def prepare_exclude_file(items, base_file, chrom=None):
"""Prepare a BED file for exclusion, incorporating variant regions and chromosome.
Excludes locally repetitive regions (if `remove_lcr` is set) and
centromere regions, both of which contribute to long run times and
false positive structural variant calls.
"""
out_file = "%s-exclude%s.bed" % (utils.splitext_plus(base_file)[0], "-%s" % chrom if chrom else "")
if not utils.file_exists(out_file) and not utils.file_exists(out_file + ".gz"):
with shared.bedtools_tmpdir(items[0]):
# Get a bedtool for the full region if no variant regions
want_bedtool = callable.get_ref_bedtool(tz.get_in(["reference", "fasta", "base"], items[0]),
items[0]["config"], chrom)
if chrom:
want_bedtool = pybedtools.BedTool(shared.subset_bed_by_chrom(want_bedtool.saveas().fn,
chrom, items[0]))
lcr_bed = shared.get_lcr_bed(items)
if lcr_bed:
want_bedtool = want_bedtool.subtract(pybedtools.BedTool(lcr_bed))
sv_exclude_bed = _get_sv_exclude_file(items)
if sv_exclude_bed and len(want_bedtool) > 0:
want_bedtool = want_bedtool.subtract(sv_exclude_bed).saveas()
want_bedtool = pybedtools.BedTool(shared.remove_highdepth_regions(want_bedtool.saveas().fn, items))
with file_transaction(items[0], out_file) as tx_out_file:
full_bedtool = callable.get_ref_bedtool(tz.get_in(["reference", "fasta", "base"], items[0]),
items[0]["config"])
if len(want_bedtool) > 0:
full_bedtool.subtract(want_bedtool).saveas(tx_out_file)
else:
full_bedtool.saveas(tx_out_file)
return out_file
def prepare_exclude_file(items, base_file, chrom=None):
"""Prepare a BED file for exclusion.
Excludes high depth and centromere regions which contribute to long run times and
false positive structural variant calls.
"""
out_file = "%s-exclude%s.bed" % (utils.splitext_plus(base_file)[0], "-%s" % chrom if chrom else "")
if not utils.file_exists(out_file) and not utils.file_exists(out_file + ".gz"):
with shared.bedtools_tmpdir(items[0]):
# Get a bedtool for the full region if no variant regions
want_bedtool = callable.get_ref_bedtool(tz.get_in(["reference", "fasta", "base"], items[0]),
items[0]["config"], chrom)
if chrom:
want_bedtool = pybedtools.BedTool(shared.subset_bed_by_chrom(want_bedtool.saveas().fn,
chrom, items[0]))
sv_exclude_bed = _get_sv_exclude_file(items)
if sv_exclude_bed and len(want_bedtool) > 0:
want_bedtool = want_bedtool.subtract(sv_exclude_bed, nonamecheck=True).saveas()
if any(dd.get_coverage_interval(d) == "genome" for d in items):
want_bedtool = pybedtools.BedTool(shared.remove_highdepth_regions(want_bedtool.saveas().fn, items))
with file_transaction(items[0], out_file) as tx_out_file:
full_bedtool = callable.get_ref_bedtool(tz.get_in(["reference", "fasta", "base"], items[0]),
items[0]["config"])
if len(want_bedtool) > 0:
full_bedtool.subtract(want_bedtool, nonamecheck=True).saveas(tx_out_file)
else:
full_bedtool.saveas(tx_out_file)
return out_file
def prepare_exclude_file(items, base_file, chrom=None):
"""Prepare a BED file for exclusion, incorporating variant regions and chromosome.
Excludes locally repetitive regions (if `remove_lcr` is set) and
centromere regions, both of which contribute to long run times and
false positive structural variant calls.
"""
out_file = "%s-exclude%s.bed" % (utils.splitext_plus(base_file)[0],
"-%s" % chrom if chrom else "")
if not utils.file_exists(out_file) and not utils.file_exists(out_file +
".gz"):
with shared.bedtools_tmpdir(items[0]):
# Get a bedtool for the full region if no variant regions
want_bedtool = callable.get_ref_bedtool(
tz.get_in(["reference", "fasta", "base"], items[0]),
items[0]["config"], chrom)
if chrom:
want_bedtool = pybedtools.BedTool(
shared.subset_bed_by_chrom(want_bedtool.saveas().fn, chrom,
items[0]))
lcr_bed = shared.get_lcr_bed(items)
if lcr_bed:
want_bedtool = want_bedtool.subtract(
pybedtools.BedTool(lcr_bed))
sv_exclude_bed = _get_sv_exclude_file(items)
if sv_exclude_bed and len(want_bedtool) > 0:
want_bedtool = want_bedtool.subtract(sv_exclude_bed).saveas()
want_bedtool = pybedtools.BedTool(
shared.remove_highdepth_regions(want_bedtool.saveas().fn,
items))
with file_transaction(items[0], out_file) as tx_out_file:
full_bedtool = callable.get_ref_bedtool(
tz.get_in(["reference", "fasta", "base"], items[0]),
items[0]["config"])
if len(want_bedtool) > 0:
full_bedtool.subtract(want_bedtool).saveas(tx_out_file)
else:
full_bedtool.saveas(tx_out_file)
return out_file
