def _merge_hla_fastq_inputs(data):
"""Merge HLA inputs from a split initial alignment.
"""
hla_key = ["hla", "fastq"]
hla_sample_files = [
x for x in (tz.get_in(hla_key, data) or []) if x and x != "None"
]
merged_hlas = None
if hla_sample_files:
out_files = collections.defaultdict(list)
for hla_file in utils.flatten(hla_sample_files):
rehla = re.search(r".hla.(?P<hlatype>[\w-]+).fq", hla_file)
if rehla:
hlatype = rehla.group("hlatype")
out_files[hlatype].append(hla_file)
if len(out_files) > 0:
hla_outdir = utils.safe_makedir(
os.path.join(dd.get_work_dir(data), "align",
dd.get_sample_name(data), "hla"))
merged_hlas = []
for hlatype, files in out_files.items():
out_file = os.path.join(
hla_outdir,
"%s-%s.fq" % (dd.get_sample_name(data), hlatype))
optitype.combine_hla_fqs([(hlatype, f) for f in files],
out_file, data)
merged_hlas.append(out_file)
data = tz.update_in(data, hla_key, lambda x: merged_hlas)
return data
def _merge_hla_fastq_inputs(data):
"""Merge HLA inputs from a split initial alignment.
"""
hla_key = ["hla", "fastq"]
hla_sample_files = [x for x in tz.get_in(hla_key, data, []) if x and x != "None"]
if hla_sample_files:
out_files = collections.defaultdict(list)
for hla_files in hla_sample_files:
for hla_file in hla_files:
rehla = re.search(".hla.(?P<hlatype>[\w-]+).fq", hla_file)
if rehla:
hlatype = rehla.group("hlatype")
out_files[hlatype].append(hla_file)
if len(out_files) > 0:
hla_outdir = utils.safe_makedir(os.path.join(dd.get_work_dir(data), "align",
dd.get_sample_name(data), "hla"))
merged_hlas = []
for hlatype, files in out_files.items():
out_file = os.path.join(hla_outdir, "%s-%s.fq" % (dd.get_sample_name(data), hlatype))
optitype.combine_hla_fqs([(hlatype, f) for f in files], out_file, data)
merged_hlas.append(out_file)
data = tz.update_in(data, hla_key, lambda x: merged_hlas)
else:
data = tz.update_in(data, hla_key, lambda x: None)
return data
def _merge_hla_fastq_inputs(data):
"""Merge HLA inputs from a split initial alignment.
"""
hla_key = ["hla", "fastq"]
hla_dirs = tz.get_in(hla_key, data)
hla_outdir = None
if hla_dirs:
hla_files = collections.defaultdict(list)
for hla_dir in hla_dirs:
if hla_dir and hla_dir != "None":
for hla_file in sorted(list(glob.glob(os.path.join(hla_dir, ".*.fq")))):
hlatype = re.search(".hla.(?P<hlatype>[\w-]+).fq", hla_file)
hla_files[hlatype].append(hla_file)
if len(hla_files) > 0:
hla_outdir = os.path.join(dd.get_work_dir(data), "align", dd.get_sample_name(data), "hla")
for hlatype, files in hla_files:
out_file = os.path.join(hla_outdir, "%s-%s.fq" % (dd.get_sample_name(data), hlatype))
optitype.combine_hla_fqs(files, out_file, data)
data = tz.update_in(data, hla_key, lambda x: hla_outdir)
return data
def _merge_hla_fastq_inputs(data):
"""Merge HLA inputs from a split initial alignment.
"""
hla_key = ["hla", "fastq"]
hla_dirs = tz.get_in(hla_key, data)
hla_outdir = None
if hla_dirs:
if not isinstance(hla_dirs, (list, tuple)):
hla_dirs = [hla_dirs]
hla_files = collections.defaultdict(list)
for hla_dir in hla_dirs:
if hla_dir and hla_dir != "None":
for hla_file in sorted(list(glob.glob(os.path.join(hla_dir, ".*.fq")))):
hlatype = re.search(".hla.(?P<hlatype>[\w-]+).fq", hla_file)
hla_files[hlatype].append(hla_file)
if len(hla_files) > 0:
hla_outdir = os.path.join(dd.get_work_dir(data), "align", dd.get_sample_name(data), "hla")
for hlatype, files in hla_files:
out_file = os.path.join(hla_outdir, "%s-%s.fq" % (dd.get_sample_name(data), hlatype))
optitype.combine_hla_fqs(files, out_file, data)
data = tz.update_in(data, hla_key, lambda x: hla_outdir)
return data
