def run(parser, args):
args = parser.parse_args()
# args = check_args(args)
if args.quiet:
logger.setLevel(logging.ERROR)
else:
logger.setLevel(logging.INFO)
DBNAME = "%s-%s" % (DB_PREFIX, args.db_name)
connect(DBNAME, host=args.db_uri)
logger.debug("Using DB %s" % DBNAME)
with open(args.reference_set) as fp:
reference_set_name = get_first_chrom_name(fp)
try:
reference_set = ReferenceSet.objects.get(name=reference_set_name)
except DoesNotExist:
reference_set = ReferenceSet.create_and_save(name=reference_set_name)
try:
reference = Reference.create_and_save(name=reference_set_name,
reference_sets=[reference_set],
md5checksum="NA")
except:
pass
vcf = VCF(args.vcf, reference_set.id, method=args.method, force=args.force)
vcf.add_to_database()
def run(parser, args):
args = parser.parse_args()
# args = check_args(args)
if args.quiet:
logger.setLevel(logging.ERROR)
else:
logger.setLevel(logging.INFO)
DBNAME = 'atlas-%s' % (args.db_name)
db = client[DBNAME]
connect(DBNAME)
logger.debug("Using DB %s" % DBNAME)
reference_set_name = ".".join(
os.path.basename(args.reference_set).split(".")[:-1])
try:
reference_set = ReferenceSet.objects.get(name=reference_set_name)
except DoesNotExist:
reference_set = ReferenceSet.create_and_save(name=reference_set_name)
# Hack
try:
reference = Reference.create_and_save(name=reference_set_name,
reference_sets=[reference_set],
md5checksum="NA")
except:
pass
vcf = VCF(args.vcf, reference_set.id, method=args.method, force=args.force)
vcf.add_to_database()
def run_make_probes_from_vcf_file(args):
# Make VariantSet from vcf
reference = os.path.basename(args.reference_filepath).split(".fa")[0]
try:
reference_set = ReferenceSet.objects.get(name=reference)
except DoesNotExist:
reference_set = ReferenceSet.create_and_save(name=reference)
# Hack
try:
reference = Reference.create_and_save(
name=reference,
reference_sets=[reference_set],
md5checksum=reference)
except NotUniqueError:
pass
vcf = VCF(
args.vcf,
reference_set.id,
method="tmp",
force=True,
append_to_global_variant_set=False)
vcf.add_to_database()