def _merge_by_batch(batch, fnames):
"""Merge all calls in a family into a single callset.
"""
merge_dir = utils.safe_makedir(os.path.join(os.getcwd(), "merged"))
clean_dir = utils.safe_makedir(os.path.join(merge_dir, "clean"))
merge_file = os.path.join(merge_dir, "%s-ensemble.bed" % batch)
if not utils.file_uptodate(merge_file, fnames[0]):
for fname in glob.glob(os.path.join(merge_dir, "%s-ensemble*" % batch)):
os.remove(fname)
ensemble.combine_bed_by_size(fnames, batch, merge_dir, {}, delim="&&")
return bedutils.clean_file(merge_file, {}, bedprep_dir=clean_dir)
def _merge_by_batch(batch, fnames):
"""Merge all calls in a family into a single callset.
"""
merge_dir = utils.safe_makedir(os.path.join(os.getcwd(), "merged"))
clean_dir = utils.safe_makedir(os.path.join(merge_dir, "clean"))
merge_file = os.path.join(merge_dir, "%s-ensemble.bed" % batch)
if not utils.file_uptodate(merge_file, fnames[0]):
for fname in glob.glob(os.path.join(merge_dir,
"%s-ensemble*" % batch)):
os.remove(fname)
ensemble.combine_bed_by_size(fnames, batch, merge_dir, {}, delim="&&")
return bedutils.clean_file(merge_file, {}, bedprep_dir=clean_dir)
def _combine_calls(in_files, sample_info):
sample_files = {}
sample_dir = utils.safe_makedir(os.path.join(os.getcwd(), "prepped"))
files_by_batch = collections.defaultdict(list)
for fname in in_files:
descr = os.path.basename(fname).split("-")[0]
sample_files[descr] = fname
cur_file = os.path.join(sample_dir, os.path.basename(fname))
files_by_batch[sample_info[descr]["batch"]].append(cur_file)
if not utils.file_uptodate(cur_file, fname):
with open(cur_file, "w") as out_handle:
with open(fname) as in_handle:
for line in in_handle:
chrom, start, end, calls = line.strip().split("\t")[:4]
info = {"sample": descr, "phenotype": sample_info[descr]["phenotype"],
"risk": sample_info[descr]["risk"],
"calls": calls.split(","), "region": "%s:%s-%s" % (chrom, start, end)}
is_cnv = any([x.startswith("cnv") for x in info["calls"]])
if int(end) - int(start) >= MIN_SIZE and (is_cnv or int(end) - int(start) < MAX_SV_SIZE):
out_handle.write("\t".join([chrom, start, end, json.dumps(info)]) + "\n")
samples_by_batch = collections.defaultdict(list)
for s, x in sample_info.items():
x["sample"] = s
samples_by_batch[x["batch"]].append(x)
ready_files = []
for batch, fnames in files_by_batch.items():
merged_file = _merge_by_batch(batch, fnames)
filtered_file = _filter_batch(merged_file, samples_by_batch[batch])
ready_files.append(filtered_file)
return ensemble.combine_bed_by_size(ready_files, "combined", os.getcwd(), {}), sample_files
def _combine_calls(in_files, sample_info):
sample_files = {}
sample_dir = utils.safe_makedir(os.path.join(os.getcwd(), "prepped"))
files_by_batch = collections.defaultdict(list)
for fname in in_files:
descr = os.path.basename(fname).split("-")[0]
sample_files[descr] = fname
cur_file = os.path.join(sample_dir, os.path.basename(fname))
files_by_batch[sample_info[descr]["batch"]].append(cur_file)
if not utils.file_uptodate(cur_file, fname):
with open(cur_file, "w") as out_handle:
with open(fname) as in_handle:
for line in in_handle:
chrom, start, end, calls = line.strip().split("\t")[:4]
info = {
"sample": descr,
"phenotype": sample_info[descr]["phenotype"],
"risk": sample_info[descr]["risk"],
"calls": calls.split(","),
"region": "%s:%s-%s" % (chrom, start, end)
}
is_cnv = any(
[x.startswith("cnv") for x in info["calls"]])
if int(end) - int(start) >= MIN_SIZE and (
is_cnv or int(end) - int(start) < MAX_SV_SIZE):
out_handle.write("\t".join(
[chrom, start, end,
json.dumps(info)]) + "\n")
samples_by_batch = collections.defaultdict(list)
for s, x in sample_info.items():
x["sample"] = s
samples_by_batch[x["batch"]].append(x)
ready_files = []
for batch, fnames in files_by_batch.items():
merged_file = _merge_by_batch(batch, fnames)
filtered_file = _filter_batch(merged_file, samples_by_batch[batch])
ready_files.append(filtered_file)
return ensemble.combine_bed_by_size(ready_files, "combined", os.getcwd(),
{}), sample_files
