def _remove_variant_set(self, variant_set_name):
vs = VariantSet.objects.get(name=variant_set_name,
reference_set=self.reference_set)
for call_set in VariantCallSet.objects(variant_sets=vs):
call_set.variant_sets.remove(vs)
call_set.save()
# Remove calls from callsets that only have this variantset
if len(call_set.variant_sets) < 2:
VariantCall.objects(call_set=call_set).delete()
call_set.delete()
# Remove variants that are ONLY from this variant set
Variant.objects(variant_sets=vs, variant_sets__size=2).delete()
VariantSetMetadata.objects(variant_set=vs).delete()
vs.delete()
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_add_variants_and_calls(self):
vcf = VCF(f="tests/vcf_tests/test.vcf",
reference_set_id=self.reference_set.id,
method="CORTEX")
vcf.add_to_database()
assert VariantCall.objects().count() == 21
assert Variant.objects().count() == 21
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 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 run(parser, args):
DB = connect('atlas-%s' % (args.db_name))
if DB is not None:
try:
Variant.objects()
logging.info(
"Connected to atlas-%s" % (args.db_name))
except (ServerSelectionTimeoutError, ConnectionError):
DB = None
logging.warning(
"Could not connect to database. Continuing without using genetic backgrounds")
mutations = []
reference = os.path.basename(args.reference_filepath).split('.fa')[0]
if args.vcf:
run_make_probes_from_vcf_file(args)
elif args.genbank:
aa2dna = GeneAminoAcidChangeToDNAVariants(
args.reference_filepath,
args.genbank)
if args.text_file:
with open(args.text_file, 'r') as infile:
reader = csv.reader(infile, delimiter="\t")
for row in reader:
gene, mutation, alphabet = row
if alphabet == "DNA":
protein_coding_var = False
else:
protein_coding_var = True
for var_name in aa2dna.get_variant_names(
gene, mutation, protein_coding_var):
mutations.append(
Mutation(reference=reference,
var_name=var_name,
gene=aa2dna.get_gene(gene),
mut=mutation))
else:
for variant in args.variant:
gene, mutation = variant.split("_")
for var_name in aa2dna.get_variant_names(gene, mutation):
mutations.append(
Mutation(reference=reference,
var_name=var_name,
gene=gene,
mut=mutation))
else:
if args.text_file:
with open(args.text_file, 'r') as infile:
reader = csv.reader(infile, delimiter="\t")
for row in reader:
gene_name, pos, ref, alt, alphabet = row
if gene_name == "ref":
mutations.append(
Mutation(
reference=reference,
var_name="".join([ref, pos, alt])))
else:
mutations.append(
Mutation(
reference=reference,
var_name=row[0]))
else:
mutations.extend(Mutation(reference=reference, var_name=v)
for v in args.variants)
al = AlleleGenerator(
reference_filepath=args.reference_filepath,
kmer=args.kmer)
for mut in mutations:
variant_panel = make_variant_probe(
al, mut.variant, args.kmer, DB=DB, no_backgrounds=args.no_backgrounds)
if variant_panel is not None:
if mut.gene:
sys.stdout.write(
">ref-%s?num_alts=%i&gene=%s&mut=%s&ref=%s\n" %
(mut.variant.var_name, len(
variant_panel.alts), mut.gene.name, mut.mut, mut.reference))
else:
sys.stdout.write(
">ref-%s?num_alts=%i\n" %
(mut.variant.var_name, len(
variant_panel.alts)))
sys.stdout.write("%s\n" % variant_panel.ref)
for a in variant_panel.alts:
sys.stdout.write(">alt-%s\n" % mut.mut)
sys.stdout.write("%s\n" % a)
else:
logging.warning(
"All variants failed for %s_%s - %s" %
(mut.gene, mut.mut, mut.variant))
