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test_Motif.py
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test_Motif.py
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# Copyright 2008 by Bartek Wilczynski. All rights reserved.
# Adapted from test_Mymodule.py by Jeff Chang
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
import os
import unittest
import warnings
from Bio import BiopythonDeprecationWarning
warnings.simplefilter('ignore', BiopythonDeprecationWarning)
from Bio.Alphabet import IUPAC
from Bio import Motif
from Bio.Seq import Seq
class MotifTestsBasic(unittest.TestCase):
def setUp(self):
self.PFMin = open("Motif/SRF.pfm")
self.SITESin = open("Motif/Arnt.sites")
self.TFout = "Motif/tf.out"
self.FAout = "Motif/fa.out"
self.PFMout = "Motif/fa.out"
self.m=Motif.Motif()
self.m.add_instance(Seq("ATATA",self.m.alphabet))
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 Motif can parse AlignAce output files.
"""
from Bio.Motif.Parsers import AlignAce
handle = open("Motif/alignace.out")
record = AlignAce.read(handle)
handle.close()
self.assertEqual(record.ver, "AlignACE 4.0 05/13/04\n")
self.assertEqual(record.cmd_line, "./AlignACE -i test.fa \n")
self.assertEqual(len(record.param_dict), 7)
self.assertEqual(record.param_dict['expect'], "10")
self.assertEqual(record.param_dict['gcback'], "0.38")
self.assertEqual(record.param_dict['minpass'], "200")
self.assertEqual(record.param_dict['seed'], "1227623309")
self.assertEqual(record.param_dict['numcols'], "10")
self.assertEqual(record.param_dict['undersample'], "1")
self.assertEqual(record.param_dict['oversample'], "1")
self.assertEqual(len(record.seq_dict), 10)
self.assertEqual(record.seq_dict[0], "SEQ1; M: CTCAATCGTAGA at 52\n")
self.assertEqual(record.seq_dict[1], "SEQ2; M: CTCAATCGTAGA at 172\n")
self.assertEqual(record.seq_dict[2], "SEQ3; M: CTCAATCGTAGA at 112\n")
self.assertEqual(record.seq_dict[3], "SEQ4; M: CTCAATCGTAGA at 173\n")
self.assertEqual(record.seq_dict[4], "SEQ5; M: CTCAATCGTAGA at 185\n")
self.assertEqual(record.seq_dict[5], "SEQ6; M: CTCAATCGTAGA at 105\n")
self.assertEqual(record.seq_dict[6], "SEQ7; M: CTCAATCGTAGA at 177\n")
self.assertEqual(record.seq_dict[7], "SEQ8; M: CTCAATCGTAGA at 172\n")
self.assertEqual(record.seq_dict[8], "SEQ9; M: CTCAATCGTAGA at 93\n")
self.assertEqual(record.seq_dict[9], "SEQ10; M: CTCAATCGTAGA at 3\n")
self.assertEqual(len(record.motifs), 16)
self.assertEqual(record.motifs[0].alphabet, IUPAC.unambiguous_dna)
self.assertEqual(len(record.motifs[0].instances), 11)
self.assertEqual(record.motifs[0].instances[0].tostring(), "TCTACGATTGAG")
self.assertEqual(record.motifs[0].instances[1].tostring(), "TCTACGATTGAG")
self.assertEqual(record.motifs[0].instances[2].tostring(), "TCTACGATTGAG")
self.assertEqual(record.motifs[0].instances[3].tostring(), "TCTACGATTGAG")
self.assertEqual(record.motifs[0].instances[4].tostring(), "TCTACGATTGAG")
self.assertEqual(record.motifs[0].instances[5].tostring(), "TCTACGATTGAG")
self.assertEqual(record.motifs[0].instances[6].tostring(), "TCTACGATTGAG")
self.assertEqual(record.motifs[0].instances[7].tostring(), "TCTACGATTGAG")
self.assertEqual(record.motifs[0].instances[8].tostring(), "TCTACGATTGAG")
self.assertEqual(record.motifs[0].instances[9].tostring(), "TCAAAGATAGAG")
self.assertEqual(record.motifs[0].instances[10].tostring(), "TCTACGATTGAG")
self.assertEqual(record.motifs[0].mask, [1,1,0,1,1,1,1,1,0,1,1,1])
self.assertAlmostEqual(record.motifs[0].score, 57.9079)
self.assertEqual(record.motifs[1].alphabet, IUPAC.unambiguous_dna)
self.assertEqual(len(record.motifs[1].instances), 22)
self.assertEqual(record.motifs[1].instances[0].tostring(), "GCGAAGGAAGCAGCGCGTGTG")
self.assertEqual(record.motifs[1].instances[1].tostring(), "GGCACCGCCTCTACGATTGAG")
self.assertEqual(record.motifs[1].instances[2].tostring(), "CAGAGCTTAGCATTGAACGCG")
self.assertEqual(record.motifs[1].instances[3].tostring(), "CTAATGAAAGCAATGAGAGTG")
self.assertEqual(record.motifs[1].instances[4].tostring(), "CTTGTGCCCTCTAAGCGTCCG")
self.assertEqual(record.motifs[1].instances[5].tostring(), "GAGCACGACGCTTTGTACCTG")
self.assertEqual(record.motifs[1].instances[6].tostring(), "CGGCACTTAGCAGCGTATCGT")
self.assertEqual(record.motifs[1].instances[7].tostring(), "CTGGTTTCATCTACGATTGAG")
self.assertEqual(record.motifs[1].instances[8].tostring(), "GGGCCAATAGCGGCGCCGGAG")
self.assertEqual(record.motifs[1].instances[9].tostring(), "GTGGAGTTATCTTAGTGCGCG")
self.assertEqual(record.motifs[1].instances[10].tostring(), "GAGAGGTTATCTACGATTGAG")
self.assertEqual(record.motifs[1].instances[11].tostring(), "CTGCTCCCCGCATACAGCGCG")
self.assertEqual(record.motifs[1].instances[12].tostring(), "CAGAACCGAGGTCCGGTACGG")
self.assertEqual(record.motifs[1].instances[13].tostring(), "GTGCCCCAAGCTTACCCAGGG")
self.assertEqual(record.motifs[1].instances[14].tostring(), "CGCCTCTGATCTACGATTGAG")
self.assertEqual(record.motifs[1].instances[15].tostring(), "GTGCTCATAGGGACGTCGCGG")
self.assertEqual(record.motifs[1].instances[16].tostring(), "CTGCCCCCCGCATAGTAGGGG")
self.assertEqual(record.motifs[1].instances[17].tostring(), "GTAAAGAAATCGATGTGCCAG")
self.assertEqual(record.motifs[1].instances[18].tostring(), "CACCTGCAATTGCTGGCAGCG")
self.assertEqual(record.motifs[1].instances[19].tostring(), "GGCGGGCCATCCCTGTATGAA")
self.assertEqual(record.motifs[1].instances[20].tostring(), "CTCCAGGTCGCATGGAGAGAG")
self.assertEqual(record.motifs[1].instances[21].tostring(), "CCTCGGATCGCTTGGGAAGAG")
self.assertEqual(record.motifs[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.motifs[1].score, 19.6235)
self.assertEqual(record.motifs[2].alphabet, IUPAC.unambiguous_dna)
self.assertEqual(len(record.motifs[2].instances), 18)
self.assertEqual(record.motifs[2].instances[0].tostring(), "GTGCGCGAAGGAAGCAGCGCG")
self.assertEqual(record.motifs[2].instances[1].tostring(), "CAGAGCTTAGCATTGAACGCG")
self.assertEqual(record.motifs[2].instances[2].tostring(), "GTGCCCGATGACCACCCGTCG")
self.assertEqual(record.motifs[2].instances[3].tostring(), "GCCCTCTAAGCGTCCGCGGAT")
self.assertEqual(record.motifs[2].instances[4].tostring(), "GAGCACGACGCTTTGTACCTG")
self.assertEqual(record.motifs[2].instances[5].tostring(), "CGGCACTTAGCAGCGTATCGT")
self.assertEqual(record.motifs[2].instances[6].tostring(), "GGGCCAATAGCGGCGCCGGAG")
self.assertEqual(record.motifs[2].instances[7].tostring(), "GCGCACTAAGATAACTCCACG")
self.assertEqual(record.motifs[2].instances[8].tostring(), "CGGCCCGTTGTCCAGCAGACG")
self.assertEqual(record.motifs[2].instances[9].tostring(), "CTGCTCCCCGCATACAGCGCG")
self.assertEqual(record.motifs[2].instances[10].tostring(), "GTGCCCCAAGCTTACCCAGGG")
self.assertEqual(record.motifs[2].instances[11].tostring(), "GTGCTCATAGGGACGTCGCGG")
self.assertEqual(record.motifs[2].instances[12].tostring(), "CTGCCCCCCGCATAGTAGGGG")
self.assertEqual(record.motifs[2].instances[13].tostring(), "CGCCGCCATGCGACGCAGAGG")
self.assertEqual(record.motifs[2].instances[14].tostring(), "AACCTCTAAGCATACTCTACG")
self.assertEqual(record.motifs[2].instances[15].tostring(), "GACCTGGAGGCTTAGACTTGG")
self.assertEqual(record.motifs[2].instances[16].tostring(), "GCGCTCTTCCCAAGCGATCCG")
self.assertEqual(record.motifs[2].instances[17].tostring(), "GGGCCGTCAGCTCTCAAGTCT")
self.assertEqual(record.motifs[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.motifs[2].score, 19.1804)
self.assertEqual(record.motifs[3].alphabet, IUPAC.unambiguous_dna)
self.assertEqual(len(record.motifs[3].instances), 16)
self.assertEqual(record.motifs[3].instances[0].tostring(), "GCCCCAAGCTTACCCAGGGAC")
self.assertEqual(record.motifs[3].instances[1].tostring(), "GCCGTCTGCTGGACAACGGGC")
self.assertEqual(record.motifs[3].instances[2].tostring(), "GCCGACGGGTGGTCATCGGGC")
self.assertEqual(record.motifs[3].instances[3].tostring(), "GCCAATAGCGGCGCCGGAGTC")
self.assertEqual(record.motifs[3].instances[4].tostring(), "GCCCCCCGCATAGTAGGGGGA")
self.assertEqual(record.motifs[3].instances[5].tostring(), "GCCCGTACCGGACCTCGGTTC")
self.assertEqual(record.motifs[3].instances[6].tostring(), "GCCTCATGTACCGGAAGGGAC")
self.assertEqual(record.motifs[3].instances[7].tostring(), "GACACGCGCCTGGGAGGGTTC")
self.assertEqual(record.motifs[3].instances[8].tostring(), "GCCTTTGGCCTTGGATGAGAA")
self.assertEqual(record.motifs[3].instances[9].tostring(), "GGCCCTCGGATCGCTTGGGAA")
self.assertEqual(record.motifs[3].instances[10].tostring(), "GCATGTTGGGAATCCGCGGAC")
self.assertEqual(record.motifs[3].instances[11].tostring(), "GACACGCGCTGTATGCGGGGA")
self.assertEqual(record.motifs[3].instances[12].tostring(), "GCCAGGTACAAAGCGTCGTGC")
self.assertEqual(record.motifs[3].instances[13].tostring(), "GCGATCAGCTTGTGGGCGTGC")
self.assertEqual(record.motifs[3].instances[14].tostring(), "GACAAATCGGATACTGGGGCA")
self.assertEqual(record.motifs[3].instances[15].tostring(), "GCACTTAGCAGCGTATCGTTA")
self.assertEqual(record.motifs[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.motifs[3].score, 18.0097)
self.assertEqual(record.motifs[4].alphabet, IUPAC.unambiguous_dna)
self.assertEqual(len(record.motifs[4].instances), 15)
self.assertEqual(record.motifs[4].instances[0].tostring(), "CGGCACAGAGCTT")
self.assertEqual(record.motifs[4].instances[1].tostring(), "ATCCGCGGACGCT")
self.assertEqual(record.motifs[4].instances[2].tostring(), "CGCCTGGGAGGGT")
self.assertEqual(record.motifs[4].instances[3].tostring(), "CGGAAGGGACGTT")
self.assertEqual(record.motifs[4].instances[4].tostring(), "ACACACAGACGGT")
self.assertEqual(record.motifs[4].instances[5].tostring(), "TGCCAGAGAGGTT")
self.assertEqual(record.motifs[4].instances[6].tostring(), "AGACTGAGACGTT")
self.assertEqual(record.motifs[4].instances[7].tostring(), "AATCGTAGAGGAT")
self.assertEqual(record.motifs[4].instances[8].tostring(), "CGTCTCGTAGGGT")
self.assertEqual(record.motifs[4].instances[9].tostring(), "CGTCGCGGAGGAT")
self.assertEqual(record.motifs[4].instances[10].tostring(), "CTTCTTAGACGCT")
self.assertEqual(record.motifs[4].instances[11].tostring(), "CGACGCAGAGGAT")
self.assertEqual(record.motifs[4].instances[12].tostring(), "ATGCTTAGAGGTT")
self.assertEqual(record.motifs[4].instances[13].tostring(), "AGACTTGGGCGAT")
self.assertEqual(record.motifs[4].instances[14].tostring(), "CGACCTGGAGGCT")
self.assertEqual(record.motifs[4].mask, [1,1,0,1,0,1,1,1,1,1,1,0,1])
self.assertAlmostEqual(record.motifs[4].score, 16.8287)
self.assertEqual(record.motifs[5].alphabet, IUPAC.unambiguous_dna)
self.assertEqual(len(record.motifs[5].instances), 18)
self.assertEqual(record.motifs[5].instances[0].tostring(), "GTGCGCGAAGGAAGCAGCGCGTG")
self.assertEqual(record.motifs[5].instances[1].tostring(), "TTGAGCCGAGTAAAGGGCTGGTG")
self.assertEqual(record.motifs[5].instances[2].tostring(), "CAATGCTAAGCTCTGTGCCGACG")
self.assertEqual(record.motifs[5].instances[3].tostring(), "CAACTCTCTATGTAGTGCCCGAG")
self.assertEqual(record.motifs[5].instances[4].tostring(), "CGACGCTTTGTACCTGGCTTGCG")
self.assertEqual(record.motifs[5].instances[5].tostring(), "CGAGTCAATGACACGCGCCTGGG")
self.assertEqual(record.motifs[5].instances[6].tostring(), "CGATACGCTGCTAAGTGCCGTCC")
self.assertEqual(record.motifs[5].instances[7].tostring(), "CCGGGCCAATAGCGGCGCCGGAG")
self.assertEqual(record.motifs[5].instances[8].tostring(), "CCACGCTTCGACACGTGGTATAG")
self.assertEqual(record.motifs[5].instances[9].tostring(), "CCGAGCCTCATGTACCGGAAGGG")
self.assertEqual(record.motifs[5].instances[10].tostring(), "CTGCTCCCCGCATACAGCGCGTG")
self.assertEqual(record.motifs[5].instances[11].tostring(), "CCGAGGTCCGGTACGGGCAAGCC")
self.assertEqual(record.motifs[5].instances[12].tostring(), "GTGCTCATAGGGACGTCGCGGAG")
self.assertEqual(record.motifs[5].instances[13].tostring(), "CCCTACTATGCGGGGGGCAGGTC")
self.assertEqual(record.motifs[5].instances[14].tostring(), "GCCAGCAATTGCAGGTGGTCGTG")
self.assertEqual(record.motifs[5].instances[15].tostring(), "CTCTGCGTCGCATGGCGGCGTGG")
self.assertEqual(record.motifs[5].instances[16].tostring(), "GGAGGCTTAGACTTGGGCGATAC")
self.assertEqual(record.motifs[5].instances[17].tostring(), "GCATGGAGAGAGATCCGGAGGAG")
self.assertEqual(record.motifs[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.motifs[5].score, 15.0441)
self.assertEqual(record.motifs[6].alphabet, IUPAC.unambiguous_dna)
self.assertEqual(len(record.motifs[6].instances), 20)
self.assertEqual(record.motifs[6].instances[0].tostring(), "GCGCGTGTGTGTAAC")
self.assertEqual(record.motifs[6].instances[1].tostring(), "GCACAGAGCTTAGCA")
self.assertEqual(record.motifs[6].instances[2].tostring(), "GGTGGTCATCGGGCA")
self.assertEqual(record.motifs[6].instances[3].tostring(), "GCGCGTGTCATTGAC")
self.assertEqual(record.motifs[6].instances[4].tostring(), "GGACGGCACTTAGCA")
self.assertEqual(record.motifs[6].instances[5].tostring(), "GCGCGTCCCGGGCCA")
self.assertEqual(record.motifs[6].instances[6].tostring(), "GCTCGGCCCGTTGTC")
self.assertEqual(record.motifs[6].instances[7].tostring(), "GCGCGTGTCCTTTAA")
self.assertEqual(record.motifs[6].instances[8].tostring(), "GCTGATCGCTGCTCC")
self.assertEqual(record.motifs[6].instances[9].tostring(), "GCCCGTACCGGACCT")
self.assertEqual(record.motifs[6].instances[10].tostring(), "GGACGTCGCGGAGGA")
self.assertEqual(record.motifs[6].instances[11].tostring(), "GCGGGGGGCAGGTCA")
self.assertEqual(record.motifs[6].instances[12].tostring(), "GGACGTACTGGCACA")
self.assertEqual(record.motifs[6].instances[13].tostring(), "GCAGGTGGTCGTGCA")
self.assertEqual(record.motifs[6].instances[14].tostring(), "GCGCATACCTTAACA")
self.assertEqual(record.motifs[6].instances[15].tostring(), "GCACGGGACTTCAAC")
self.assertEqual(record.motifs[6].instances[16].tostring(), "GCACGTAGCTGGTAA")
self.assertEqual(record.motifs[6].instances[17].tostring(), "GCTCGTCTATGGTCA")
self.assertEqual(record.motifs[6].instances[18].tostring(), "GCGCATGCTGGATCC")
self.assertEqual(record.motifs[6].instances[19].tostring(), "GGCCGTCAGCTCTCA")
self.assertEqual(record.motifs[6].mask, [1,1,0,1,1,1,1,0,1,0,1,0,0,1,1])
self.assertAlmostEqual(record.motifs[6].score, 13.3145)
self.assertEqual(record.motifs[7].alphabet, IUPAC.unambiguous_dna)
self.assertEqual(len(record.motifs[7].instances), 20)
self.assertEqual(record.motifs[7].instances[0].tostring(), "GAACCGAGGTCCGGTACGGGC")
self.assertEqual(record.motifs[7].instances[1].tostring(), "GCCCCCCGCATAGTAGGGGGA")
self.assertEqual(record.motifs[7].instances[2].tostring(), "GTCCCTGGGTAAGCTTGGGGC")
self.assertEqual(record.motifs[7].instances[3].tostring(), "ACTCCACGCTTCGACACGTGG")
self.assertEqual(record.motifs[7].instances[4].tostring(), "ATCCTCTGCGTCGCATGGCGG")
self.assertEqual(record.motifs[7].instances[5].tostring(), "GTTCAATGCTAAGCTCTGTGC")
self.assertEqual(record.motifs[7].instances[6].tostring(), "GCTCATAGGGACGTCGCGGAG")
self.assertEqual(record.motifs[7].instances[7].tostring(), "GTCCCGGGCCAATAGCGGCGC")
self.assertEqual(record.motifs[7].instances[8].tostring(), "GCACTTAGCAGCGTATCGTTA")
self.assertEqual(record.motifs[7].instances[9].tostring(), "GGCCCTCGGATCGCTTGGGAA")
self.assertEqual(record.motifs[7].instances[10].tostring(), "CTGCTGGACAACGGGCCGAGC")
self.assertEqual(record.motifs[7].instances[11].tostring(), "GGGCACTACATAGAGAGTTGC")
self.assertEqual(record.motifs[7].instances[12].tostring(), "AGCCTCCAGGTCGCATGGAGA")
self.assertEqual(record.motifs[7].instances[13].tostring(), "AATCGTAGATCAGAGGCGAGA")
self.assertEqual(record.motifs[7].instances[14].tostring(), "GAACTCCACTAAGACTTGAGA")
self.assertEqual(record.motifs[7].instances[15].tostring(), "GAGCAGCGATCAGCTTGTGGG")
self.assertEqual(record.motifs[7].instances[16].tostring(), "GCCAGGTACAAAGCGTCGTGC")
self.assertEqual(record.motifs[7].instances[17].tostring(), "AGTCAATGACACGCGCCTGGG")
self.assertEqual(record.motifs[7].instances[18].tostring(), "GGTCATGGAATCTTATGTAGC")
self.assertEqual(record.motifs[7].instances[19].tostring(), "GTAGATAACAGAGGTCGGGGG")
self.assertEqual(record.motifs[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.motifs[7].score, 11.6098)
self.assertEqual(record.motifs[8].alphabet, IUPAC.unambiguous_dna)
self.assertEqual(len(record.motifs[8].instances), 14)
self.assertEqual(record.motifs[8].instances[0].tostring(), "CCGAGTAAAGGGCTG")
self.assertEqual(record.motifs[8].instances[1].tostring(), "GTGGTCATCGGGCAC")
self.assertEqual(record.motifs[8].instances[2].tostring(), "GATAACAGAGGTCGG")
self.assertEqual(record.motifs[8].instances[3].tostring(), "CGGCGCCGGAGTCTG")
self.assertEqual(record.motifs[8].instances[4].tostring(), "GCGCGTCCCGGGCCA")
self.assertEqual(record.motifs[8].instances[5].tostring(), "CTGGACAACGGGCCG")
self.assertEqual(record.motifs[8].instances[6].tostring(), "CGGATACTGGGGCAG")
self.assertEqual(record.motifs[8].instances[7].tostring(), "GGGAGCAGCGATCAG")
self.assertEqual(record.motifs[8].instances[8].tostring(), "CAGAACCGAGGTCCG")
self.assertEqual(record.motifs[8].instances[9].tostring(), "GGGTCCCTGGGTAAG")
self.assertEqual(record.motifs[8].instances[10].tostring(), "GTGCTCATAGGGACG")
self.assertEqual(record.motifs[8].instances[11].tostring(), "GAGATCCGGAGGAGG")
self.assertEqual(record.motifs[8].instances[12].tostring(), "GCGATCCGAGGGCCG")
self.assertEqual(record.motifs[8].instances[13].tostring(), "GAGTTCACATGGCTG")
self.assertEqual(record.motifs[8].mask, [1,0,1,0,0,1,1,0,1,1,1,1,1,0,1])
self.assertAlmostEqual(record.motifs[8].score, 11.2943)
self.assertEqual(record.motifs[9].alphabet, IUPAC.unambiguous_dna)
self.assertEqual(len(record.motifs[9].instances), 18)
self.assertEqual(record.motifs[9].instances[0].tostring(), "TAGAGGCGGTG")
self.assertEqual(record.motifs[9].instances[1].tostring(), "GCTAAGCTCTG")
self.assertEqual(record.motifs[9].instances[2].tostring(), "TGGAAGCAGTG")
self.assertEqual(record.motifs[9].instances[3].tostring(), "GCGAGGCTGTG")
self.assertEqual(record.motifs[9].instances[4].tostring(), "ACGACGCTTTG")
self.assertEqual(record.motifs[9].instances[5].tostring(), "GGGACGCGCAC")
self.assertEqual(record.motifs[9].instances[6].tostring(), "TCGAAGCGTGG")
self.assertEqual(record.motifs[9].instances[7].tostring(), "TGTATGCGGGG")
self.assertEqual(record.motifs[9].instances[8].tostring(), "GGTAAGCTTGG")
self.assertEqual(record.motifs[9].instances[9].tostring(), "TGTACGCTGGG")
self.assertEqual(record.motifs[9].instances[10].tostring(), "ACTATGCGGGG")
self.assertEqual(record.motifs[9].instances[11].tostring(), "GGTATGCGCTG")
self.assertEqual(record.motifs[9].instances[12].tostring(), "GGTACCCGGAG")
self.assertEqual(record.motifs[9].instances[13].tostring(), "GCGACGCAGAG")
self.assertEqual(record.motifs[9].instances[14].tostring(), "TGGCGGCGTGG")
self.assertEqual(record.motifs[9].instances[15].tostring(), "TCTAGGCGGGC")
self.assertEqual(record.motifs[9].instances[16].tostring(), "AGTATGCTTAG")
self.assertEqual(record.motifs[9].instances[17].tostring(), "TGGAGGCTTAG")
self.assertEqual(record.motifs[9].mask, [1,1,1,1,0,1,1,1,1,1,1])
self.assertAlmostEqual(record.motifs[9].score, 9.7924)
self.assertEqual(record.motifs[10].alphabet, IUPAC.unambiguous_dna)
self.assertEqual(len(record.motifs[10].instances), 13)
self.assertEqual(record.motifs[10].instances[0].tostring(), "GCACAGAGCTTAGCATTGAAC")
self.assertEqual(record.motifs[10].instances[1].tostring(), "GTCCGCGGATTCCCAACATGC")
self.assertEqual(record.motifs[10].instances[2].tostring(), "ATACACAGCCTCGCAAGCCAG")
self.assertEqual(record.motifs[10].instances[3].tostring(), "GGCCCGGGACGCGCACTAAGA")
self.assertEqual(record.motifs[10].instances[4].tostring(), "GCCCGTTGTCCAGCAGACGGC")
self.assertEqual(record.motifs[10].instances[5].tostring(), "GAGCAGCGATCAGCTTGTGGG")
self.assertEqual(record.motifs[10].instances[6].tostring(), "GAACCGAGGTCCGGTACGGGC")
self.assertEqual(record.motifs[10].instances[7].tostring(), "GTCCCTGGGTAAGCTTGGGGC")
self.assertEqual(record.motifs[10].instances[8].tostring(), "GACCTGCCCCCCGCATAGTAG")
self.assertEqual(record.motifs[10].instances[9].tostring(), "AACCAGCGCATACCTTAACAG")
self.assertEqual(record.motifs[10].instances[10].tostring(), "ATCCTCTGCGTCGCATGGCGG")
self.assertEqual(record.motifs[10].instances[11].tostring(), "GACCATAGACGAGCATCAAAG")
self.assertEqual(record.motifs[10].instances[12].tostring(), "GGCCCTCGGATCGCTTGGGAA")
self.assertEqual(record.motifs[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.motifs[10].score, 9.01393)
self.assertEqual(record.motifs[11].alphabet, IUPAC.unambiguous_dna)
self.assertEqual(len(record.motifs[11].instances), 16)
self.assertEqual(record.motifs[11].instances[0].tostring(), "GCCGTCCGTC")
self.assertEqual(record.motifs[11].instances[1].tostring(), "GGCGTGCGCG")
self.assertEqual(record.motifs[11].instances[2].tostring(), "GGCGCGTGTC")
self.assertEqual(record.motifs[11].instances[3].tostring(), "AGCGCGTGTG")
self.assertEqual(record.motifs[11].instances[4].tostring(), "GCGGTGCGTG")
self.assertEqual(record.motifs[11].instances[5].tostring(), "AGCGCGTGTC")
self.assertEqual(record.motifs[11].instances[6].tostring(), "AGCGTCCGCG")
self.assertEqual(record.motifs[11].instances[7].tostring(), "ACCGTCTGTG")
self.assertEqual(record.motifs[11].instances[8].tostring(), "GCCATGCGAC")
self.assertEqual(record.motifs[11].instances[9].tostring(), "ACCACCCGTC")
self.assertEqual(record.motifs[11].instances[10].tostring(), "GGCGCCGGAG")
self.assertEqual(record.motifs[11].instances[11].tostring(), "ACCACGTGTC")
self.assertEqual(record.motifs[11].instances[12].tostring(), "GGCTTGCGAG")
self.assertEqual(record.motifs[11].instances[13].tostring(), "GCGATCCGAG")
self.assertEqual(record.motifs[11].instances[14].tostring(), "AGTGCGCGTC")
self.assertEqual(record.motifs[11].instances[15].tostring(), "AGTGCCCGAG")
self.assertEqual(record.motifs[11].mask, [1,1,1,1,1,1,1,1,1,1])
self.assertAlmostEqual(record.motifs[11].score, 7.51121)
self.assertEqual(record.motifs[12].alphabet, IUPAC.unambiguous_dna)
self.assertEqual(len(record.motifs[12].instances), 16)
self.assertEqual(record.motifs[12].instances[0].tostring(), "GCCGACGGGTGGTCATCGGG")
self.assertEqual(record.motifs[12].instances[1].tostring(), "GCACGACGCTTTGTACCTGG")
self.assertEqual(record.motifs[12].instances[2].tostring(), "CCTGGGAGGGTTCAATAACG")
self.assertEqual(record.motifs[12].instances[3].tostring(), "GCGCGTCCCGGGCCAATAGC")
self.assertEqual(record.motifs[12].instances[4].tostring(), "GCCGTCTGCTGGACAACGGG")
self.assertEqual(record.motifs[12].instances[5].tostring(), "GTCCCTTCCGGTACATGAGG")
self.assertEqual(record.motifs[12].instances[6].tostring(), "GCTGCTCCCCGCATACAGCG")
self.assertEqual(record.motifs[12].instances[7].tostring(), "GCCCCAAGCTTACCCAGGGA")
self.assertEqual(record.motifs[12].instances[8].tostring(), "ACCGGCTGACGCTAATACGG")
self.assertEqual(record.motifs[12].instances[9].tostring(), "GCGGGGGGCAGGTCATTACA")
self.assertEqual(record.motifs[12].instances[10].tostring(), "GCTGGCAGCGTCTAAGAAGG")
self.assertEqual(record.motifs[12].instances[11].tostring(), "GCAGGTGGTCGTGCAATACG")
self.assertEqual(record.motifs[12].instances[12].tostring(), "GCTGGTTGAAGTCCCGTGCG")
self.assertEqual(record.motifs[12].instances[13].tostring(), "GCACGTAGCTGGTAAATAGG")
self.assertEqual(record.motifs[12].instances[14].tostring(), "GCGGCGTGGATTTCATACAG")
self.assertEqual(record.motifs[12].instances[15].tostring(), "CCTGGAGGCTTAGACTTGGG")
self.assertEqual(record.motifs[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.motifs[12].score, 5.63667)
self.assertEqual(record.motifs[13].alphabet, IUPAC.unambiguous_dna)
self.assertEqual(len(record.motifs[13].instances), 15)
self.assertEqual(record.motifs[13].instances[0].tostring(), "GCCGACGGGTGGTCATCGGG")
self.assertEqual(record.motifs[13].instances[1].tostring(), "ATCCGCGGACGCTTAGAGGG")
self.assertEqual(record.motifs[13].instances[2].tostring(), "ACGCTTTGTACCTGGCTTGC")
self.assertEqual(record.motifs[13].instances[3].tostring(), "ACGGACGGCACTTAGCAGCG")
self.assertEqual(record.motifs[13].instances[4].tostring(), "GCCGTCTGCTGGACAACGGG")
self.assertEqual(record.motifs[13].instances[5].tostring(), "ACACACAGACGGTTGAAAGG")
self.assertEqual(record.motifs[13].instances[6].tostring(), "GCCGATAGTGCTTAAGTTCG")
self.assertEqual(record.motifs[13].instances[7].tostring(), "CTTGCCCGTACCGGACCTCG")
self.assertEqual(record.motifs[13].instances[8].tostring(), "ACCGGCTGACGCTAATACGG")
self.assertEqual(record.motifs[13].instances[9].tostring(), "GCCCCCCGCATAGTAGGGGG")
self.assertEqual(record.motifs[13].instances[10].tostring(), "GCTGGCAGCGTCTAAGAAGG")
self.assertEqual(record.motifs[13].instances[11].tostring(), "GCAGGTGGTCGTGCAATACG")
self.assertEqual(record.motifs[13].instances[12].tostring(), "ACGCACGGGACTTCAACCAG")
self.assertEqual(record.motifs[13].instances[13].tostring(), "GCACGTAGCTGGTAAATAGG")
self.assertEqual(record.motifs[13].instances[14].tostring(), "ATCCTCTGCGTCGCATGGCG")
self.assertEqual(record.motifs[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.motifs[13].score, 3.89842)
self.assertEqual(record.motifs[14].alphabet, IUPAC.unambiguous_dna)
self.assertEqual(len(record.motifs[14].instances), 14)
self.assertEqual(record.motifs[14].instances[0].tostring(), "GAGGCTGTGTAT")
self.assertEqual(record.motifs[14].instances[1].tostring(), "GAGGTCGGGGGT")
self.assertEqual(record.motifs[14].instances[2].tostring(), "GACGGACGGCAC")
self.assertEqual(record.motifs[14].instances[3].tostring(), "TTGGCCCGGGAC")
self.assertEqual(record.motifs[14].instances[4].tostring(), "GAGGCTCGGCCC")
self.assertEqual(record.motifs[14].instances[5].tostring(), "CACGCGCTGTAT")
self.assertEqual(record.motifs[14].instances[6].tostring(), "TAGGCCAGGTAT")
self.assertEqual(record.motifs[14].instances[7].tostring(), "GAGGTCCGGTAC")
self.assertEqual(record.motifs[14].instances[8].tostring(), "TACGCTGGGGAT")
self.assertEqual(record.motifs[14].instances[9].tostring(), "GTCGCGGAGGAT")
self.assertEqual(record.motifs[14].instances[10].tostring(), "TACGCACGGGAC")
self.assertEqual(record.motifs[14].instances[11].tostring(), "TACTCCGGGTAC")
self.assertEqual(record.motifs[14].instances[12].tostring(), "GACGCAGAGGAT")
self.assertEqual(record.motifs[14].instances[13].tostring(), "TAGGCGGGCCAT")
self.assertEqual(record.motifs[14].mask, [1,1,1,1,1,0,1,1,1,0,1,1])
self.assertAlmostEqual(record.motifs[14].score, 3.33444)
self.assertEqual(record.motifs[15].alphabet, IUPAC.unambiguous_dna)
self.assertEqual(len(record.motifs[15].instances), 21)
self.assertEqual(record.motifs[15].instances[0].tostring(), "CGGCTCAATCGTAGAGGC")
self.assertEqual(record.motifs[15].instances[1].tostring(), "CGACGGGTGGTCATCGGG")
self.assertEqual(record.motifs[15].instances[2].tostring(), "CGCTTAGAGGGCACAAGC")
self.assertEqual(record.motifs[15].instances[3].tostring(), "TGACACGCGCCTGGGAGG")
self.assertEqual(record.motifs[15].instances[4].tostring(), "CGATACGCTGCTAAGTGC")
self.assertEqual(record.motifs[15].instances[5].tostring(), "CGTCCCGGGCCAATAGCG")
self.assertEqual(record.motifs[15].instances[6].tostring(), "CCACGCTTCGACACGTGG")
self.assertEqual(record.motifs[15].instances[7].tostring(), "CGTCTGCTGGACAACGGG")
self.assertEqual(record.motifs[15].instances[8].tostring(), "ACACAGACGGTTGAAAGG")
self.assertEqual(record.motifs[15].instances[9].tostring(), "TGCTCCCCGCATACAGCG")
self.assertEqual(record.motifs[15].instances[10].tostring(), "TGAGGCTTGCCCGTACCG")
self.assertEqual(record.motifs[15].instances[11].tostring(), "TGCCCCAAGCTTACCCAG")
self.assertEqual(record.motifs[15].instances[12].tostring(), "CGGCTGACGCTAATACGG")
self.assertEqual(record.motifs[15].instances[13].tostring(), "CGCGACGTCCCTATGAGC")
self.assertEqual(record.motifs[15].instances[14].tostring(), "TGCCCCCCGCATAGTAGG")
self.assertEqual(record.motifs[15].instances[15].tostring(), "CGTTGCCTTCTTAGACGC")
self.assertEqual(record.motifs[15].instances[16].tostring(), "TGACTCAATCGTAGACCC")
self.assertEqual(record.motifs[15].instances[17].tostring(), "AGTCCCGTGCGTATGTGG")
self.assertEqual(record.motifs[15].instances[18].tostring(), "AGGCTCGCACGTAGCTGG")
self.assertEqual(record.motifs[15].instances[19].tostring(), "CCACGCCGCCATGCGACG")
self.assertEqual(record.motifs[15].instances[20].tostring(), "AGCCTCCAGGTCGCATGG")
self.assertEqual(record.motifs[15].mask, [1,1,0,1,0,1,0,0,1,1,0,1,1,0,0,0,1,1])
self.assertAlmostEqual(record.motifs[15].score, 1.0395)
def test_pfm_parsing(self):
"""Test to be sure that Motif can parse pfm files.
"""
motif= Motif.read(self.PFMin,"jaspar-pfm")
assert motif.length==12
def test_sites_parsing(self):
"""Test to be sure that Motif can parse sites files.
"""
motif= Motif.read(self.SITESin,"jaspar-sites")
assert motif.length==6
def test_FAoutput(self):
"""Ensure that we can write proper FASTA output files.
"""
output_handle = open(self.FAout, "w")
output_handle.write(self.m.format("fasta"))
output_handle.close()
def test_TFoutput(self):
"""Ensure that we can write proper TransFac output files.
"""
output_handle = open(self.TFout, "w")
output_handle.write(self.m.format("transfac"))
output_handle.close()
def test_pfm_output(self):
"""Ensure that we can write proper pfm output files.
"""
output_handle = open(self.PFMout, "w")
output_handle.write(self.m.format("jaspar-pfm"))
output_handle.close()
class TestMEME(unittest.TestCase):
def test_meme_parser_1(self):
"""Test if Motif can parse MEME output files (first test)
"""
from Bio.Motif.Parsers import MEME
handle = open("Motif/meme.out")
record = MEME.read(handle)
self.assertEqual(record.version, '3.5.7')
self.assertEqual(record.datafile, 'test.fa')
self.assertEqual(record.alphabet, IUPAC.unambiguous_dna)
self.assertEqual(len(record.sequence_names), 10)
self.assertEqual(record.sequence_names[0], 'SEQ1;')
self.assertEqual(record.sequence_names[1], 'SEQ2;')
self.assertEqual(record.sequence_names[2], 'SEQ3;')
self.assertEqual(record.sequence_names[3], 'SEQ4;')
self.assertEqual(record.sequence_names[4], 'SEQ5;')
self.assertEqual(record.sequence_names[5], 'SEQ6;')
self.assertEqual(record.sequence_names[6], 'SEQ7;')
self.assertEqual(record.sequence_names[7], 'SEQ8;')
self.assertEqual(record.sequence_names[8], 'SEQ9;')
self.assertEqual(record.sequence_names[9], 'SEQ10;')
self.assertEqual(record.command, 'meme test.fa -dna -w 10 -dir /home/bartek/MetaMotif/meme')
self.assertEqual(len(record.motifs), 1)
motif = record.motifs[0]
self.assertEqual(motif.num_occurrences, 10)
self.assertAlmostEqual(motif.evalue, 1.1e-22)
self.assertEqual(motif.alphabet, IUPAC.unambiguous_dna)
self.assertEqual(motif.name, "Motif 1")
self.assertEqual(len(motif.instances), 10)
self.assertAlmostEqual(motif.instances[0].pvalue, 8.71e-07)
self.assertAlmostEqual(motif.instances[1].pvalue, 8.71e-07)
self.assertAlmostEqual(motif.instances[2].pvalue, 8.71e-07)
self.assertAlmostEqual(motif.instances[3].pvalue, 8.71e-07)
self.assertAlmostEqual(motif.instances[4].pvalue, 8.71e-07)
self.assertAlmostEqual(motif.instances[5].pvalue, 8.71e-07)
self.assertAlmostEqual(motif.instances[6].pvalue, 8.71e-07)
self.assertAlmostEqual(motif.instances[7].pvalue, 8.71e-07)
self.assertAlmostEqual(motif.instances[8].pvalue, 8.71e-07)
self.assertAlmostEqual(motif.instances[9].pvalue, 8.71e-07)
self.assertEqual(motif.instances[0].sequence_name, 'SEQ10;')
self.assertEqual(motif.instances[1].sequence_name, 'SEQ9;')
self.assertEqual(motif.instances[2].sequence_name, 'SEQ8;')
self.assertEqual(motif.instances[3].sequence_name, 'SEQ7;')
self.assertEqual(motif.instances[4].sequence_name, 'SEQ6;')
self.assertEqual(motif.instances[5].sequence_name, 'SEQ5;')
self.assertEqual(motif.instances[6].sequence_name, 'SEQ4;')
self.assertEqual(motif.instances[7].sequence_name, 'SEQ3;')
self.assertEqual(motif.instances[8].sequence_name, 'SEQ2;')
self.assertEqual(motif.instances[9].sequence_name, 'SEQ1;')
self.assertEqual(motif.instances[0].start, 3)
self.assertEqual(motif.instances[1].start, 93)
self.assertEqual(motif.instances[2].start, 172)
self.assertEqual(motif.instances[3].start, 177)
self.assertEqual(motif.instances[4].start, 105)
self.assertEqual(motif.instances[5].start, 185)
self.assertEqual(motif.instances[6].start, 173)
self.assertEqual(motif.instances[7].start, 112)
self.assertEqual(motif.instances[8].start, 172)
self.assertEqual(motif.instances[9].start, 52)
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[0].length, 10)
self.assertEqual(motif.instances[1].length, 10)
self.assertEqual(motif.instances[2].length, 10)
self.assertEqual(motif.instances[3].length, 10)
self.assertEqual(motif.instances[4].length, 10)
self.assertEqual(motif.instances[5].length, 10)
self.assertEqual(motif.instances[6].length, 10)
self.assertEqual(motif.instances[7].length, 10)
self.assertEqual(motif.instances[8].length, 10)
self.assertEqual(motif.instances[9].length, 10)
self.assertEqual(motif.instances[0].motif_name, 'Motif 1')
self.assertEqual(motif.instances[1].motif_name, 'Motif 1')
self.assertEqual(motif.instances[2].motif_name, 'Motif 1')
self.assertEqual(motif.instances[3].motif_name, 'Motif 1')
self.assertEqual(motif.instances[4].motif_name, 'Motif 1')
self.assertEqual(motif.instances[5].motif_name, 'Motif 1')
self.assertEqual(motif.instances[6].motif_name, 'Motif 1')
self.assertEqual(motif.instances[7].motif_name, 'Motif 1')
self.assertEqual(motif.instances[8].motif_name, 'Motif 1')
self.assertEqual(motif.instances[9].motif_name, 'Motif 1')
self.assertEqual(motif.instances[0].alphabet, IUPAC.unambiguous_dna)
self.assertEqual(motif.instances[1].alphabet, IUPAC.unambiguous_dna)
self.assertEqual(motif.instances[2].alphabet, IUPAC.unambiguous_dna)
self.assertEqual(motif.instances[3].alphabet, IUPAC.unambiguous_dna)
self.assertEqual(motif.instances[4].alphabet, IUPAC.unambiguous_dna)
self.assertEqual(motif.instances[5].alphabet, IUPAC.unambiguous_dna)
self.assertEqual(motif.instances[6].alphabet, IUPAC.unambiguous_dna)
self.assertEqual(motif.instances[7].alphabet, IUPAC.unambiguous_dna)
self.assertEqual(motif.instances[8].alphabet, IUPAC.unambiguous_dna)
self.assertEqual(motif.instances[9].alphabet, IUPAC.unambiguous_dna)
self.assertEqual(motif.instances[0].tostring(), "CTCAATCGTA")
self.assertEqual(motif.instances[1].tostring(), "CTCAATCGTA")
self.assertEqual(motif.instances[2].tostring(), "CTCAATCGTA")
self.assertEqual(motif.instances[3].tostring(), "CTCAATCGTA")
self.assertEqual(motif.instances[4].tostring(), "CTCAATCGTA")
self.assertEqual(motif.instances[5].tostring(), "CTCAATCGTA")
self.assertEqual(motif.instances[6].tostring(), "CTCAATCGTA")
self.assertEqual(motif.instances[7].tostring(), "CTCAATCGTA")
self.assertEqual(motif.instances[8].tostring(), "CTCAATCGTA")
self.assertEqual(motif.instances[9].tostring(), "CTCAATCGTA")
handle.close()
def test_meme_parser_2(self):
"""Test if Motif can parse MEME output files (second test)
"""
from Bio.Motif.Parsers import MEME
handle = open("Motif/meme.dna.oops.txt")
record = MEME.read(handle)
self.assertEqual(record.version, '3.0')
self.assertEqual(record.datafile, 'INO_up800.s')
self.assertEqual(record.alphabet, IUPAC.unambiguous_dna)
self.assertEqual(len(record.sequence_names), 7)
self.assertEqual(record.sequence_names[0], 'CHO1')
self.assertEqual(record.sequence_names[1], 'CHO2')
self.assertEqual(record.sequence_names[2], 'FAS1')
self.assertEqual(record.sequence_names[3], 'FAS2')
self.assertEqual(record.sequence_names[4], 'ACC1')
self.assertEqual(record.sequence_names[5], 'INO1')
self.assertEqual(record.sequence_names[6], 'OPI3')
self.assertEqual(record.command, 'meme -mod oops -dna -revcomp -nmotifs 2 -bfile yeast.nc.6.freq INO_up800.s')
self.assertEqual(len(record.motifs), 2)
motif = record.motifs[0]
self.assertEqual(motif.num_occurrences, 7)
self.assertAlmostEqual(motif.evalue, 0.2)
self.assertEqual(motif.alphabet, IUPAC.unambiguous_dna)
self.assertEqual(motif.name, "Motif 1")
self.assertEqual(len(motif.instances), 7)
self.assertAlmostEqual(motif.instances[0].pvalue, 1.85e-08)
self.assertAlmostEqual(motif.instances[1].pvalue, 1.85e-08)
self.assertAlmostEqual(motif.instances[2].pvalue, 1.52e-07)
self.assertAlmostEqual(motif.instances[3].pvalue, 2.52e-07)
self.assertAlmostEqual(motif.instances[4].pvalue, 4.23e-07)
self.assertAlmostEqual(motif.instances[5].pvalue, 9.43e-07)
self.assertAlmostEqual(motif.instances[6].pvalue, 3.32e-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].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, 12)
self.assertEqual(motif.instances[1].length, 12)
self.assertEqual(motif.instances[2].length, 12)
self.assertEqual(motif.instances[3].length, 12)
self.assertEqual(motif.instances[4].length, 12)
self.assertEqual(motif.instances[5].length, 12)
self.assertEqual(motif.instances[6].length, 12)
self.assertEqual(motif.instances[0].start, 620)
self.assertEqual(motif.instances[1].start, 95)
self.assertEqual(motif.instances[2].start, 83)
self.assertEqual(motif.instances[3].start, 354)
self.assertEqual(motif.instances[4].start, 611)
self.assertEqual(motif.instances[5].start, 567)
self.assertEqual(motif.instances[6].start, 340)
self.assertEqual(motif.instances[0].tostring(), "TTCACATGCCGC")
self.assertEqual(motif.instances[1].tostring(), "TTCACATGCCGC")
self.assertEqual(motif.instances[2].tostring(), "TTCACATGGCCC")
self.assertEqual(motif.instances[3].tostring(), "TTCTCATGCCGC")
self.assertEqual(motif.instances[4].tostring(), "TTCACACGGCAC")
self.assertEqual(motif.instances[5].tostring(), "TTCACATGCTAC")
self.assertEqual(motif.instances[6].tostring(), "TTCAGATCGCTC")
motif = record.motifs[1]
self.assertEqual(motif.num_occurrences, 7)
self.assertAlmostEqual(motif.evalue, 110)
self.assertEqual(motif.alphabet, IUPAC.unambiguous_dna)
self.assertEqual(motif.name, "Motif 2")
self.assertEqual(len(motif.instances), 7)
self.assertAlmostEqual(motif.instances[0].pvalue, 3.24e-07)
self.assertAlmostEqual(motif.instances[1].pvalue, 3.24e-07)
self.assertAlmostEqual(motif.instances[2].pvalue, 3.24e-07)
self.assertAlmostEqual(motif.instances[3].pvalue, 5.29e-06)
self.assertAlmostEqual(motif.instances[4].pvalue, 6.25e-06)
self.assertAlmostEqual(motif.instances[5].pvalue, 8.48e-06)
self.assertAlmostEqual(motif.instances[6].pvalue, 8.48e-06)
self.assertEqual(motif.instances[0].sequence_name, 'OPI3')
self.assertEqual(motif.instances[1].sequence_name, 'ACC1')
self.assertEqual(motif.instances[2].sequence_name, 'CHO1')
self.assertEqual(motif.instances[3].sequence_name, 'INO1')
self.assertEqual(motif.instances[4].sequence_name, 'FAS1')
self.assertEqual(motif.instances[5].sequence_name, 'FAS2')
self.assertEqual(motif.instances[6].sequence_name, 'CHO2')
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, 10)
self.assertEqual(motif.instances[1].length, 10)
self.assertEqual(motif.instances[2].length, 10)
self.assertEqual(motif.instances[3].length, 10)
self.assertEqual(motif.instances[4].length, 10)
self.assertEqual(motif.instances[5].length, 10)
self.assertEqual(motif.instances[6].length, 10)
self.assertEqual(motif.instances[0].start, 186)
self.assertEqual(motif.instances[1].start, 232)
self.assertEqual(motif.instances[2].start, 559)
self.assertEqual(motif.instances[3].start, 283)
self.assertEqual(motif.instances[4].start, 44)
self.assertEqual(motif.instances[5].start, 185)
self.assertEqual(motif.instances[6].start, 413)
self.assertEqual(motif.instances[0].tostring(), "TCTGGCACAG")
self.assertEqual(motif.instances[1].tostring(), "TCTGGCACAG")
self.assertEqual(motif.instances[2].tostring(), "TCTGGCACAG")
self.assertEqual(motif.instances[3].tostring(), "GCGGGCGCAG")
self.assertEqual(motif.instances[4].tostring(), "GCAGGCACGG")
self.assertEqual(motif.instances[5].tostring(), "TCTGGCACTC")
self.assertEqual(motif.instances[6].tostring(), "TCTGGCATCG")
handle.close()
def test_meme_parser_3(self):
"""Test if Motif can parse MEME output files (third test)
"""
from Bio.Motif.Parsers import MEME
handle = open("Motif/meme.protein.oops.txt")
record = MEME.read(handle)
self.assertEqual(record.version, '3.0')
self.assertEqual(record.datafile, 'adh.s')
self.assertEqual(record.alphabet, IUPAC.protein)
self.assertEqual(len(record.sequence_names), 33)
self.assertEqual(record.sequence_names[0], "2BHD_STREX")
self.assertEqual(record.sequence_names[1], "3BHD_COMTE")
self.assertEqual(record.sequence_names[2], "ADH_DROME")
self.assertEqual(record.sequence_names[3], "AP27_MOUSE")
self.assertEqual(record.sequence_names[4], "BA72_EUBSP")
self.assertEqual(record.sequence_names[5], "BDH_HUMAN")
self.assertEqual(record.sequence_names[6], "BPHB_PSEPS")
self.assertEqual(record.sequence_names[7], "BUDC_KLETE")
self.assertEqual(record.sequence_names[8], "DHES_HUMAN")
self.assertEqual(record.sequence_names[9], "DHGB_BACME")
self.assertEqual(record.sequence_names[10], "DHII_HUMAN")
self.assertEqual(record.sequence_names[11], "DHMA_FLAS1")
self.assertEqual(record.sequence_names[12], "ENTA_ECOLI")
self.assertEqual(record.sequence_names[13], "FIXR_BRAJA")
self.assertEqual(record.sequence_names[14], "GUTD_ECOLI")
self.assertEqual(record.sequence_names[15], "HDE_CANTR")
self.assertEqual(record.sequence_names[16], "HDHA_ECOLI")
self.assertEqual(record.sequence_names[17], "LIGD_PSEPA")
self.assertEqual(record.sequence_names[18], "NODG_RHIME")
self.assertEqual(record.sequence_names[19], "RIDH_KLEAE")
self.assertEqual(record.sequence_names[20], "YINL_LISMO")
self.assertEqual(record.sequence_names[21], "YRTP_BACSU")
self.assertEqual(record.sequence_names[22], "CSGA_MYXXA")
self.assertEqual(record.sequence_names[23], "DHB2_HUMAN")
self.assertEqual(record.sequence_names[24], "DHB3_HUMAN")
self.assertEqual(record.sequence_names[25], "DHCA_HUMAN")
self.assertEqual(record.sequence_names[26], "FABI_ECOLI")
self.assertEqual(record.sequence_names[27], "FVT1_HUMAN")
self.assertEqual(record.sequence_names[28], "HMTR_LEIMA")
self.assertEqual(record.sequence_names[29], "MAS1_AGRRA")
self.assertEqual(record.sequence_names[30], "PCR_PEA")
self.assertEqual(record.sequence_names[31], "RFBB_NEIGO")
self.assertEqual(record.sequence_names[32], "YURA_MYXXA")
self.assertEqual(record.command, 'meme adh.s -mod oops -protein -nmotifs 2')
self.assertEqual(len(record.motifs), 2)
motif = record.motifs[0]
self.assertEqual(motif.num_occurrences, 33)
self.assertAlmostEqual(motif.evalue, 3.6e-165)
self.assertEqual(motif.alphabet, IUPAC.protein)
self.assertEqual(motif.name, "Motif 1")
self.assertEqual(len(motif.instances), 33)
self.assertAlmostEqual(motif.instances[0].pvalue, 1.64e-22)
self.assertAlmostEqual(motif.instances[1].pvalue, 6.32e-22)
self.assertAlmostEqual(motif.instances[2].pvalue, 1.13e-21)
self.assertAlmostEqual(motif.instances[3].pvalue, 4.04e-21)
self.assertAlmostEqual(motif.instances[4].pvalue, 6.12e-21)
self.assertAlmostEqual(motif.instances[5].pvalue, 7.52e-20)
self.assertAlmostEqual(motif.instances[6].pvalue, 3.35e-19)
self.assertAlmostEqual(motif.instances[7].pvalue, 4.82e-19)
self.assertAlmostEqual(motif.instances[8].pvalue, 4.82e-19)
self.assertAlmostEqual(motif.instances[9].pvalue, 1.11e-18)
self.assertAlmostEqual(motif.instances[10].pvalue, 1.25e-18)
self.assertAlmostEqual(motif.instances[11].pvalue, 2.23e-18)
self.assertAlmostEqual(motif.instances[12].pvalue, 5.53e-18)
self.assertAlmostEqual(motif.instances[13].pvalue, 9.65e-18)
self.assertAlmostEqual(motif.instances[14].pvalue, 2.86e-17)
self.assertAlmostEqual(motif.instances[15].pvalue, 8.20e-17)
self.assertAlmostEqual(motif.instances[16].pvalue, 9.09e-17)
self.assertAlmostEqual(motif.instances[17].pvalue, 1.37e-16)
self.assertAlmostEqual(motif.instances[18].pvalue, 2.52e-16)
self.assertAlmostEqual(motif.instances[19].pvalue, 1.21e-15)
self.assertAlmostEqual(motif.instances[20].pvalue, 1.61e-15)
self.assertAlmostEqual(motif.instances[21].pvalue, 1.77e-15)
self.assertAlmostEqual(motif.instances[22].pvalue, 7.81e-15)
self.assertAlmostEqual(motif.instances[23].pvalue, 8.55e-15)
self.assertAlmostEqual(motif.instances[24].pvalue, 1.47e-14)
self.assertAlmostEqual(motif.instances[25].pvalue, 3.24e-14)
self.assertAlmostEqual(motif.instances[26].pvalue, 1.80e-12)
self.assertAlmostEqual(motif.instances[27].pvalue, 2.10e-12)
self.assertAlmostEqual(motif.instances[28].pvalue, 4.15e-12)
self.assertAlmostEqual(motif.instances[29].pvalue, 5.20e-12)
self.assertAlmostEqual(motif.instances[30].pvalue, 4.80e-10)
self.assertAlmostEqual(motif.instances[31].pvalue, 2.77e-08)
self.assertAlmostEqual(motif.instances[32].pvalue, 5.72e-08)
self.assertEqual(motif.instances[0].sequence_name, 'YRTP_BACSU')
self.assertEqual(motif.instances[1].sequence_name, 'AP27_MOUSE')
self.assertEqual(motif.instances[2].sequence_name, 'NODG_RHIME')
self.assertEqual(motif.instances[3].sequence_name, 'BUDC_KLETE')
self.assertEqual(motif.instances[4].sequence_name, 'FIXR_BRAJA')
self.assertEqual(motif.instances[5].sequence_name, 'DHGB_BACME')
self.assertEqual(motif.instances[6].sequence_name, 'HMTR_LEIMA')
self.assertEqual(motif.instances[7].sequence_name, 'YURA_MYXXA')
self.assertEqual(motif.instances[8].sequence_name, 'GUTD_ECOLI')
self.assertEqual(motif.instances[9].sequence_name, '2BHD_STREX')
self.assertEqual(motif.instances[10].sequence_name, 'HDHA_ECOLI')
self.assertEqual(motif.instances[11].sequence_name, 'DHB2_HUMAN')
self.assertEqual(motif.instances[12].sequence_name, 'DHMA_FLAS1')
self.assertEqual(motif.instances[13].sequence_name, 'HDE_CANTR')
self.assertEqual(motif.instances[14].sequence_name, 'FVT1_HUMAN')
self.assertEqual(motif.instances[15].sequence_name, 'BDH_HUMAN')
self.assertEqual(motif.instances[16].sequence_name, 'RIDH_KLEAE')
self.assertEqual(motif.instances[17].sequence_name, 'DHES_HUMAN')
self.assertEqual(motif.instances[18].sequence_name, 'BA72_EUBSP')
self.assertEqual(motif.instances[19].sequence_name, 'LIGD_PSEPA')
self.assertEqual(motif.instances[20].sequence_name, 'DHII_HUMAN')
self.assertEqual(motif.instances[21].sequence_name, 'ENTA_ECOLI')
self.assertEqual(motif.instances[22].sequence_name, '3BHD_COMTE')
self.assertEqual(motif.instances[23].sequence_name, 'DHB3_HUMAN')
self.assertEqual(motif.instances[24].sequence_name, 'RFBB_NEIGO')
self.assertEqual(motif.instances[25].sequence_name, 'YINL_LISMO')
self.assertEqual(motif.instances[26].sequence_name, 'BPHB_PSEPS')
self.assertEqual(motif.instances[27].sequence_name, 'CSGA_MYXXA')
self.assertEqual(motif.instances[28].sequence_name, 'FABI_ECOLI')
self.assertEqual(motif.instances[29].sequence_name, 'ADH_DROME')
self.assertEqual(motif.instances[30].sequence_name, 'DHCA_HUMAN')
self.assertEqual(motif.instances[31].sequence_name, 'PCR_PEA')
self.assertEqual(motif.instances[32].sequence_name, 'MAS1_AGRRA')
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, 29)
self.assertEqual(motif.instances[1].length, 29)
self.assertEqual(motif.instances[2].length, 29)
self.assertEqual(motif.instances[3].length, 29)
self.assertEqual(motif.instances[4].length, 29)
self.assertEqual(motif.instances[5].length, 29)
self.assertEqual(motif.instances[6].length, 29)
self.assertEqual(motif.instances[7].length, 29)
self.assertEqual(motif.instances[8].length, 29)
self.assertEqual(motif.instances[9].length, 29)
self.assertEqual(motif.instances[10].length, 29)
self.assertEqual(motif.instances[11].length, 29)
self.assertEqual(motif.instances[12].length, 29)
self.assertEqual(motif.instances[13].length, 29)
self.assertEqual(motif.instances[14].length, 29)
self.assertEqual(motif.instances[15].length, 29)
self.assertEqual(motif.instances[16].length, 29)
self.assertEqual(motif.instances[17].length, 29)
self.assertEqual(motif.instances[18].length, 29)
self.assertEqual(motif.instances[19].length, 29)
self.assertEqual(motif.instances[20].length, 29)
self.assertEqual(motif.instances[21].length, 29)
self.assertEqual(motif.instances[22].length, 29)
self.assertEqual(motif.instances[23].length, 29)
self.assertEqual(motif.instances[24].length, 29)
self.assertEqual(motif.instances[25].length, 29)
self.assertEqual(motif.instances[26].length, 29)
self.assertEqual(motif.instances[27].length, 29)
self.assertEqual(motif.instances[28].length, 29)
self.assertEqual(motif.instances[29].length, 29)
self.assertEqual(motif.instances[30].length, 29)
self.assertEqual(motif.instances[31].length, 29)
self.assertEqual(motif.instances[32].length, 29)
self.assertEqual(motif.instances[0].start, 155)
self.assertEqual(motif.instances[1].start, 149)
self.assertEqual(motif.instances[2].start, 152)
self.assertEqual(motif.instances[3].start, 152)
self.assertEqual(motif.instances[4].start, 189)
self.assertEqual(motif.instances[5].start, 160)
self.assertEqual(motif.instances[6].start, 193)
self.assertEqual(motif.instances[7].start, 160)
self.assertEqual(motif.instances[8].start, 154)
self.assertEqual(motif.instances[9].start, 152)
self.assertEqual(motif.instances[10].start, 159)
self.assertEqual(motif.instances[11].start, 232)
self.assertEqual(motif.instances[12].start, 165)
self.assertEqual(motif.instances[13].start, 467)
self.assertEqual(motif.instances[14].start, 186)
self.assertEqual(motif.instances[15].start, 208)
self.assertEqual(motif.instances[16].start, 160)
self.assertEqual(motif.instances[17].start, 155)
self.assertEqual(motif.instances[18].start, 157)
self.assertEqual(motif.instances[19].start, 157)
self.assertEqual(motif.instances[20].start, 183)
self.assertEqual(motif.instances[21].start, 144)
self.assertEqual(motif.instances[22].start, 151)
self.assertEqual(motif.instances[23].start, 198)
self.assertEqual(motif.instances[24].start, 165)
self.assertEqual(motif.instances[25].start, 154)
self.assertEqual(motif.instances[26].start, 153)
self.assertEqual(motif.instances[27].start, 88)
self.assertEqual(motif.instances[28].start, 159)
self.assertEqual(motif.instances[29].start, 152)
self.assertEqual(motif.instances[30].start, 193)
self.assertEqual(motif.instances[31].start, 26)
self.assertEqual(motif.instances[32].start, 349)
self.assertEqual(motif.instances[0].tostring(), "YSASKFAVLGLTESLMQEVRKHNIRVSAL")
self.assertEqual(motif.instances[1].tostring(), "YSSTKGAMTMLTKAMAMELGPHKIRVNSV")
self.assertEqual(motif.instances[2].tostring(), "YCASKAGMIGFSKSLAQEIATRNITVNCV")
self.assertEqual(motif.instances[3].tostring(), "YSSSKFAVRGLTQTAARDLAPLGITVNGF")
self.assertEqual(motif.instances[4].tostring(), "YATSKAALASLTRELAHDYAPHGIRVNAI")
self.assertEqual(motif.instances[5].tostring(), "YAASKGGMKLMTETLALEYAPKGIRVNNI")
self.assertEqual(motif.instances[6].tostring(), "YTMAKGALEGLTRSAALELAPLQIRVNGV")
self.assertEqual(motif.instances[7].tostring(), "YSASKAFLSTFMESLRVDLRGTGVRVTCI")
self.assertEqual(motif.instances[8].tostring(), "YSAAKFGGVGLTQSLALDLAEYGITVHSL")
self.assertEqual(motif.instances[9].tostring(), "YGASKWGVRGLSKLAAVELGTDRIRVNSV")
self.assertEqual(motif.instances[10].tostring(), "YASSKAAASHLVRNMAFDLGEKNIRVNGI")
self.assertEqual(motif.instances[11].tostring(), "YGSSKAAVTMFSSVMRLELSKWGIKVASI")
self.assertEqual(motif.instances[12].tostring(), "YVAAKGGVAMLTRAMAVDLARHGILVNMI")
self.assertEqual(motif.instances[13].tostring(), "YSSSKAGILGLSKTMAIEGAKNNIKVNIV")
self.assertEqual(motif.instances[14].tostring(), "YSASKFAIRGLAEALQMEVKPYNVYITVA")
self.assertEqual(motif.instances[15].tostring(), "YCITKFGVEAFSDCLRYEMYPLGVKVSVV")
self.assertEqual(motif.instances[16].tostring(), "YTASKFAVQAFVHTTRRQVAQYGVRVGAV")
self.assertEqual(motif.instances[17].tostring(), "YCASKFALEGLCESLAVLLLPFGVHLSLI")
self.assertEqual(motif.instances[18].tostring(), "YPASKASVIGLTHGLGREIIRKNIRVVGV")
self.assertEqual(motif.instances[19].tostring(), "YSAAKAASINLMEGYRQGLEKYGIGVSVC")
self.assertEqual(motif.instances[20].tostring(), "YSASKFALDGFFSSIRKEYSVSRVNVSIT")
self.assertEqual(motif.instances[21].tostring(), "YGASKAALKSLALSVGLELAGSGVRCNVV")
self.assertEqual(motif.instances[22].tostring(), "YSASKAAVSALTRAAALSCRKQGYAIRVN")
self.assertEqual(motif.instances[23].tostring(), "YSASKAFVCAFSKALQEEYKAKEVIIQVL")
self.assertEqual(motif.instances[24].tostring(), "YSASKAAADHLVRAWQRTYRLPSIVSNCS")
self.assertEqual(motif.instances[25].tostring(), "YGATKWAVRDLMEVLRMESAQEGTNIRTA")
self.assertEqual(motif.instances[26].tostring(), "YTAAKQAIVGLVRELAFELAPYVRVNGVG")
self.assertEqual(motif.instances[27].tostring(), "YRMSKAALNMAVRSMSTDLRPEGFVTVLL")
self.assertEqual(motif.instances[28].tostring(), "MGLAKASLEANVRYMANAMGPEGVRVNAI")
self.assertEqual(motif.instances[29].tostring(), "YSGTKAAVVNFTSSLAKLAPITGVTAYTV")
self.assertEqual(motif.instances[30].tostring(), "YGVTKIGVTVLSRIHARKLSEQRKGDKIL")
self.assertEqual(motif.instances[31].tostring(), "KDSTLFGVSSLSDSLKGDFTSSALRCKEL")
self.assertEqual(motif.instances[32].tostring(), "YINCVAPLRMTELCLPHLYETGSGRIVNI")
motif = record.motifs[1]
self.assertEqual(motif.num_occurrences, 33)
self.assertAlmostEqual(motif.evalue, 2.3e-159)
self.assertEqual(motif.alphabet, IUPAC.protein)
self.assertEqual(motif.name, "Motif 2")
self.assertEqual(len(motif.instances), 33)
self.assertAlmostEqual(motif.instances[0].pvalue, 2.44e-23)
self.assertAlmostEqual(motif.instances[1].pvalue, 5.50e-23)
self.assertAlmostEqual(motif.instances[2].pvalue, 5.38e-22)
self.assertAlmostEqual(motif.instances[3].pvalue, 5.65e-20)
self.assertAlmostEqual(motif.instances[4].pvalue, 1.17e-19)
self.assertAlmostEqual(motif.instances[5].pvalue, 1.17e-19)
self.assertAlmostEqual(motif.instances[6].pvalue, 4.74e-19)
self.assertAlmostEqual(motif.instances[7].pvalue, 9.31e-19)
self.assertAlmostEqual(motif.instances[8].pvalue, 2.50e-18)
self.assertAlmostEqual(motif.instances[9].pvalue, 3.45e-18)
self.assertAlmostEqual(motif.instances[10].pvalue, 5.86e-18)
self.assertAlmostEqual(motif.instances[11].pvalue, 9.86e-18)
self.assertAlmostEqual(motif.instances[12].pvalue, 2.47e-17)
self.assertAlmostEqual(motif.instances[13].pvalue, 3.01e-17)
self.assertAlmostEqual(motif.instances[14].pvalue, 3.33e-17)
self.assertAlmostEqual(motif.instances[15].pvalue, 4.06e-17)
self.assertAlmostEqual(motif.instances[16].pvalue, 4.06e-17)
self.assertAlmostEqual(motif.instances[17].pvalue, 8.05e-17)
self.assertAlmostEqual(motif.instances[18].pvalue, 1.90e-16)
self.assertAlmostEqual(motif.instances[19].pvalue, 2.77e-16)
self.assertAlmostEqual(motif.instances[20].pvalue, 3.65e-16)
self.assertAlmostEqual(motif.instances[21].pvalue, 8.31e-16)
self.assertAlmostEqual(motif.instances[22].pvalue, 4.05e-15)
self.assertAlmostEqual(motif.instances[23].pvalue, 5.24e-15)
self.assertAlmostEqual(motif.instances[24].pvalue, 3.00e-14)
self.assertAlmostEqual(motif.instances[25].pvalue, 8.47e-14)
self.assertAlmostEqual(motif.instances[26].pvalue, 1.46e-13)
self.assertAlmostEqual(motif.instances[27].pvalue, 1.46e-13)
self.assertAlmostEqual(motif.instances[28].pvalue, 1.59e-12)
self.assertAlmostEqual(motif.instances[29].pvalue, 6.97e-10)
self.assertAlmostEqual(motif.instances[30].pvalue, 3.15e-09)
self.assertAlmostEqual(motif.instances[31].pvalue, 2.77e-07)
self.assertAlmostEqual(motif.instances[32].pvalue, 4.24e-07)
self.assertEqual(motif.instances[0].sequence_name, 'HDE_CANTR')
self.assertEqual(motif.instances[1].sequence_name, 'DHII_HUMAN')
self.assertEqual(motif.instances[2].sequence_name, 'YINL_LISMO')
self.assertEqual(motif.instances[3].sequence_name, 'HDHA_ECOLI')
self.assertEqual(motif.instances[4].sequence_name, 'RIDH_KLEAE')
self.assertEqual(motif.instances[5].sequence_name, 'BUDC_KLETE')
self.assertEqual(motif.instances[6].sequence_name, 'ENTA_ECOLI')
self.assertEqual(motif.instances[7].sequence_name, 'AP27_MOUSE')
self.assertEqual(motif.instances[8].sequence_name, 'DHMA_FLAS1')
self.assertEqual(motif.instances[9].sequence_name, 'YRTP_BACSU')
self.assertEqual(motif.instances[10].sequence_name, 'DHGB_BACME')
self.assertEqual(motif.instances[11].sequence_name, 'DHB3_HUMAN')
self.assertEqual(motif.instances[12].sequence_name, 'PCR_PEA')
self.assertEqual(motif.instances[13].sequence_name, 'BDH_HUMAN')
self.assertEqual(motif.instances[14].sequence_name, 'BA72_EUBSP')
self.assertEqual(motif.instances[15].sequence_name, 'FIXR_BRAJA')
self.assertEqual(motif.instances[16].sequence_name, '3BHD_COMTE')
self.assertEqual(motif.instances[17].sequence_name, '2BHD_STREX')
self.assertEqual(motif.instances[18].sequence_name, 'HMTR_LEIMA')
self.assertEqual(motif.instances[19].sequence_name, 'FVT1_HUMAN')
self.assertEqual(motif.instances[20].sequence_name, 'DHB2_HUMAN')
self.assertEqual(motif.instances[21].sequence_name, 'LIGD_PSEPA')
self.assertEqual(motif.instances[22].sequence_name, 'NODG_RHIME')
self.assertEqual(motif.instances[23].sequence_name, 'DHCA_HUMAN')
self.assertEqual(motif.instances[24].sequence_name, 'MAS1_AGRRA')
self.assertEqual(motif.instances[25].sequence_name, 'BPHB_PSEPS')
self.assertEqual(motif.instances[26].sequence_name, 'GUTD_ECOLI')
self.assertEqual(motif.instances[27].sequence_name, 'DHES_HUMAN')
self.assertEqual(motif.instances[28].sequence_name, 'RFBB_NEIGO')
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, 'YURA_MYXXA')
self.assertEqual(motif.instances[32].sequence_name, 'CSGA_MYXXA')
self.assertEqual(motif.instances[0].start, 323)
self.assertEqual(motif.instances[1].start, 35)
self.assertEqual(motif.instances[2].start, 6)
self.assertEqual(motif.instances[3].start, 12)
self.assertEqual(motif.instances[4].start, 15)
self.assertEqual(motif.instances[5].start, 3)
self.assertEqual(motif.instances[6].start, 6)
self.assertEqual(motif.instances[7].start, 8)
self.assertEqual(motif.instances[8].start, 15)
self.assertEqual(motif.instances[9].start, 7)
self.assertEqual(motif.instances[10].start, 8)
self.assertEqual(motif.instances[11].start, 49)
self.assertEqual(motif.instances[12].start, 87)
self.assertEqual(motif.instances[13].start, 56)
self.assertEqual(motif.instances[14].start, 7)
self.assertEqual(motif.instances[15].start, 37)
self.assertEqual(motif.instances[16].start, 7)
self.assertEqual(motif.instances[17].start, 7)