def listFromCIGAR(cls, cigarstring,position_b0, refname, strand):
read_parts = []
if strand == MINUS: # need to reverse the CIGAR
logger.debug("Reversing CIGAR for minus strand read fragment")
cigarstring = "".join(reversed(re.findall("\d+[MIDNSHP=X]", cigarstring)))
op_type_list = []
for op in HTSeq.parse_cigar(cigarstring, position_b0, refname, strand):
logger.debug(map(str,(op, op.query_from, op.query_to, op.ref_iv)))
if op.type == "M":
if "M" in op_type_list:
if len(op_type_list) >=2 and op_type_list[-1] == "D" and op_type_list[-2] == "M":
logger.debug(map(str,("extending (D):", op, op.query_from, op.query_to, op.ref_iv)))
read_parts[-1].extend(op.query_from, op.query_to,op.ref_iv.start,op.ref_iv.end,op.ref_iv.chrom,strand)
elif len(op_type_list) >=2 and op_type_list[-1] == "I" and op_type_list[-2] == "M":
logger.debug(map(str,("extending (I):", op, op.query_from, op.query_to, op.ref_iv)))
read_parts[-1].extend(op.query_from, op.query_to,op.ref_iv.start,op.ref_iv.end,op.ref_iv.chrom,strand)
else:
logger.debug("CIGAR WARNING: Number of matches > 1: {0}".format(cigarstring))
else:
logger.debug(map(str,("appending:", op, op.query_from, op.query_to, op.ref_iv)))
suppl_frag = cls(op.query_from, op.query_to,op.ref_iv.start,op.ref_iv.end,op.ref_iv.chrom,strand)
read_parts.append(suppl_frag)
op_type_list.append(op.type)
return read_parts
def fromCigar(cls,
cigar,
drop=None,
dropEmpty=None,
start=None,
chrom=None,
strand=None):
if drop is None:
drop = 'DNS'
assert isinstance(cigar, basestring), cigar
args = [cigar]
if start is not None:
args += [start]
if chrom is not None:
args += [chrom]
if strand is not None:
args += [strand]
cos = HTSeq.parse_cigar(*args)
cos = [co for co in cos if co.type not in drop]
# if dropEmpty is None:
# dropEmpty = True
# if dropEmpty:
# cos = [co for co in cos if co.size ]
ivdq = GenomicIntervalDeque([co.ref_iv for co in cos],
cigarstring=cigar)
# if start is not None:
# for iv in ivdq:
# iv.start+= start
# iv.end += start
return ivdq
def listFromCIGAR(cls, cigarstring, position_b0, refname, strand):
read_parts = []
if strand == MINUS: # need to reverse the CIGAR
logger.debug("Reversing CIGAR for minus strand read fragment")
cigarstring = "".join(
reversed(re.findall("\d+[MIDNSHP=X]", cigarstring)))
op_type_list = []
for op in HTSeq.parse_cigar(cigarstring, position_b0, refname, strand):
logger.debug(map(str, (op, op.query_from, op.query_to, op.ref_iv)))
if op.type == "M":
if "M" in op_type_list:
if len(op_type_list) >= 2 and op_type_list[
-1] == "D" and op_type_list[-2] == "M":
logger.debug(
map(str, ("extending (D):", op, op.query_from,
op.query_to, op.ref_iv)))
read_parts[-1].extend(op.query_from, op.query_to,
op.ref_iv.start, op.ref_iv.end,
op.ref_iv.chrom, strand)
elif len(op_type_list) >= 2 and op_type_list[
-1] == "I" and op_type_list[-2] == "M":
logger.debug(
map(str, ("extending (I):", op, op.query_from,
op.query_to, op.ref_iv)))
read_parts[-1].extend(op.query_from, op.query_to,
op.ref_iv.start, op.ref_iv.end,
op.ref_iv.chrom, strand)
else:
logger.debug(
"CIGAR WARNING: Number of matches > 1: {0}".format(
cigarstring))
else:
logger.debug(
map(str, ("appending:", op, op.query_from, op.query_to,
op.ref_iv)))
suppl_frag = cls(op.query_from, op.query_to,
op.ref_iv.start, op.ref_iv.end,
op.ref_iv.chrom, strand)
read_parts.append(suppl_frag)
op_type_list.append(op.type)
return read_parts
def annotate_pairs(pairs_path, ant, ant_mode, ant_col, strand_type, min_over,
cigar_col, output, **kwargs):
instream = (_fileio.auto_open(pairs_path,
mode='r',
nproc=kwargs.get('nproc_in'),
command=kwargs.get('cmd_in', None))
if pairs_path else sys.stdin)
outstream = (_fileio.auto_open(output,
mode='w',
nproc=kwargs.get('nproc_out'),
command=kwargs.get('cmd_out', None))
if output else sys.stdout)
header, body_stream = _headerops.get_header(instream)
header = _headerops.append_new_pg(header, ID=UTIL_NAME, PN=UTIL_NAME)
if len(header) == 0:
sys.stderr.write('.pairs file doesn\'t have header rows!\n')
raise SystemExit(1)
col_names = header[-1].split(' ')
if col_names[0] != '#columns:':
sys.stderr.write(
'The last row of .pairs header is not a valid col_names row (start with \'#columns:\')!\n'
)
raise SystemExit(1)
col_names.pop(0)
ant_col = ant_col.split(',')
for i in ant_col:
if i in col_names:
sys.stderr.write(
'Annotation col names already exist in .pairs file!\n')
raise SystemExit(1)
for i in strand_type:
if i not in ['s', 'r', 'n']:
sys.stderr.write('Invalid strand specific type for annotation!\n')
raise SystemExit(1)
if ant_mode.lower() == 'both':
header[-1] = header[-1] + ' ' + ' '.join(ant_col)
else:
header[-1] = header[-1] + ' ' + ant_col[0]
min_over = [int(i) for i in min_over.split(',')]
cigar_col = cigar_col.split(',')
cigar_idx = []
for i in cigar_col:
if i not in col_names and i.lower() != 'false':
sys.stderr.write(
'Cigar col names doesn\'t exist in .pairs file!\n')
raise SystemExit(1)
else:
cigar_idx += [col_names.index(i)]
outstream.writelines(l + '\n' for l in header)
count_line = 1
for line in body_stream:
if count_line % 1000000 == 0:
print("%d records processed ..." % count_line)
count_line += 1
cols = line.rstrip().split(_pairsam_format.PAIRSAM_SEP)
if ant_mode.lower() == 'rna':
chrom1, pos1, strand1, cigar1 = cols[_pairsam_format.COL_C1], int(cols[_pairsam_format.COL_P1]), \
cols[_pairsam_format.COL_S1], cols[cigar_idx[0]]
if cigar_idx[0] == 'false':
match_length1 = 1
else:
if cigar1 == '*':
cigar1 = '1M'
match_length1 = sum(
[i.ref_iv.length for i in HTSeq.parse_cigar(cigar1)])
ant_str = annotate_region(ant, chrom1, pos1, strand1,
match_length1, min_over[0],
strand_type[0])
elif ant_mode.lower() == 'dna':
chrom2, pos2, strand2, cigar2 = cols[_pairsam_format.COL_C2], int(cols[_pairsam_format.COL_P2]), \
cols[_pairsam_format.COL_S2], cols[cigar_idx[0]]
if cigar_idx[0] == 'false':
match_length2 = 1
else:
if cigar2 == '*':
cigar2 = '1M'
match_length2 = sum(
[i.ref_iv.length for i in HTSeq.parse_cigar(cigar2)])
ant_str = annotate_region(ant, chrom2, pos2, strand2,
match_length2, min_over[0],
strand_type[0])
else:
chrom1, pos1, strand1, cigar1 = cols[_pairsam_format.COL_C1], int(cols[_pairsam_format.COL_P1]), \
cols[_pairsam_format.COL_S1], cols[cigar_idx[0]]
if cigar_idx[0] == 'false':
match_length1 = 1
else:
if cigar1 == '*':
cigar1 = '1M'
match_length1 = sum(
[i.ref_iv.length for i in HTSeq.parse_cigar(cigar1)])
ant_str = annotate_region(ant, chrom1, pos1, strand1,
match_length1, min_over[0],
strand_type[0])
chrom2, pos2, strand2, cigar2 = cols[_pairsam_format.COL_C2], int(cols[_pairsam_format.COL_P2]), \
cols[_pairsam_format.COL_S2], cols[cigar_idx[1]]
if cigar_idx[1] == 'false':
match_length2 = 1
else:
if cigar2 == '*':
cigar2 = '1M'
match_length2 = sum(
[i.ref_iv.length for i in HTSeq.parse_cigar(cigar2)])
ant_str += _pairsam_format.PAIRSAM_SEP + \
annotate_region(ant, chrom2, pos2, strand2, match_length2, min_over[1], strand_type[1])
outstream.write(
_pairsam_format.PAIRSAM_SEP.join([line.rstrip(), ant_str]))
outstream.write('\n')
if instream != sys.stdin:
instream.close()
if outstream != sys.stdout:
outstream.close()
