def _setup_variant_regions(data, out_dir):
"""Ensure we have variant regions for calling, using transcript if not present.
Respects noalt_calling by removing additional contigs to improve
speeds.
"""
vr_file = dd.get_variant_regions(data)
if not vr_file:
vr_file = regions.get_sv_bed(data, "transcripts", out_dir=out_dir)
contigs = set([c.name for c in ref.file_contigs(dd.get_ref_file(data))])
out_file = os.path.join(utils.safe_makedir(os.path.join(dd.get_work_dir(data), "bedprep")),
"%s-rnaseq_clean.bed" % utils.splitext_plus(os.path.basename(vr_file))[0])
if not utils.file_uptodate(out_file, vr_file):
with file_transaction(data, out_file) as tx_out_file:
with open(tx_out_file, "w") as out_handle:
with shared.bedtools_tmpdir(data):
for r in pybedtools.BedTool(vr_file):
if r.chrom in contigs:
if chromhacks.is_nonalt(r.chrom):
out_handle.write(str(r))
data = dd.set_variant_regions(data, out_file)
return data
def _setup_variant_regions(data, out_dir):
"""Ensure we have variant regions for calling, using transcript if not present.
Respects noalt_calling by removing additional contigs to improve
speeds.
"""
vr_file = dd.get_variant_regions(data)
if not vr_file:
vr_file = regions.get_sv_bed(data, "transcripts", out_dir=out_dir)
contigs = set([c.name for c in ref.file_contigs(dd.get_ref_file(data))])
out_file = os.path.join(utils.safe_makedir(os.path.join(dd.get_work_dir(data), "bedprep")),
"%s-rnaseq_clean.bed" % utils.splitext_plus(os.path.basename(vr_file))[0])
if not utils.file_uptodate(out_file, vr_file):
with file_transaction(data, out_file) as tx_out_file:
with open(tx_out_file, "w") as out_handle:
with shared.bedtools_tmpdir(data):
for r in pybedtools.BedTool(vr_file):
if r.chrom in contigs:
if chromhacks.is_nonalt(r.chrom):
out_handle.write(str(r))
data = dd.set_variant_regions(data, out_file)
return data