def testOverlap(self): t0 = classes.trfHit(['seq1','12','224','55','2.1','55','91','0','300','33','19','15','30','1.93','CTCTAAAAACCTTGATTCATTGTTTAACGAGCTTGACACAAGACAAGGAACTATG','CTCTAAAAACCTTGATTCATTGTTTAACGAGCTTGACACAAGACAAGGAACTATGCTCTAAAATCCTTGATTCATTTTTTAATGAGCTTGACACAAGGTAAGGAACTATGCTC']) t1 = classes.trfHit(['seq1','225','337','55','2.1','55','91','0','181','33','19','15','30','1.93','CTCTAAAAACCTTGATTCATTGTTTAACGAGCTTGACACAAGACAAGGAACTATG','CTCTAAAAACCTTGATTCATTGTTTAACGAGCTTGACACAAGACAAGGAACTATGCTCTAAAATCCTTGATTCATTTTTTAATGAGCTTGACACAAGGTAAGGAACTATGCTC']) t2 = classes.trfHit(['seq1','230','330','55','2.1','55','91','0','180','33','19','15','30','1.93','CTCTAAAAACCTTGATTCATTGTTTAACGAGCTTGACACAAGACAAGGAACTATG','CTCTAAAAACCTTGATTCATTGTTTAACGAGCTTGACACAAGACAAGGAACTATGCTCTAAAATCCTTGATTCATTTTTTAATGAGCTTGACACAAGGTAAGGAACTATGCTC']) t3 = classes.trfHit(['seq2','225','337','55','2.1','55','91','0','181','33','19','15','30','1.93','CTCTAAAAACCTTGATTCATTGTTTAACGAGCTTGACACAAGACAAGGAACTATG','CTCTAAAAACCTTGATTCATTGTTTAACGAGCTTGACACAAGACAAGGAACTATGCTCTAAAATCCTTGATTCATTTTTTAATGAGCTTGACACAAGGTAAGGAACTATGCTC']) self.assertFalse(trfStats.overlap(t0,t1)) self.assertTrue(trfStats.overlap(t1,t2)) self.assertFalse(trfStats.overlap(t0,t3))
def parseDat(args):
trfDict = defaultdict(list)
seq_name = ''
for line in open(args.trf_output).read().split('\n'):
if line.startswith('Seq'):
seq_name = line[len('Sequence: '):]
if line != '' and line.split()[0].isdigit():
fields = line.split()
fields.insert(0,seq_name)
newTandem = trfHit(fields)
if args.filter_monomers:
filterTRFDict(newTandem,trfDict,"monomers")
elif args.filter_multimers:
filterTRFDict(newTandem,trfDict,"multimers")
else:
trfDict[seq_name].append(newTandem)
return trfDict
def parseNGS(args):
trfDict = defaultdict(list)
seq_name = ''
count = 0
for line in open(args.trf_output).read().split('\n'):
if line.startswith('@'):
seq_name = line[1:]
elif line != '':
fields = line.split()
fields.insert(0,seq_name)
newTandem = trfHit(fields)
if args.filter_monomers:
filterTRFDict(newTandem,trfDict,"monomers")
elif args.filter_multimers:
filterTRFDict(newTandem,trfDict,"multimers")
else:
trfDict[seq_name].append(newTandem)
return trfDict