def coverage(data):
bed_file = dd.get_coverage_experimental(data)
if not bed_file:
return data
work_dir = os.path.join(dd.get_work_dir(data), "report", "coverage")
with chdir(work_dir):
in_bam = data['work_bam']
sample = os.path.splitext(os.path.basename(in_bam))[0]
logger.debug("doing coverage for %s" % sample)
region_bed = pybedtools.BedTool(bed_file)
parse_file = os.path.join(sample + "_coverage.bed")
parse_total_file = os.path.join(sample + "_cov_total.tsv")
if not file_exists(parse_file):
total_cov = cov_class(0, None, sample)
bam_api = pysam.AlignmentFile(in_bam)
with file_transaction(parse_file) as out_tx:
with open(out_tx, 'w') as out_handle:
print >>out_handle, "#chrom\tstart\tend\tregion\treads\tstrand\tsize\tsample\tmean\tsdt\tq10\tq20\tq4\tq50"
with tmpfile() as tx_tmp_file:
# tx_tmp_file = "tmpintersect"
for line in region_bed:
chrom = line.chrom
start = max(line.start, 0)
end = line.end
region_file = pybedtools.BedTool(str(line), from_string=True).saveas().fn
coords = "%s:%s-%s" % (chrom, start, end)
cmd = ("samtools view -b {in_bam} {coords} | "
"bedtools coverage -a {region_file} -b - -hist > {tx_tmp_file}")
_silence_run(cmd.format(**locals()))
total_cov = _get_exome_coverage_stats(os.path.abspath(tx_tmp_file), sample, out_tx, total_cov)
total_cov.write_coverage(parse_total_file)
data['coverage'] = os.path.abspath(parse_file)
return data
def coverage(data):
AVERAGE_REGION_STRING_LENGTH = 100
bed_file = dd.get_coverage_experimental(data)
if not bed_file:
return data
work_dir = os.path.join(dd.get_work_dir(data), "report", "coverage")
batch_size = max_command_length() / AVERAGE_REGION_STRING_LENGTH
with chdir(work_dir):
in_bam = data['work_bam']
sample = dd.get_sample_name(data)
logger.debug("doing coverage for %s" % sample)
region_bed = pybedtools.BedTool(bed_file)
parse_file = os.path.join(sample + "_coverage.bed")
parse_total_file = os.path.join(sample + "_cov_total.tsv")
if not file_exists(parse_file):
total_cov = cov_class(0, None, sample)
with file_transaction(parse_file) as out_tx:
with open(out_tx, 'w') as out_handle:
HEADER = ["#chrom", "start", "end", "region", "reads",
"strand", "size", "sample", "mean", "sd", "cutoff10",
"cutoff20", "cutoff4", "cutoff50"]
out_handle.write("\t".join(HEADER) + "\n")
with tmpfile() as tx_tmp_file:
lcount = 0
for chunk in robust_partition_all(batch_size, region_bed):
coord_batch = []
line_batch = ""
for line in chunk:
lcount += 1
chrom = line.chrom
start = max(line.start, 0)
end = line.end
coords = "%s:%s-%s" % (chrom, start, end)
coord_batch.append(coords)
line_batch += str(line)
if not coord_batch:
continue
region_file = pybedtools.BedTool(line_batch,
from_string=True).saveas().fn
coord_string = " ".join(coord_batch)
cmd = ("samtools view -b {in_bam} {coord_string} | "
"bedtools coverage -a {region_file} -b - "
"-hist > {tx_tmp_file}")
_silence_run(cmd.format(**locals()))
total_cov = _get_exome_coverage_stats(os.path.abspath(tx_tmp_file), sample, out_tx, total_cov)
logger.debug("Processed %d regions." % lcount)
total_cov.write_coverage(parse_total_file)
data['coverage'] = os.path.abspath(parse_file)
return data
def coverage(data):
bed_file = dd.get_coverage_experimental(data)
if not bed_file:
return data
work_dir = os.path.join(dd.get_work_dir(data), "report", "coverage")
with chdir(work_dir):
in_bam = data['work_bam']
sample = os.path.splitext(os.path.basename(in_bam))[0]
logger.debug("doing coverage for %s" % sample)
region_bed = pybedtools.BedTool(bed_file)
parse_file = os.path.join(sample + "_coverage.bed")
parse_total_file = os.path.join(sample + "_cov_total.tsv")
if not file_exists(parse_file):
total_cov = cov_class(0, None, sample)
bam_api = pysam.AlignmentFile(in_bam)
with file_transaction(parse_file) as out_tx:
with open(out_tx, 'w') as out_handle:
print >> out_handle, "#chrom\tstart\tend\tregion\treads\tstrand\tsize\tsample\tmean\tsdt\tq10\tq20\tq4\tq50"
with tmpfile() as tx_tmp_file:
# tx_tmp_file = "tmpintersect"
for line in region_bed:
chrom = line.chrom
start = max(line.start, 0)
end = line.end
region_file = pybedtools.BedTool(
str(line), from_string=True).saveas().fn
coords = "%s:%s-%s" % (chrom, start, end)
cmd = (
"samtools view -b {in_bam} {coords} | "
"bedtools coverage -a {region_file} -b - -hist > {tx_tmp_file}"
)
_silence_run(cmd.format(**locals()))
total_cov = _get_exome_coverage_stats(
os.path.abspath(tx_tmp_file), sample, out_tx,
total_cov)
total_cov.write_coverage(parse_total_file)
data['coverage'] = os.path.abspath(parse_file)
return data