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 setup(self):
DB.drop_database("mykrobe-test")
self.reference_set = ReferenceSet().create_and_save(name="ref_set")
self.reference = Reference().create_and_save(
name="NC_000962.3",
md5checksum="sre",
reference_sets=[self.reference_set])
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 setup(self):
DB.drop_database('mykrobe-test')
self.reference_set = ReferenceSet().create_and_save(name="ref_set")
self.variant_set = VariantSet.create_and_save(
name="this_vcf_file2", reference_set=self.reference_set)
self.variant_sets = [self.variant_set]
self.reference = Reference().create_and_save(
name="ref", md5checksum="sre", reference_sets=[self.reference_set])
self.call_set = VariantCallSet.create(sample_id="C00123",
name="C00123",
variant_sets=self.variant_sets)
self.variant_snp = Variant.create(variant_sets=self.variant_sets,
start=0,
end=1,
reference_bases="A",
alternate_bases=["T"],
reference=self.reference)
self.variant_snp_mult_alts = Variant.create(
variant_sets=self.variant_sets,
start=0,
end=1,
reference_bases="T",
alternate_bases=["A", "C"],
reference=self.reference)
def setup(self):
DB.drop_database('mykrobe-test')
self.reference_set = ReferenceSet().create_and_save(name="ref_set")
self.variant_set = VariantSet.create_and_save(
name="this_vcf_file2", reference_set=self.reference_set)
self.variant_sets = [self.variant_set]
self.reference = Reference().create_and_save(
name="ref", md5checksum="sre", reference_sets=[self.reference_set])
def setup(self):
DB.drop_database('mykrobe-test')
self.pg = AlleleGenerator(
reference_filepath="src/mykrobe/data/BX571856.1.fasta")
self.reference_set = ReferenceSet().create_and_save(name="ref_set")
self.variant_set = VariantSet.create_and_save(
name="this_vcf_file", reference_set=self.reference_set)
self.variant_sets = [self.variant_set]
self.reference = Reference().create_and_save(
name="ref", md5checksum="sre", reference_sets=[self.reference_set])
def setup(self):
DB.drop_database("mykrobe-test")
self.pg = AlleleGenerator(
reference_filepath=f"{DATA_DIR}/NC_000962.3.fasta", kmer=31)
self.reference_set = ReferenceSet().create_and_save(name="ref_set")
self.variant_set = VariantSet.create_and_save(
name="this_vcf_file", reference_set=self.reference_set)
self.variant_sets = [self.variant_set]
self.reference = Reference().create_and_save(
name="ref", md5checksum="sre", reference_sets=[self.reference_set])
def setup(self):
DB.drop_database('mykrobe-test')
self.reference_set = ReferenceSet().create_and_save(name="ref_set")
self.reference = Reference().create_and_save(
name="NC_000962.3",
md5checksum="sre",
reference_sets=[self.reference_set])
vcf = VCF(f="tests/vcf_tests/test.vcf",
reference_set_id=self.reference_set.id,
method="CORTEX")
vcf.add_to_database()
def setup(self):
DB.drop_database('mykrobe-test')
with open("src/mykrobe/data/NC_000962.3.fasta", 'r') as infile:
self.reference_seq = list(SeqIO.parse(infile, "fasta"))[0].seq
self.gm = GeneAminoAcidChangeToDNAVariants(
reference="src/mykrobe/data/NC_000962.3.fasta",
genbank="src/mykrobe/data/NC_000962.3.gb")
self.reference_set = ReferenceSet().create_and_save(name="ref_set")
self.variant_set = VariantSet.create_and_save(
name="this_vcf_file", reference_set=self.reference_set)
self.variant_sets = [self.variant_set]
self.reference_id = Reference().create_and_save(
name="ref", md5checksum="sre", reference_sets=[self.reference_set])
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()