def read_gtf(lines, scaffolds, contig_prefix):
table = {} # gene_id -> transcript_id -> exon_number -> feature -> [items]
for gtf in text.parse_lines(lines, pysam.asGTF()):
if not filter_gtf_record(gtf):
update_gtf_table(table, gtf, scaffolds, contig_prefix)
return table
def read_bed_file(filename):
"""Parses a (gzip/bzip2 compressed) BED file, and yields
a sequence of records. Comments and empty lines are skipped."""
handle = None
try:
handle = fileutils.open_ro(filename)
for record in text.parse_lines(handle, BEDRecord):
yield record
finally:
if handle:
handle.close()
def read_bed_file(filename):
"""Parses a (gzip/bzip2 compressed) BED file, and yields
a sequence of records. Comments and empty lines are skipped."""
handle = None
try:
handle = fileutils.open_ro(filename)
for record in text.parse_lines(handle, BEDRecord):
yield record
finally:
if handle:
handle.close()
def read_bed_file(filename):
"""Parses a (gzip/bzip2 compressed) BED file, and yields
a sequence of records. Comments and empty lines are skipped."""
handle = None
try:
handle = fileutils.open_ro(filename)
parser = pysam.asBed()
for record in text.parse_lines(handle, parser):
# Force evaluation of (lazily parsed) properties
_ = record.start
_ = record.end
yield record
finally:
if handle:
handle.close()
def read_bed_file(filename):
"""Parses a (gzip/bzip2 compressed) BED file, and yields
a sequence of records. Comments and empty lines are skipped."""
handle = None
try:
handle = fileutils.open_ro(filename)
parser = pysam.asBed()
for record in text.parse_lines(handle, parser):
# Force evaluation of (lazily parsed) properties
_ = record.start
_ = record.end
yield record
finally:
if handle:
handle.close()
def _parse_lines(*args, **kwargs):
return list(parse_lines(*args, **kwargs))
def _parse_lines(*args, **kwargs):
return list(parse_lines(*args, **kwargs))
