def _write_combined_features(in_handle, out_handle):
"""Prepare BED file with intersecting feature identifiers combined.
"""
def _write_combined(pos, ids):
if len(ids) == 0:
ids.append(".")
else:
ids = sorted(list(set(ids)))
out_handle.write("{0}\t{1}\n".format("\t".join(pos), ";".join(ids)))
last = None
ids = []
for parts in (l.split("\t") for l in in_handle):
cur_id = parts[:3]
cur_attr = parts[-2]
if cur_id != last:
if last is not None:
_write_combined(last, ids)
last = cur_id
ids = []
if cur_attr != ".":
attrs = parse_attributes(cur_attr)
ids.append(attrs.get("ensembl_gene_id", attrs["ID"]))
if last:
_write_combined(last, ids)
def _write_combined_features(in_handle, out_handle):
"""Prepare BED file with intersecting feature identifiers combined.
"""
def _write_combined(pos, ids):
if len(ids) == 0:
ids.append(".")
else:
ids = sorted(list(set(ids)))
out_handle.write("{0}\t{1}\n".format("\t".join(pos), ";".join(ids)))
last = None
ids = []
for parts in (l.split("\t") for l in in_handle):
cur_id = parts[:3]
cur_attr = parts[-2]
if cur_id != last:
if last is not None:
_write_combined(last, ids)
last = cur_id
ids = []
if cur_attr != ".":
attrs = parse_attributes(cur_attr)
ids.append(attrs.get("ensembl_gene_id", attrs["ID"]))
if last:
_write_combined(last, ids)
def get_gff_name(field):
attrs = parse_attributes(field)
for key in ("ID", "gene_name", "transcript_id", "gene_id", "Parent"):
if key in attrs: return attrs[key]
def get_gff_name(field):
attrs = parse_attributes(field)
for key in ("ID", "gene_name", "transcript_id", "gene_id", "Parent"):
if key in attrs:
return attrs[key]
