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_file", reference_set=self.reference_set)
self.variant_sets = [self.variant_set]
def global_variant_set(self):
try:
vs = VariantSet.objects.get(name=GLOBAL_VARIANT_SET_NAME)
except:
vs = VariantSet.create_and_save(name=GLOBAL_VARIANT_SET_NAME,
reference_set=self.reference_set)
return vs
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 _create_new_variant_set(self):
variant_set_name = os.path.basename(self.f)
if VariantSet.objects(name=variant_set_name,
reference_set=self.reference_set):
if not self.force:
raise NotUniqueError(
"VariantSet %s already exists. Rerun with -f to recreate."
% variant_set_name)
else:
self._remove_variant_set(variant_set_name)
self.vcf_variant_set = VariantSet.create_and_save(
name=variant_set_name, reference_set=self.reference_set)
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 test_create_new_variant(self):
variant_set = VariantSet.create_and_save(
name="this_vcf_file", reference_set=self.reference_set)
vs = VariantSet.objects.get(name="this_vcf_file")
assert variant_set == vs
assert vs.reference_set.name == "ref_set"