def coordinate_map(an_alignment_row):
global args
range_accumulator = []
cigar = an_alignment_row.CIGAR
start_pos = an_alignment_row.POS + args.systematic_offset
label = an_alignment_row.QNAME
read_start_range = (0, 0)
ref_start_range = (start_pos, start_pos)
read_last_range = read_start_range
ref_last_range = ref_start_range
try:
parse_results = parse_cigar_string(cigar)
except ParseException:
logger.critical("Parse error for cigar string %s", cigar)
return []
for length, type in parse_results:
if type == "M":
read_current_range = (read_last_range[1], read_last_range[1] + length)
ref_current_range = (ref_last_range[1], ref_last_range[1] + length)
elif type == "I":
read_current_range = (read_last_range[1], read_last_range[1] + length)
ref_current_range = (ref_last_range[1], ref_last_range[1])
elif type == "D":
read_current_range = (read_last_range[1], read_last_range[1])
ref_current_range = (ref_last_range[1], ref_last_range[1] + length)
elif type == "S":
read_current_range = (read_last_range[1], read_last_range[1] + length)
ref_current_range = (ref_last_range[1], ref_last_range[1])
range_accumulator.append(
{"label": label, "type": type, "length": length, "ref_coord": ref_current_range, "read_coord": read_current_range})
read_last_range = read_current_range
ref_last_range = ref_current_range
return range_accumulator
def coordinate_map(an_alignment_row):
global args
range_accumulator = []
cigar = an_alignment_row.CIGAR
start_pos = an_alignment_row.POS + args.systematic_offset
label = an_alignment_row.QNAME
read_start_range = (0, 0)
ref_start_range = (start_pos, start_pos)
read_last_range = read_start_range
ref_last_range = ref_start_range
try:
parse_results = parse_cigar_string(cigar)
except ParseException:
logger.critical("Parse error for cigar string %s", cigar)
return []
for length, type in parse_results:
if type == "M":
read_current_range = (read_last_range[1],
read_last_range[1] + length)
ref_current_range = (ref_last_range[1], ref_last_range[1] + length)
elif type == "I":
read_current_range = (read_last_range[1],
read_last_range[1] + length)
ref_current_range = (ref_last_range[1], ref_last_range[1])
elif type == "D":
read_current_range = (read_last_range[1], read_last_range[1])
ref_current_range = (ref_last_range[1], ref_last_range[1] + length)
elif type == "S":
read_current_range = (read_last_range[1],
read_last_range[1] + length)
ref_current_range = (ref_last_range[1], ref_last_range[1])
range_accumulator.append({
"label": label,
"type": type,
"length": length,
"ref_coord": ref_current_range,
"read_coord": read_current_range
})
read_last_range = read_current_range
ref_last_range = ref_current_range
return range_accumulator
def test_parse_cigar_string(self): starting_file = data_dir + "/alignments/C_model_GMAPno40_NM_000546.5.sam" reads = parse_sam_file(starting_file) for i,r in enumerate(reads.CIGAR): print i,parse_cigar_string(r)
def test_parse_cigar_string(self):
starting_file = data_dir + "/alignments/C_model_GMAPno40_NM_000546.5.sam"
reads = parse_sam_file(starting_file)
for i, r in enumerate(reads.CIGAR):
print i, parse_cigar_string(r)
