records = list()
query_records = list()
for record in vcf_reader:
if len(record.FILTER
) == 0 and record.is_indel and cp.requires_mt_provean(record):
query_records.append(record)
records.append(record)
if len(query_records) > 0 and not args.no_remote:
# run mutation taster
for record in records:
if 'MT_pred' not in record.INFO:
query_mutation_taster(record)
if args.run_local:
import provean_query
query_manager = provean_query.ProveanQueryManager(
query_records,
args.provean_script,
args.num_provean_threads,
args.mem_per_thread,
cluster_mode=args.cluster_mode)
query_manager.run_queries()
else:
query = rpq.RemoteProveanQuery(query_records)
query.run_query()
for record in records:
if len(record.FILTER) == 0 and record.is_indel:
cp.classify_pathogenicity(record, no_remote=args.no_remote)
vcf_writer.write_record(record)
vcf_writer.close()
desc="mutation taster score (run if necessary)",
source=None, version=None)
vcf_writer = vcf.Writer(sys.stdout, vcf_reader)
records = list()
query_records = list()
for record in vcf_reader:
if cp.requires_mt_provean(record):
query_records.append(record)
records.append(record)
if len(query_records) > 0 and not args.no_remote:
# run mutation taster
for record in records:
if 'MT_pred' not in record.INFO:
query_mutation_taster(record)
if args.run_local:
import provean_query
query_manager = provean_query.ProveanQueryManager(query_records, args.provean_script,
args.num_provean_threads, args.mem_per_thread,
cluster_mode=args.cluster_mode)
query_manager.run_queries()
else:
query = rpq.RemoteProveanQuery(query_records)
query.run_query()
for record in records:
cp.classify_pathogenicity(record, no_remote=args.no_remote)
vcf_writer.write_record(record)
vcf_writer.close()
import vcf
import sys
import classify_pathogenicity_vcf as cp
if __name__ == "__main__":
parser = argparse.ArgumentParser(prog='classify_pathogenicity_vcf.py',
description='Add pathogenicity to vcf file')
parser.add_argument('vcf_infile')
args = parser.parse_args()
vcf_reader = vcf.Reader(open(args.vcf_infile, 'r'))
assert "ANN" in vcf_reader.infos
assert "HOTSPOT" in vcf_reader.infos or "hotspot" in vcf_reader.infos
assert "fathmm_pred" in vcf_reader.infos
assert "facetsLOH" in vcf_reader.infos
assert "MutationTaster_pred" in vcf_reader.infos
# add necessary info headers
vcf_reader.infos['pathogenicity'] = vcf.parser._Info(id='pathogenicity', num=-1, type='String',
desc="Classification of pathogenicity",
source=None, version=None)
vcf_writer = vcf.Writer(sys.stdout, vcf_reader)
records = list()
for record in vcf_reader:
cp.classify_pathogenicity(record)
vcf_writer.write_record(record)
vcf_writer.close()
import classify_pathogenicity_vcf as cp
if __name__ == "__main__":
parser = argparse.ArgumentParser(prog='classify_snv_pathogenicity_vcf.py',
description='Add pathogenicity to vcf file')
parser.add_argument('vcf_infile')
args = parser.parse_args()
vcf_reader = vcf.Reader(open(args.vcf_infile, 'r'))
assert "ANN" in vcf_reader.infos
assert "HOTSPOT" in vcf_reader.infos or "hotspot" in vcf_reader.infos
assert "FATHMM_pred" in vcf_reader.infos
assert "facetsLOH" in vcf_reader.infos or "LOH" in vcf_reader.infos
assert "MutationTaster_pred" in vcf_reader.infos
# add necessary info headers
vcf_reader.infos['pathogenicity'] = vcf.parser._Info(id='pathogenicity', num=-1, type='String',
desc="Classification of pathogenicity",
source=None, version=None)
records = [x for x in vcf_reader]
for record in records:
if len(record.FILTER) == 0 and record.is_snp:
cp.classify_pathogenicity(record)
vcf_writer = vcf.Writer(sys.stdout, vcf_reader)
for record in records:
vcf_writer.write_record(record)
vcf_writer.close()