def test_delete_case_and_variants(vcf_path, ped_path, real_mongo_adapter,
case_id, case_obj):
mongo_adapter = real_mongo_adapter
db = mongo_adapter.db
load_database(
adapter=mongo_adapter,
variant_file=vcf_path,
family_file=ped_path,
family_type='ped',
)
mongo_case = db.case.find_one()
assert mongo_case['case_id'] == case_id
delete(
adapter=mongo_adapter,
case_obj=case_obj,
)
mongo_case = db.case.find_one()
assert mongo_case == None
mongo_variant = db.case.find_one()
assert mongo_variant == None
def test_load_database_wrong_ped(vcf_path, funny_ped_path, real_mongo_adapter):
mongo_adapter = real_mongo_adapter
## GIVEN a vcf and ped file with wrong individuals
## WHEN loading the information
## THEN Error should be raised since individuals is not in vcf
with pytest.raises(CaseError):
load_database(
adapter=mongo_adapter,
variant_file=vcf_path,
family_file=funny_ped_path,
family_type="ped",
)
def test_load_database(vcf_path, ped_path, real_mongo_adapter, case_id):
mongo_adapter = real_mongo_adapter
db = mongo_adapter.db
load_database(
adapter=mongo_adapter,
variant_file=vcf_path,
family_file=ped_path,
family_type="ped",
)
mongo_case = db.case.find_one()
assert mongo_case["case_id"] == case_id
def test_load_database_alternative_ped(vcf_path, ped_path, real_mongo_adapter,
case_id):
mongo_adapter = real_mongo_adapter
db = mongo_adapter.db
load_database(adapter=mongo_adapter,
variant_file=vcf_path,
family_file=ped_path,
family_type='ped',
case_id='alternative')
mongo_case = db.case.find_one()
mongo_variant = db.variant.find_one()
assert mongo_case['case_id'] == 'alternative'
assert mongo_variant['families'] == ['alternative']
def load(ctx, variant_file, sv_variants, family_file, family_type,
skip_case_id, gq_treshold, case_id, ensure_index, max_window,
check_profile, hard_threshold, soft_threshold):
"""Load the variants of a case
A variant is loaded if it is observed in any individual of a case
If no family file is provided all individuals in vcf file will be considered.
"""
if not (family_file or case_id):
LOG.warning("Please provide a family file or a case id")
ctx.abort()
if not (variant_file or sv_variants):
LOG.warning("Please provide a VCF file")
ctx.abort()
variant_path = None
if variant_file:
variant_path = os.path.abspath(variant_file)
variant_sv_path = None
if sv_variants:
variant_sv_path = os.path.abspath(sv_variants)
variant_profile_path = None
if check_profile:
variant_profile_path = os.path.abspath(check_profile)
adapter = ctx.obj['adapter']
genome_build = ctx.obj['genome_build']
start_inserting = datetime.now()
try:
nr_inserted = load_database(adapter=adapter,
variant_file=variant_path,
sv_file=variant_sv_path,
family_file=family_file,
family_type=family_type,
skip_case_id=skip_case_id,
case_id=case_id,
gq_treshold=gq_treshold,
max_window=max_window,
profile_file=variant_profile_path,
hard_threshold=hard_threshold,
soft_threshold=soft_threshold,
genome_build=genome_build)
except (SyntaxError, CaseError, IOError) as error:
LOG.warning(error)
ctx.abort()
LOG.info("Nr variants inserted: %s", nr_inserted)
LOG.info("Time to insert variants: {0}".format(datetime.now() -
start_inserting))
if ensure_index:
adapter.ensure_indexes()
else:
adapter.check_indexes()
def test_load_database_alternative_ped(vcf_path, ped_path, real_mongo_adapter,
case_id):
mongo_adapter = real_mongo_adapter
db = mongo_adapter.db
load_database(
adapter=mongo_adapter,
variant_file=vcf_path,
family_file=ped_path,
family_type="ped",
case_id="alternative",
)
mongo_case = db.case.find_one()
mongo_variant = db.variant.find_one()
assert mongo_case["case_id"] == "alternative"
assert mongo_variant["families"] == ["alternative"]
def test_delete_structural_variants(vcf_path, ped_path, real_mongo_adapter, case_id, sv_case_obj):
# GIVEN a mongo adapter with an inserted case with SVs
mongo_adapter = real_mongo_adapter
db = mongo_adapter.db
load_database(
adapter=mongo_adapter,
variant_file=sv_case_obj['vcf_path'],
family_file=ped_path,
family_type='ped',
sv_file=sv_case_obj['vcf_sv_path']
)
mongo_svs = db.structural_variant.find()
assert len(list(mongo_svs)) == 19
# WHEN deleteing the case
delete(adapter=mongo_adapter, case_obj=sv_case_obj)
# All structural variants should be deleted.
mongo_svs = db.structural_variant.find()
assert len(list(mongo_svs)) == 0