def _prepare_calls(result_file, out_dir, data):
"""Write summary file of results of HLA typing by allele.
"""
sample = dd.get_sample_name(data)
out_file = os.path.join(out_dir, "%s-optitype.csv" % (sample))
if not utils.file_uptodate(out_file, result_file):
hla_truth = bwakit.get_hla_truthset(data)
with file_transaction(data, out_file) as tx_out_file:
with open(tx_out_file, "w") as out_handle:
writer = csv.writer(out_handle)
allele_info = _parse_result_file(result_file)
if len(allele_info) == 1:
writer.writerow([
"sample", "locus", "alleles", "expected", "validates"
])
else:
writer.writerow(
["sample", "local", "index", "alleles", "score"])
for j, (alleles, score) in enumerate(allele_info):
for hla_locus, call_alleles in alleles:
truth_alleles = tz.get_in([sample, hla_locus],
hla_truth, [])
if len(allele_info) == 1:
writer.writerow([
sample, hla_locus, ";".join(call_alleles),
";".join(truth_alleles),
bwakit.matches_truth(call_alleles,
truth_alleles, data)
])
else:
writer.writerow([
sample, hla_locus, j, ";".join(call_alleles),
score
])
return out_file
def _prepare_calls(result_file, hla_dir, data):
"""Write summary file of results of HLA typing by allele.
"""
sample = dd.get_sample_name(data)
out_file = os.path.join(hla_dir, "%s-optitype.csv" % (sample))
if not utils.file_uptodate(out_file, result_file):
hla_truth = bwakit.get_hla_truthset(data)
with file_transaction(data, out_file) as tx_out_file:
with open(tx_out_file, "w") as out_handle:
writer = csv.writer(out_handle)
allele_info = _parse_result_file(result_file)
if len(allele_info) == 1:
writer.writerow(["sample", "locus", "alleles", "expected", "validates"])
else:
writer.writerow(["sample", "local", "index", "alleles", "score"])
for j, (alleles, score) in enumerate(allele_info):
for hla_locus, call_alleles in alleles:
truth_alleles = tz.get_in([sample, hla_locus], hla_truth, [])
if len(allele_info) == 1:
writer.writerow([sample, hla_locus,
";".join(call_alleles), ";".join(truth_alleles),
bwakit.matches_truth(call_alleles, truth_alleles, data)])
else:
writer.writerow([sample, hla_locus, j, ";".join(call_alleles), score])
return out_file
def _combine_calls(hla_calls, hla_dir, data):
"""Write summary file of results of HLA typing by allele.
"""
sample = dd.get_sample_name(data)
out_file = os.path.join(hla_dir, "%s-optitype.csv" % (sample))
if not utils.file_uptodate(out_file, hla_calls[0][1]):
hla_truth = bwakit.get_hla_truthset(data)
with file_transaction(data, out_file) as tx_out_file:
with open(tx_out_file, "w") as out_handle:
writer = csv.writer(out_handle)
writer.writerow(["sample", "locus", "alleles", "expected", "validates"])
for hla_locus, result_file in hla_calls:
truth_alleles = tz.get_in([sample, hla_locus], hla_truth, [])
call_alleles, score = _parse_result_file(result_file, hla_locus)
writer.writerow([sample, hla_locus,
";".join(call_alleles), ";".join(truth_alleles),
bwakit.matches_truth(call_alleles, truth_alleles, data)])
return out_file
