqual(t[i0], 45.0, msg=msg) self.assertAlmostEqual(t[i1], 0.0, msg=msg) self.assertAlmostEqual(t[i2], 0.0, msg=msg) # str, int self.assertAlmostEqual(counts["T", i4], 13.0, msg=msg) def test_simple(self): """Test if Bio.motifs PWM scoring works.""" counts = self.m.counts pwm = counts.normalize(pseudocounts=0.25) pssm = pwm.log_odds() result = pssm.calculate(self.s) self.assertEqual(6, len(result)) # The fast C-code in Bio/motifs/_pwm.c stores all results as 32-bit # floats; the slower Python code in Bio/motifs/__init__.py uses 64-bit # doubles. The C-code and Python code results will therefore not be # exactly equal. Test the first 5 decimal places only to avoid either # the C-code or the Python code to inadvertently fail this test. self.assertAlmostEqual(result[0], -29.18363571, places=5) self.assertAlmostEqual(result[1], -38.3365097, places=5) self.assertAlmostEqual(result[2], -29.17756271, places=5) self.assertAlmostEqual(result[3], -38.04542542, places=5) self.assertAlmostEqual(result[4], -20.3014183, places=5) self.assertAlmostEqual(result[5], -25.18009186, places=5) def test_with_mixed_case(self): """Test if Bio.motifs PWM scoring works with mixed case.""" counts = self.m.counts pwm = counts.normalize(pseudocounts=0.25) pssm = pwm.log_odds() result = pssm.calculate(Seq("AcGTgTGCGtaGTGCGT")) self.assertEqual(6, len(result)) self.assertAlmostEqual(result[0], -29.18363571, places=5) self.assertAlmostEqual(result[1], -38.3365097, places=5) self.assertAlmostEqual(result[2], -29.17756271, places=5) self.assertAlmostEqual(result[3], -38.04542542, places=5) self.assertAlmostEqual(result[4], -20.3014183, places=5) self.assertAlmostEqual(result[5], -25.18009186, places=5) def test_with_bad_char(self): """Test if Bio.motifs PWM scoring works with unexpected letters like N.""" counts = self.m.counts pwm = counts.normalize(pseudocounts=0.25) pssm = pwm.log_odds() result = pssm.calculate(Seq("ACGTGTGCGTAGTGCGTN")) self.assertEqual(7, len(result)) self.assertAlmostEqual(result[0], -29.18363571, places=5) self.assertAlmostEqual(result[1], -38.3365097, places=5) self.assertAlmostEqual(result[2], -29.17756271, places=5) self.assertAlmostEqual(result[3], -38.04542542, places=5) self.assertAlmostEqual(result[4], -20.3014183, places=5) self.assertAlmostEqual(result[5], -25.18009186, places=5) self.assertTrue(math.isnan(result[6]), f"Expected nan, not {result[6]!r}") def test_calculate_pseudocounts(self): pseudocounts = motifs.jaspar.calculate_pseudocounts(self.m) self.assertAlmostEqual(pseudocounts["A"], 1.695582495781317, places=5) self.assertAlmostEqual(pseudocounts["C"], 1.695582495781317, places=5) self.assertAlmostEqual(pseudocounts["G"], 1.695582495781317, places=5) self.assertAlmostEqual(pseudocounts["T"], 1.695582495781317, places=5) if __name__ == "__main__": runner = unittest.TextTestRunner(verbosity=2) unittest.main(testRunner=runner)