def setUp(self):
readf = Read('AAAGGGCCCTTT', pos=3,
qname='matchonly')
readr = Read('AGGGCCCTTTCCC', pos=5,
qname='matchonly',
is_reverse=True)
fix_pair((readf, readr))
self.pair = (readr, readf)
def setUp(self):
readf = Read('AAAGGGCCCTTT', pos=3, qname='matchonly')
readr = Read('AGGGCCCTTTCCC',
pos=5,
qname='matchonly',
is_reverse=True)
fix_pair((readf, readr))
self.pair = (readr, readf)
def test(self):
'''Test match only pairs'''
pair = deepcopy(self.pair)
pair[0].seq = pair[0].seq[7:]
pair[0].qual = pair[0].qual[7:]
pair[0].pos = 1
pair[0].cigar = [(0, len(pair[0].seq))]
pair[1].mpos = 1
fix_pair(pair)
# Call the function
pair_type = filter_read_pair(self.pair, self.ref,
trim_bad_cigars=1,
match_len_min=3)
self.assertEqual(pair_type, 'good')
self.assertEqual(self.pair, pair)
def test(self):
'''Test match only pairs'''
pair = deepcopy(self.pair)
pair[0].seq = pair[0].seq[7:]
pair[0].qual = pair[0].qual[7:]
pair[0].pos = 1
pair[0].cigar = [(0, len(pair[0].seq))]
pair[1].mpos = 1
fix_pair(pair)
# Call the function
pair_type = filter_read_pair(self.pair,
self.ref,
trim_bad_cigars=1,
match_len_min=3)
self.assertEqual(pair_type, 'good')
self.assertEqual(self.pair, pair)
