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 test_get_first_chrom_name_multiple_chroms_gets_first():
fp = StringIO(">ch1\nA\n>ch2\nG")
actual = get_first_chrom_name(fp)
expected = "ch1"
assert actual == expected
def test_get_first_chrom_name_pointer_is_past_start_gets_first():
fp = StringIO(">ch1\nA\n>ch2\nG")
_ = fp.readline()
actual = get_first_chrom_name(fp)
expected = "ch1"
assert actual == expected
def test_get_first_chrom_name_not_fasta_raises_error():
fp = StringIO("@chrom1\nACGT")
with pytest.raises(ValueError):
get_first_chrom_name(fp)