def test_add_new_vcf_variant_set(self):
vcf = VCF(f="tests/vcf_tests/test.vcf",
reference_set_id=self.reference_set.id,
method="CORTEX")
vcf.add_to_database()
# We create a global variant set as well as one for the individual VCF
assert VariantSet.objects().count() == 2
vs = VariantSet.objects()[0]
assert len(Variant.objects()[0].variant_sets) == 2
assert vs.name == "test.vcf"
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):
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):
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 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 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"
def setUp(self):
DB.drop_database('ga4ghmongo-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]
self.reference = Reference().create_and_save(
name="ref", md5checksum="sre", reference_sets=[self.reference_set])
def setUp(self):
DB.drop_database('atlas-test')
self.pg = AlleleGenerator(
reference_filepath="atlasvar/data/NC_000962.2.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('ga4ghmongo-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]
self.reference = Reference().create_and_save(
name="ref",
md5checksum="sre",
reference_sets=[
self.reference_set])
def setUp(self):
DB.drop_database('atlas-test')
with open("mykatlas/data/NC_000962.3.fasta", 'r') as infile:
self.reference_seq = list(SeqIO.parse(infile, "fasta"))[0].seq
self.gm = GeneAminoAcidChangeToDNAVariants(
reference="mykatlas/data/NC_000962.3.fasta",
genbank="mykatlas/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_add_second_vcf_variant_set(self):
# This VCF only has one Variant which is not in the first VCF
vcf = VCF(f="tests/vcf_tests/test2.vcf",
reference_set_id=self.reference_set.id,
method="CORTEX")
vcf.add_to_database()
assert VariantSet.objects().count() == 3
assert VariantCallSet.objects().count() == 2
assert VariantCall.objects().count() == 42
assert Variant.objects().count() == 22
assert len(Variant.objects()[0].variant_sets) == 3
assert len(
Variant.objects.get(
names="UNION_BC_k31_var_147").variant_sets) == 3
def test_add_second_vcf_variant_set(self):
# This VCF only has one Variant which is not in the first VCF
vcf = VCF(f="tests/vcf_tests/test3.vcf",
reference_set_id=self.reference_set.id,
method="CORTEX")
vcf.add_to_database()
assert VariantSet.objects().count() == 2
assert VariantCallSet.objects().count() == 1
assert VariantCall.objects().count() == 106
assert Variant.objects().count() == 106
assert Variant.snps().count() == 89
assert Variant.indels().count() == 17
assert Variant.insertions().count() == 8
assert Variant.deletions().count() == 8
assert Variant.ph_snps.count() == 1
def setUp(self):
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 setUp(self):
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]