def _parse_tx_infos(self, gtf_path):
"""Parse transcript infos from GTF file or load from cache
In case of successful loading from GTF, result will be cached.
"""
if os.path.exists('_tx_cache.bin'):
with open('_tx_cache.bin', 'rb') as f:
return pickle.load(f)
result = []
with gzip.open(gtf_path, 'rt') as f:
for i, line in enumerate(f):
if i % 1000 == 0:
print('processed {}'.format(i), file=sys.stderr)
if line.startswith('#'):
continue
if line.split('\t', 3)[2] != 'transcript':
continue
record = GTFFeature.parse(line)
if record.feature != 'transcript':
continue
result.append(
TranscriptInfo(record.attrs['gene_id'],
record.attrs['transcript_id'],
record.attrs['transcript_type'],
record.seqname,
record.start,
record.end))
with open('_tx_cache.bin', 'wb') as g:
pickle.dump(result, g)
print(len(result), file=sys.stderr)
return result
def handle_match(self, linc_tx, match, nm):
"""Handle one match of a lincRNA against the genome
For each match, look at all overlapping exons and consider them
as candidate lincRNA-to-coding gene interactions.
"""
# look for exons overlapping with the lincRNA match
match_strand = ('-' if match.flag & 16 else '+')
region = Region(self.sam_file.getrname(match.reference_id),
match.pos, match.reference_end)
#print('Querying for exons...', file=sys.stderr)
try:
first = True
for arr in self.tabix.query(*region.to_tuple()):
exon = GTFFeature.parse(arr=arr)
if exon.feature != 'exon':
continue # we look for overlapping transcripts
if exon.attrs['transcript_type'] != 'protein_coding':
continue # we are only interested in these
if match_strand == exon.strand:
continue # must be on different strands
overlap_type = self.classify_overlap(
[region.start, region.end],
[exon.start, exon.end])
if first:
# print('MATCH', match, file=sys.stderr)
first = False
# print('TARGET', exon, file=sys.stderr)
window_5 = exon.get_5_prime_window(region)
window_3 = exon.get_3_prime_window(region)
classes = self.compute_classes(exon, window_5, window_3)
def ali_length(cigar):
OP = 'MIDNSHP=X'
return sum(num for op, num in cigar if OP[op] in 'MI=X')
# generate and write out OutputRecord
out = OutputRecord(
region, exon, linc_tx, len(match.query_sequence),
ali_length(match.cigar), int(nm),
window_5, window_3, classes)
print(out.to_tsv(), file=self.args.output_tsv)
except tabix.TabixError as e:
pass # swallow, probably some unplaced region
