def test_sv_end_BND():
"""Test the function that calculates the end coordinate of a BND structural variant.
Example:
2 321681 bnd_W G G]17:198982] 6 PASS SVTYPE=BND;MATEID=bnd_Y GT 0/1
"""
end = sv_end(pos=321681, alt=ALT, svend=None, svlen=None)
assert end == 198981
def test_sv_end_SVEND():
"""Test the function that calculates the end coordinate of a structural variant in the presence of SVEND.
Example:
2 321682 . T <DEL> 6 PASS SVTYPE=DEL;END=321887;SVLEN=-205;CIPOS=-56,20;CIEND=-10,62 GT:GQ 0/1:12
"""
end = sv_end(pos=321682, alt="<DEL>", svend=321887, svlen=-205)
assert end == 321886
def add_variants(database, vcf_obj, samples, assembly, dataset_id, nr_variants):
"""Build variant objects from a cyvcf2 VCF iterator
Accepts:
database(pymongo.database.Database)
vcf_obj(cyvcf2.VCF): a VCF object
samples(set): set of samples to add variants for
assembly(str): chromosome build
dataset_id(str): dataset id
nr_variant(int): number of variants contained in VCF file
Returns:
inserted_vars, samples(tuple): (int,list)
"""
LOG.info("Parsing variants..\n")
new_samples = set()
# Collect position to check genotypes for (only samples provided by user)
gt_positions = []
for i, sample in enumerate(vcf_obj.samples):
if sample in samples:
gt_positions.append(i)
vcf_samples = vcf_obj.samples
inserted_vars = 0
with Bar("Processing", max=nr_variants) as bar:
for vcf_variant in vcf_obj:
chrom = vcf_variant.CHROM.replace("chr", "")
if chrom not in CHROMOSOMES:
LOG.warning(
f"chromosome '{vcf_variant.CHROM}' not included in canonical chromosome list, skipping it."
)
continue
# Check if variant was called in provided samples
sample_calls = variant_called(
vcf_samples, gt_positions, vcf_variant.gt_types
)
if sample_calls == {}:
continue # variant was not called in samples of interest
parsed_variant = dict(
chromosome=chrom,
start=vcf_variant.start, # 0-based coordinate
end=vcf_variant.end, # 0-based coordinate
reference_bases=vcf_variant.REF,
alternate_bases=vcf_variant.ALT,
)
if vcf_variant.var_type == "sv":
sv_type = vcf_variant.INFO["SVTYPE"]
parsed_variant["variant_type"] = sv_type
alt = vcf_variant.ALT[0]
# Check if a better variant end can be extracted from INFO field
end = sv_end(
pos=vcf_variant.POS,
alt=alt,
svend=vcf_variant.INFO.get("END"),
svlen=vcf_variant.INFO.get("SVLEN"),
)
parsed_variant["end"] = end
if sv_type == "BND":
parsed_variant["mate_name"] = bnd_mate_name(alt, chrom)
else:
parsed_variant["variant_type"] = vcf_variant.var_type.upper()
dataset_dict = {dataset_id: {"samples": sample_calls}}
# Create standard variant object with specific _id
variant = Variant(parsed_variant, dataset_dict, assembly)
# Load variant into database or update an existing one with new samples and dataset
result = add_variant(
database=database, variant=variant, dataset_id=dataset_id
)
if result is not None:
inserted_vars += 1
bar.next()
return inserted_vars