def combine_bed_by_size(input_beds, sample, work_dir, data, delim=","):
"""Combine a set of BED files, breaking into individual size chunks.
"""
out_file = os.path.join(work_dir, "%s-ensemble.bed" % sample)
if len(input_beds) > 0:
size_beds = []
for e_start, e_end in validate.EVENT_SIZES:
base, ext = os.path.splitext(out_file)
size_out_file = "%s-%s_%s%s" % (base, e_start, e_end, ext)
if not utils.file_exists(size_out_file):
with file_transaction(data, size_out_file) as tx_out_file:
with shared.bedtools_tmpdir(data):
all_file = "%s-all.bed" % utils.splitext_plus(tx_out_file)[0]
has_regions = False
with open(all_file, "w") as out_handle:
for line in fileinput.input(input_beds):
chrom, start, end, event_str = line.split()[:4]
event = event_str.split("_", 1)[0]
size = int(end) - int(start)
if size >= e_start and size < e_end or event == "BND":
out_handle.write(line)
has_regions = True
if has_regions:
pybedtools.BedTool(all_file).sort(stream=True)\
.merge(c=4, o="distinct", delim=delim).saveas(tx_out_file)
if utils.file_exists(size_out_file):
ann_size_out_file = annotate.add_genes(size_out_file, data)
size_beds.append(ann_size_out_file)
if len(size_beds) > 0:
out_file = bedutils.combine(size_beds, out_file, data)
return out_file
def combine_bed_by_size(input_beds, sample, work_dir, data, delim=","):
"""Combine a set of BED files, breaking into individual size chunks.
"""
out_file = os.path.join(work_dir, "%s-ensemble.bed" % sample)
if len(input_beds) > 0:
size_beds = []
for e_start, e_end in validate.EVENT_SIZES:
base, ext = os.path.splitext(out_file)
size_out_file = "%s-%s_%s%s" % (base, e_start, e_end, ext)
if not utils.file_exists(size_out_file):
with file_transaction(data, size_out_file) as tx_out_file:
with shared.bedtools_tmpdir(data):
all_file = "%s-all.bed" % utils.splitext_plus(tx_out_file)[0]
has_regions = False
with open(all_file, "w") as out_handle:
for line in fileinput.input(input_beds):
chrom, start, end, event_str = line.split()[:4]
event = event_str.split("_", 1)[0]
size = int(end) - int(start)
if size >= e_start and size < e_end or event == "BND":
out_handle.write(line)
has_regions = True
if has_regions:
pybedtools.BedTool(all_file).sort(stream=True)\
.merge(c=4, o="distinct", delim=delim).saveas(tx_out_file)
if utils.file_exists(size_out_file):
ann_size_out_file = annotate.add_genes(size_out_file, data)
size_beds.append(ann_size_out_file)
if len(size_beds) > 0:
out_file = bedutils.combine(size_beds, out_file, data)
return out_file
def summarize(calls, data):
"""Summarize results from multiple callers into a single flattened BED file.
"""
import pybedtools
sample = tz.get_in(["rgnames", "sample"], data)
work_dir = utils.safe_makedir(os.path.join(data["dirs"]["work"], "structural",
sample, "ensemble"))
out_file = os.path.join(work_dir, "%s-ensemble.bed" % sample)
with shared.bedtools_tmpdir(data):
input_beds = filter(lambda x: x is not None,
[_create_bed(c, out_file, data) for c in calls])
if len(input_beds) > 0:
size_beds = []
for e_start, e_end in validate.EVENT_SIZES:
base, ext = os.path.splitext(out_file)
size_out_file = "%s-%s_%s%s" % (base, e_start, e_end, ext)
if not utils.file_exists(size_out_file):
with file_transaction(data, size_out_file) as tx_out_file:
with shared.bedtools_tmpdir(data):
all_file = "%s-all.bed" % utils.splitext_plus(tx_out_file)[0]
with open(all_file, "w") as out_handle:
for line in fileinput.input(input_beds):
chrom, start, end = line.split()[:3]
size = int(end) - int(start)
if size >= e_start and size < e_end:
out_handle.write(line)
pybedtools.BedTool(all_file).sort(stream=True)\
.merge(c=4, o="distinct", delim=",").saveas(tx_out_file)
size_beds.append(size_out_file)
out_file = bedutils.combine(size_beds, out_file, data["config"])
if utils.file_exists(out_file):
bedprep_dir = utils.safe_makedir(os.path.join(os.path.dirname(out_file), "bedprep"))
calls.append({"variantcaller": "ensemble",
"vrn_file": bedutils.clean_file(out_file, data, bedprep_dir=bedprep_dir)})
return calls
def combine_bed(*args):
return bedutils.combine(*args)
def combine_bed(*args):
return bedutils.combine(*args)
