def sample_callable_bed(bam_file, ref_file, data):
"""Retrieve callable regions for a sample subset by defined analysis regions.
"""
CovInfo = collections.namedtuple(
"CovInfo", "callable, highdepth, avg_coverage, coverage")
config = data["config"]
out_file = "%s-callable_sample.bed" % os.path.splitext(bam_file)[0]
with shared.bedtools_tmpdir({"config": config}):
coverage_file, callable_bed, highdepth_bed, variant_regions_avg_cov = coverage.calculate(
bam_file, data)
input_regions_bed = config["algorithm"].get("variant_regions", None)
if not utils.file_uptodate(out_file, callable_bed):
with file_transaction(config, out_file) as tx_out_file:
callable_regions = pybedtools.BedTool(callable_bed)
filter_regions = callable_regions.filter(
lambda x: x.name == "CALLABLE")
if input_regions_bed:
if not utils.file_uptodate(out_file, input_regions_bed):
input_regions = pybedtools.BedTool(input_regions_bed)
filter_regions.intersect(
input_regions,
nonamecheck=True).saveas(tx_out_file)
else:
filter_regions.saveas(tx_out_file)
return CovInfo(out_file, highdepth_bed, variant_regions_avg_cov,
coverage_file)
def sample_callable_bed(bam_file, ref_file, data):
"""Retrieve callable regions for a sample subset by defined analysis regions.
"""
from bcbio.heterogeneity import chromhacks
CovInfo = collections.namedtuple("CovInfo",
"callable, raw_callable, depth_files")
noalt_calling = "noalt_calling" in dd.get_tools_on(
data) or "altcontigs" in dd.get_exclude_regions(data)
def callable_chrom_filter(r):
"""Filter to callable region, potentially limiting by chromosomes.
"""
return r.name == "CALLABLE" and (not noalt_calling
or chromhacks.is_nonalt(r.chrom))
out_file = "%s-callable_sample.bed" % os.path.splitext(bam_file)[0]
with shared.bedtools_tmpdir(data):
sv_bed = regions.get_sv_bed(data)
callable_bed, depth_files = coverage.calculate(bam_file, data, sv_bed)
input_regions_bed = dd.get_variant_regions(data)
if not utils.file_uptodate(out_file, callable_bed):
with file_transaction(data, out_file) as tx_out_file:
callable_regions = pybedtools.BedTool(callable_bed)
filter_regions = callable_regions.filter(callable_chrom_filter)
if input_regions_bed:
if not utils.file_uptodate(out_file, input_regions_bed):
input_regions = pybedtools.BedTool(input_regions_bed)
filter_regions.intersect(
input_regions,
nonamecheck=True).saveas(tx_out_file)
else:
filter_regions.saveas(tx_out_file)
return CovInfo(out_file, callable_bed, depth_files)
def sample_callable_bed(bam_file, ref_file, data):
"""Retrieve callable regions for a sample subset by defined analysis regions.
"""
from bcbio.heterogeneity import chromhacks
CovInfo = collections.namedtuple("CovInfo", "callable, raw_callable, depth_files")
noalt_calling = "noalt_calling" in dd.get_tools_on(data) or "altcontigs" in dd.get_exclude_regions(data)
def callable_chrom_filter(r):
"""Filter to callable region, potentially limiting by chromosomes.
"""
return r.name == "CALLABLE" and (not noalt_calling or chromhacks.is_nonalt(r.chrom))
out_file = "%s-callable_sample.bed" % os.path.splitext(bam_file)[0]
with shared.bedtools_tmpdir(data):
sv_bed = regions.get_sv_bed(data)
callable_bed, depth_files = coverage.calculate(bam_file, data, sv_bed)
input_regions_bed = dd.get_variant_regions(data)
if not utils.file_uptodate(out_file, callable_bed):
with file_transaction(data, out_file) as tx_out_file:
callable_regions = pybedtools.BedTool(callable_bed)
filter_regions = callable_regions.filter(callable_chrom_filter)
if input_regions_bed:
if not utils.file_uptodate(out_file, input_regions_bed):
input_regions = pybedtools.BedTool(input_regions_bed)
filter_regions.intersect(input_regions, nonamecheck=True).saveas(tx_out_file)
else:
filter_regions.saveas(tx_out_file)
return CovInfo(out_file, callable_bed, depth_files)
def sample_callable_bed(bam_file, ref_file, data):
"""Retrieve callable regions for a sample subset by defined analysis regions.
"""
CovInfo = collections.namedtuple("CovInfo", "callable, highdepth, avg_coverage, coverage")
config = data["config"]
out_file = "%s-callable_sample.bed" % os.path.splitext(bam_file)[0]
with shared.bedtools_tmpdir({"config": config}):
coverage_file, callable_bed, highdepth_bed, variant_regions_avg_cov = coverage.calculate(bam_file, data)
input_regions_bed = config["algorithm"].get("variant_regions", None)
if not utils.file_uptodate(out_file, callable_bed):
with file_transaction(config, out_file) as tx_out_file:
callable_regions = pybedtools.BedTool(callable_bed)
filter_regions = callable_regions.filter(lambda x: x.name == "CALLABLE")
if input_regions_bed:
if not utils.file_uptodate(out_file, input_regions_bed):
input_regions = pybedtools.BedTool(input_regions_bed)
filter_regions.intersect(input_regions, nonamecheck=True).saveas(tx_out_file)
else:
filter_regions.saveas(tx_out_file)
return CovInfo(out_file, highdepth_bed, variant_regions_avg_cov, coverage_file)
