def split_aligment(x, split_length=CIGAR_OPS_LIMIT):
read_len = x.query_length
ref = x.get_reference_sequence()
cigar = butil.decompress_cigar_pairs(x.cigar)
if read_len < split_length:
return [x]
ret = []
prev_query_end = 0
ref_len = 0
for id, i in enumerate(range(0, len(cigar), split_length)):
prefix_cigar = cigar[i:i + split_length]
prefix_len = butil.get_read_len_from_cigar(prefix_cigar)
prefix = deepcopy(x)
prefix.reference_start += ref_len
prefix.cigar = butil.compress_cigar(prefix_cigar, 'ints')
prefix.set_tag('MD', butil.generate_md_tag(ref[ref_len:],
prefix.cigar))
prefix.query_sequence = x.query_sequence[
prev_query_end:prev_query_end + prefix_len]
prev_query_end += prefix_len
ref_len += butil.get_ref_len_from_cigar(prefix_cigar)
ret.append(prefix)
return ret
def extend_cigar(read_seq, ref_seq, cigar_pairs, mode='ints'):
cigar_str = butil.decompress_cigar_pairs(cigar_pairs, mode)
ref_seq = butil.reference_align_string(ref_seq, cigar_pairs)
read_seq = butil.query_align_string(read_seq, cigar_pairs)
assert len(ref_seq) == len(cigar_str) and len(read_seq) == len(cigar_str)
def _resolve_m(i, op):
if op.upper() == 'M':
return '=' if ref_seq[i].upper() == read_seq[i].upper() else 'X'
return op.upper()
cigar_str = ''.join(_resolve_m(*p) for p in enumerate(cigar_str))
pairs = butil.compress_cigar(cigar_str)
cigar = butil.cigar_pairs_to_str(pairs, 'chars')
return cigar
def get_target_sequences(sam_path):
result_dict = {}
cnt = defaultdict(int)
with pysam.AlignmentFile(sam_path, "r") as samfile:
for x in tqdm(samfile.fetch(), desc='Building ref'):
name = x.query_name
cnt['total'] += 1
if x.is_unmapped:
cnt['unmapped'] += 1
#logging.warning("%s unmapped" % name)
continue
try:
# hack to bypass segfault
full_cigar = butil.decompress_cigar_pairs(x.cigartuples)
r_len = butil.get_read_len_from_cigar(full_cigar)
ref_len = butil.get_ref_len_from_cigar(full_cigar)
if r_len != x.query_length or ref_len != x.reference_length:
logging.error(
"%s cigar operations do not match alignment info in md",
name)
cnt['invalid_md_cigar'] += 1
continue
target = x.get_reference_sequence()
except (ValueError, AssertionError) as e:
cnt['missign_ref'] += 1
logging.error(
"%s Mapped but reference len equals 0, md tag: %s", name,
x.has_tag('MD'))
continue
ref_name = x.reference_name
length = x.reference_length
start_pos = x.reference_start
cigar_pairs = x.cigartuples
if x.is_reverse:
target = butil.reverse_complement(target)
cigar_pairs = list(reversed(cigar_pairs))
cigar_str = butil.decompress_cigar_pairs(cigar_pairs, mode='ints')
if name in result_dict:
prev_target, _, prev_start_pos, _, prev_cigar_str = result_dict[
name]
merged = _merge_circular_aligment(prev_target, prev_start_pos,
prev_cigar_str, target,
start_pos, cigar_str,
x.is_reverse, x.query_name)
if not merged:
continue
target, start_pos, cigar_str = merged
length = len(target)
result_dict[name] = [
target, ref_name, start_pos, length, cigar_str
]
logging.warning("Results: %s", str(cnt.items()))
return result_dict