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)