def test_nopad(self): read = Read(seq=self.read.seq[8:8+13], pos=48) read.cigar = [(0, 13)] trim_short_cigars(self.read, match_len_min=5, trim_pad=0) self.assertEqual(read, self.read)
def test_pad(self): read = Read(seq=self.read.seq[8+2:8+13-2], pos=50) read.cigar = [(0, 9)] trim_short_cigars(self.read, match_len_min=5, trim_pad=2) self.assertEqual(read, self.read)
def setUp(self): read = Read(seq=''.join(chr(i) for i in xrange(65, 91))) read.cigar = [(1, 3), (0, 3), (2, 45), (1, 2), (0, 13), (1, 3)] read.cigar.append( (0, (len(read.seq) - sum(bl for (bt, bl) in read.cigar if bt in (0, 1))))) self.read = read
def setUp(self): readf = Read('GGCCAACCCAAAGGG', pos=0, qname='startsbefore') readf.cigar = [(1, 6), (0, len(readf.seq) - 6)] readr = Read('CCAAAGGGCCCTTT', pos=1, qname='startsbefore', is_reverse=True) self.pair = (readf, readr)
def setUp(self): read = Read(seq=''.join(chr(i) for i in xrange(65, 91))) read.cigar = [(1, 3), (0, 3), (2, 45), (1, 2), (0, 13), (1, 3)] read.cigar.append((0, (len(read.seq) - sum(bl for (bt, bl) in read.cigar if bt in (0, 1))) )) self.read = read
def test_pad(self): read = Read(seq=self.read.seq[8 + 2:8 + 13 - 2], pos=50) read.cigar = [(0, 9)] trim_short_cigars(self.read, match_len_min=5, trim_pad=2) self.assertEqual(read, self.read)
def test_nopad(self): read = Read(seq=self.read.seq[8:8 + 13], pos=48) read.cigar = [(0, 13)] trim_short_cigars(self.read, match_len_min=5, trim_pad=0) self.assertEqual(read, self.read)
def setUp(self): read = Read('AAAGGGTTTCCC', pos=1) read.cigar = [(0, 3), (1, 2), (0, 7)] self.read = read