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):
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):
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):
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
def setUp(self):
self.read = Read('AAAGGGTTTCCC', pos=1)