def run(parser, args):
db_name = '%s-%s' % (DB_PREFIX, args.db_name)
DB = connect(db_name, host=args.db_uri)
if args.verbose:
logger.setLevel(level=logging.DEBUG)
else:
logger.setLevel(level=logging.INFO)
al = AlleleGenerator(reference_filepath=args.reference_filepath,
kmer=args.kmer)
_variant_ids = get_non_singelton_variants(db_name)
total = Variant.snps(id__in=_variant_ids).count()
N = 100
pages = math.ceil(total / N)
for page in range(pages):
logger.info("%i of %i - %f%%" %
(page * N, total, round(100 * (page * N) / total, 2)))
for variant in Variant.snps(
id__in=_variant_ids).order_by("start").skip(N * page).limit(N):
# for variant in Variant.snps().order_by("start"):
variant_panel = make_variant_probe(al, variant, args.kmer, DB=DB)
for i, ref in enumerate(variant_panel.refs):
sys.stdout.write(
">ref-%s?var_name=%snum_alts=%i&ref=%s&enum=%i\n" %
(variant_panel.variant.var_hash, variant.var_name[:100],
len(variant_panel.alts),
variant_panel.variant.reference.id, i))
sys.stdout.write("%s\n" % ref)
for i, a in enumerate(variant_panel.alts):
sys.stdout.write(">alt-%s?var_name=%s&enum=%i\n" %
(variant_panel.variant.var_hash,
variant.var_name[:100], i))
sys.stdout.write("%s\n" % a)
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