def priority_total_coverage(data, out_dir):
"""
calculate coverage at 10 depth intervals in the priority regions
"""
from bcbio.structural import prioritize
bed_file = dd.get_svprioritize(data)
if not bed_file and not file_exists(bed_file) or prioritize.is_gene_list(
bed_file):
return {}
in_bam = dd.get_align_bam(data) or dd.get_work_bam(data)
cleaned_bed = clean_file(bed_file, data, prefix="svprioritize-")
work_dir = safe_makedir(out_dir)
sample = dd.get_sample_name(data)
out_file = os.path.join(work_dir, sample + "_priority_total_coverage.bed")
if utils.file_uptodate(out_file, cleaned_bed) and utils.file_uptodate(
out_file, in_bam):
return out_file
cmdl = sambamba.make_command(
data,
"depth region",
in_bam,
cleaned_bed,
depth_thresholds=[10, 20, 30, 40, 50, 60, 70, 80, 90, 100])
with file_transaction(out_file) as tx_out_file:
message = "Calculating region coverage of {bed_file} in {in_bam}"
do.run(cmdl + " -o " + tx_out_file, message.format(**locals()))
logger.debug("Saved svprioritize coverage into " + out_file)
return out_file
def priority_coverage(data, out_dir):
from bcbio.structural import prioritize
bed_file = dd.get_svprioritize(data)
if not bed_file or not file_exists(bed_file) or prioritize.is_gene_list(
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 = clean_file(bed_file, data, prefix="cov-", simple=True)
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_total_coverage(data, out_dir):
"""
calculate coverage at 10 depth intervals in the priority regions
"""
from bcbio.structural import prioritize
bed_file = dd.get_svprioritize(data)
if not bed_file and not file_exists(bed_file) or prioritize.is_gene_list(
bed_file):
return {}
work_dir = safe_makedir(out_dir)
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 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 = clean_file(bed_file, data)
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 out_file
def priority_total_coverage(data, out_dir):
"""
calculate coverage at 10 depth intervals in the priority regions
"""
from bcbio.structural import prioritize
bed_file = dd.get_svprioritize(data)
if not bed_file and not file_exists(bed_file) or prioritize.is_gene_list(bed_file):
return {}
work_dir = safe_makedir(out_dir)
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 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 = clean_file(bed_file, data)
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 out_file
def priority_coverage(data, out_dir):
from bcbio.structural import prioritize
bed_file = dd.get_svprioritize(data)
if not bed_file or not file_exists(bed_file) or prioritize.is_gene_list(bed_file):
return data
work_dir = safe_makedir(out_dir)
sample = dd.get_sample_name(data)
cleaned_bed = clean_file(bed_file, data, prefix="cov-", simple=True)
out_file = os.path.join(work_dir, sample + "_priority_depth.bed")
in_bam = dd.get_align_bam(data) or dd.get_work_bam(data)
if utils.file_uptodate(out_file, cleaned_bed) and utils.file_uptodate(out_file, in_bam):
return out_file
with file_transaction(data, out_file) as tx_out_file:
cmdl = sambamba.make_command(data, "depth base", in_bam, cleaned_bed)
parse_cmd = "awk '{print $1\"\t\"$2\"\t\"$2\"\t\"$3\"\t\"$10}' | sed '1d'"
cmdl += " | {parse_cmd} > {tx_out_file}"
message = "Calculating base coverage of {bed_file} in {in_bam}"
do.run(cmdl.format(**locals()), message.format(**locals()))
return out_file
def priority_coverage(data, out_dir):
from bcbio.structural import prioritize
bed_file = dd.get_svprioritize(data)
if not bed_file or not file_exists(bed_file) or prioritize.is_gene_list(bed_file):
return data
work_dir = safe_makedir(out_dir)
sample = dd.get_sample_name(data)
cleaned_bed = clean_file(bed_file, data, prefix="cov-", simple=True)
out_file = os.path.join(work_dir, sample + "_priority_depth.bed")
in_bam = dd.get_align_bam(data) or dd.get_work_bam(data)
if utils.file_uptodate(out_file, cleaned_bed) and utils.file_uptodate(out_file, in_bam):
return out_file
with file_transaction(out_file) as tx_out_file:
cmdl = sambamba.make_command(data, "depth base", in_bam, cleaned_bed)
parse_cmd = "awk '{print $1\"\t\"$2\"\t\"$2\"\t\"$3\"\t\"$10}' | sed '1d'"
cmdl += " | {parse_cmd} > {tx_out_file}"
message = "Calculating base coverage of {bed_file} in {in_bam}"
do.run(cmdl.format(**locals()), message.format(**locals()))
return out_file
def priority_total_coverage(data, out_dir):
"""
calculate coverage at 10 depth intervals in the priority regions
"""
from bcbio.structural import prioritize
bed_file = dd.get_svprioritize(data)
if not bed_file and not file_exists(bed_file) or prioritize.is_gene_list(bed_file):
return {}
in_bam = dd.get_align_bam(data) or dd.get_work_bam(data)
cleaned_bed = clean_file(bed_file, data, prefix="svprioritize-")
work_dir = safe_makedir(out_dir)
sample = dd.get_sample_name(data)
out_file = os.path.join(work_dir, sample + "_priority_total_coverage.bed")
if utils.file_uptodate(out_file, cleaned_bed) and utils.file_uptodate(out_file, in_bam):
return out_file
cmdl = sambamba.make_command(data, "depth region", in_bam, cleaned_bed,
depth_thresholds=[10, 20, 30, 40, 50, 60, 70, 80, 90, 100])
with file_transaction(out_file) as tx_out_file:
message = "Calculating region coverage of {bed_file} in {in_bam}"
do.run(cmdl + " -o " + tx_out_file, message.format(**locals()))
logger.debug("Saved svprioritize coverage into " + out_file)
return out_file
def priority_coverage(data, out_dir):
from bcbio.structural import prioritize
bed_file = dd.get_svprioritize(data)
if not bed_file or not file_exists(bed_file) or prioritize.is_gene_list(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 = clean_file(bed_file, data, prefix="cov-", simple=True)
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