def test_fetch_decimal(self):
first = True
for col in self.bamfile.pileup(region="IL4:5879-5880"):
count = 0
for r in col.pileups:
if first:
if count == self.foc:
self.read = r
first = False
count = count + 1
self.assertEquals(82, ref2querypos(self.read.alignment, 5959.01))
def test_fetch_decimal(self):
first = True
for col in self.bamfile.pileup(region="IL4:5879-5880"):
count = 0
for r in col.pileups:
if first:
if count == self.foc:
self.read = r
first = False
count = count + 1
self.assertEquals(82, ref2querypos(self.read.alignment, 5959.01))
def test_get_indel_matches_pileupread_pos(self):
first = True
for col in self.bamfile.pileup(region="IL4:5879-5880"):
count = 0
for r in col.pileups:
if first:
if count == self.foc:
self.read = r
first = False
count = count + 1
if self.read is not None and self.read.alignment.query_name == r.alignment.query_name:
if not r.is_del:
self.assertEquals(r.query_position, ref2querypos(r.alignment, col.reference_pos))
def test_get_indel_matches_pileupread_pos(self):
first = True
for col in self.bamfile.pileup(region="IL4:5879-5880"):
count = 0
for r in col.pileups:
if first:
if count == self.foc:
self.read = r
first = False
count = count + 1
if self.read is not None and self.read.alignment.query_name == r.alignment.query_name:
if not r.is_del:
self.assertEquals(
r.query_position,
ref2querypos(r.alignment, col.reference_pos))
# THIS IS GOOD CODE
read = None
foc = 0
seq = ""
first = True
for pileup_column in samfile.pileup(region="IL4:5879-5880"):
count = 0
for r in pileup_column.pileups:
if first:
if count == foc:
read = r
first = False
count = count + 1
if read is not None and read.alignment.query_name == r.alignment.query_name:
if not r.is_del:
print str(r.query_position) + " " + str(ref2querypos(r.alignment, pileup_column.reference_pos)) + " " + str(pileup_column.reference_pos)
print read.alignment.cigarstring
print read.alignment.query_sequence
"""
read_dict['RB40W:00428:02640'] = []
ref_spacer = []
for each column:
max_indel = 0
for each read:
find max indel
ref_spacer.append((ref_pos, max_indel))
# Now generate printing view (numeric header)