def priority_total_coverage(data):
"""
calculate coverage at 10 depth intervals in the priority regions
"""
bed_file = dd.get_svprioritize(data)
if not bed_file and not file_exists(bed_file):
return data
work_dir = os.path.join(dd.get_work_dir(data), "report", "coverage")
sample = dd.get_sample_name(data)
out_file = os.path.join(work_dir, sample + "_priority_total_coverage.bed")
if file_exists(out_file):
data['priority_total_coverage'] = os.path.abspath(out_file)
return data
nthreads = dd.get_num_cores(data)
in_bam = dd.get_align_bam(data) or dd.get_work_bam(data)
sambamba = config_utils.get_program("sambamba", data, default="sambamba")
with tx_tmpdir(data, work_dir) as tmp_dir:
cleaned_bed = os.path.join(tmp_dir, os.path.basename(bed_file))
cleaned_bed = bed.decomment(bed_file, cleaned_bed)
with file_transaction(out_file) as tx_out_file:
cmd = ("{sambamba} depth region -t {nthreads} -L {cleaned_bed} "
"-F \"not unmapped\" "
"-T 10 -T 20 -T 30 -T 40 -T 50 -T 60 -T 70 -T 80 -T 90 -T 100 "
"{in_bam} -o {tx_out_file}")
message = "Calculating coverage of {bed_file} regions in {in_bam}"
do.run(cmd.format(**locals()), message.format(**locals()))
data['priority_total_coverage'] = os.path.abspath(out_file)
return data
def priority_total_coverage(data):
"""
calculate coverage at 10 depth intervals in the priority regions
"""
bed_file = dd.get_svprioritize(data)
if not bed_file and not file_exists(bed_file):
return data
work_dir = os.path.join(dd.get_work_dir(data), "report", "coverage")
sample = dd.get_sample_name(data)
out_file = os.path.join(work_dir, sample + "_priority_total_coverage.bed")
if file_exists(out_file):
data['priority_total_coverage'] = os.path.abspath(out_file)
return data
nthreads = dd.get_num_cores(data)
in_bam = dd.get_align_bam(data) or dd.get_work_bam(data)
sambamba = config_utils.get_program("sambamba", data, default="sambamba")
with tx_tmpdir(data, work_dir) as tmp_dir:
cleaned_bed = os.path.join(tmp_dir, os.path.basename(bed_file))
cleaned_bed = bed.decomment(bed_file, cleaned_bed)
with file_transaction(out_file) as tx_out_file:
cmd = (
"{sambamba} depth region -t {nthreads} -L {cleaned_bed} "
"-F \"not unmapped\" "
"-T 10 -T 20 -T 30 -T 40 -T 50 -T 60 -T 70 -T 80 -T 90 -T 100 "
"{in_bam} -o {tx_out_file}")
message = "Calculating coverage of {bed_file} regions in {in_bam}"
do.run(cmd.format(**locals()), message.format(**locals()))
data['priority_total_coverage'] = os.path.abspath(out_file)
return data
def coverage(data):
"""
Calculate coverage at different completeness cutoff
for region in coverage option.
"""
bed_file = dd.get_coverage(data)
sambamba = config_utils.get_program("sambamba", data["config"])
work_dir = safe_makedir(os.path.join(dd.get_work_dir(data), "report", "coverage"))
if not bed_file:
return data
cleaned_bed = os.path.join(work_dir, os.path.splitext(os.path.basename(bed_file))[0] + ".cleaned.bed")
cleaned_bed = bed.decomment(bed_file, cleaned_bed)
with chdir(work_dir):
in_bam = dd.get_align_bam(data) or dd.get_work_bam(data)
sample = dd.get_sample_name(data)
logger.debug("doing coverage for %s" % sample)
parse_file = os.path.join(sample + "_coverage.bed")
parse_total_file = os.path.join(sample + "_cov_total.tsv")
cores = dd.get_num_cores(data)
if not file_exists(parse_file):
with tx_tmpdir(data, work_dir) as tmp_dir:
with file_transaction(parse_file) as out_tx:
cmd = ("{sambamba} depth region -F \"not unmapped\" -t {cores} "
"%s -T 1 -T 5 -T 10 -T 20 -T 40 -T 50 -T 60 -T 70 "
"-T 80 -T 100 -L {cleaned_bed} {in_bam} | sed 's/# "
"chrom/chrom/' > {out_tx}")
do.run(cmd.format(**locals()) % "-C 1000", "Run coverage for {}".format(sample))
parse_file = _add_high_covered_regions(parse_file, cleaned_bed, sample)
_calculate_percentiles(os.path.abspath(parse_file), sample)
data['coverage'] = os.path.abspath(parse_file)
return data
def coverage(data):
"""
Calculate coverage at different completeness cutoff
for region in coverage option.
"""
bed_file = dd.get_coverage(data)
if not bed_file:
return data
cleaned_bed = os.path.splitext(
os.path.basename(bed_file))[0] + ".cleaned.bed"
work_dir = os.path.join(dd.get_work_dir(data), "report", "coverage")
with chdir(work_dir):
in_bam = data['work_bam']
sample = dd.get_sample_name(data)
logger.debug("doing coverage for %s" % sample)
parse_file = os.path.join(sample + "_coverage.bed")
parse_total_file = os.path.join(sample + "_cov_total.tsv")
cores = dd.get_num_cores(data)
if not file_exists(parse_file):
with tx_tmpdir(data, work_dir) as tmp_dir:
cleaned_bed = os.path.join(tmp_dir, os.path.basename(bed_file))
cleaned_bed = bed.decomment(bed_file, cleaned_bed)
with file_transaction(parse_file) as out_tx:
cmd = (
"sambamba depth region -F \"not unmapped\" -t {cores} "
"-C 1000 -T 1 -T 5 -T 10 -T 20 -T 40 -T 50 -T 60 -T 70 "
"-T 80 -T 100 -L {cleaned_bed} {in_bam} | sed 's/# "
"chrom/chrom/' > {out_tx}")
do.run(cmd.format(**locals()),
"Run coverage for {}".format(sample))
parse_file = _add_high_covered_regions(parse_file, bed_file, sample)
_calculate_percentiles(parse_file, sample)
data['coverage'] = os.path.abspath(parse_file)
return data
def coverage(data, out_dir):
"""
Calculate coverage at different completeness cutoff
for region in coverage option.
"""
bed_file = dd.get_coverage(data)
sambamba = config_utils.get_program("sambamba", data["config"])
work_dir = safe_makedir(out_dir)
if not bed_file:
return {}
cleaned_bed = os.path.join(
work_dir,
os.path.splitext(os.path.basename(bed_file))[0] + ".cleaned.bed")
cleaned_bed = bed.decomment(bed_file, cleaned_bed)
with chdir(work_dir):
in_bam = dd.get_align_bam(data) or dd.get_work_bam(data)
sample = dd.get_sample_name(data)
logger.debug("doing coverage for %s" % sample)
parse_file = os.path.join(sample + "_coverage.bed")
parse_total_file = os.path.join(sample + "_cov_total.tsv")
cores = dd.get_num_cores(data)
if not file_exists(parse_file):
with tx_tmpdir(data, work_dir) as tmp_dir:
with file_transaction(parse_file) as out_tx:
cmd = (
"{sambamba} depth region -F \"not unmapped\" -t {cores} "
"%s -T 1 -T 5 -T 10 -T 20 -T 40 -T 50 -T 60 -T 70 "
"-T 80 -T 100 -L {cleaned_bed} {in_bam} | sed 's/# "
"chrom/chrom/' > {out_tx}")
do.run(
cmd.format(**locals()) % "-C 1000",
"Run coverage for {}".format(sample))
parse_file = _add_high_covered_regions(parse_file, cleaned_bed, sample)
parse_file = _calculate_percentiles(os.path.abspath(parse_file),
sample)
return os.path.abspath(parse_file)
def priority_coverage(data, out_dir):
bed_file = dd.get_svprioritize(data)
if not bed_file or not file_exists(bed_file):
return data
work_dir = safe_makedir(out_dir)
sample = dd.get_sample_name(data)
out_file = os.path.join(work_dir, sample + "_priority_depth.bed")
if file_exists(out_file):
return out_file
nthreads = dd.get_num_cores(data)
in_bam = dd.get_align_bam(data) or dd.get_work_bam(data)
sambamba = config_utils.get_program("sambamba", data, default="sambamba")
with tx_tmpdir(data, work_dir) as tmp_dir:
cleaned_bed = os.path.join(tmp_dir, os.path.basename(bed_file))
cleaned_bed = bed.decomment(bed_file, cleaned_bed)
with file_transaction(out_file) as tx_out_file:
parse_cmd = "awk '{print $1\"\t\"$2\"\t\"$2\"\t\"$3\"\t\"$10}' | sed '1d'"
cmd = ("{sambamba} depth base -t {nthreads} -L {cleaned_bed} "
"-F \"not unmapped\" "
"{in_bam} | {parse_cmd} > {tx_out_file}")
message = "Calculating coverage of {bed_file} regions in {in_bam}"
do.run(cmd.format(**locals()), message.format(**locals()))
return out_file
def priority_coverage(data, out_dir):
bed_file = dd.get_svprioritize(data)
if not bed_file or not file_exists(bed_file):
return data
work_dir = safe_makedir(out_dir)
sample = dd.get_sample_name(data)
out_file = os.path.join(work_dir, sample + "_priority_depth.bed")
if file_exists(out_file):
return out_file
nthreads = dd.get_num_cores(data)
in_bam = dd.get_align_bam(data) or dd.get_work_bam(data)
sambamba = config_utils.get_program("sambamba", data, default="sambamba")
with tx_tmpdir(data, work_dir) as tmp_dir:
cleaned_bed = os.path.join(tmp_dir, os.path.basename(bed_file))
cleaned_bed = bed.decomment(bed_file, cleaned_bed)
with file_transaction(out_file) as tx_out_file:
parse_cmd = "awk '{print $1\"\t\"$2\"\t\"$2\"\t\"$3\"\t\"$10}' | sed '1d'"
cmd = ("{sambamba} depth base -t {nthreads} -L {cleaned_bed} "
"-F \"not unmapped\" "
"{in_bam} | {parse_cmd} > {tx_out_file}")
message = "Calculating coverage of {bed_file} regions in {in_bam}"
do.run(cmd.format(**locals()), message.format(**locals()))
return out_file