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)