def test_delete_case_and_variants(vcf_path, ped_path, mongo_adapter, case_id):
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,
variant_file=vcf_path,
family_file=ped_path,
family_type='ped',
)
mongo_case = db.case.find_one()
assert mongo_case == None
mongo_variant = db.case.find_one()
assert mongo_variant == None
def test_delete_case_and_variants(vcf_path, ped_path, mongo_adapter, case_id):
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,
variant_file=vcf_path,
family_file=ped_path,
family_type='ped',
)
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, mongo_adapter):
db = mongo_adapter.db
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_wrong_ped(vcf_path, funny_ped_path, mongo_adapter):
db = mongo_adapter.db
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_wrong_ped(vcf_path, funny_ped_path, 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_alternative_ped(vcf_path, ped_path, mongo_adapter,
case_id):
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(self, family_id: str, ped_path: str, vcf_path: str) -> dict:
"""Add observations from a VCF."""
variant_handle = get_file_handle(vcf_path)
nr_variants = check_vcf(variant_handle)
load_database(
adapter=self,
variant_file=vcf_path,
family_file=ped_path,
family_type='ped',
case_id=family_id,
gq_treshold=20,
nr_variants=nr_variants,
)
self.check_indexes()
return dict(variants=nr_variants)
def test_load_database_alternative_ped(vcf_path, ped_path, mongo_adapter, case_id):
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, family_file, family_type, skip_case_id, gq_treshold, case_id):
"""Load the variants of a case
The loading is based on if the variant is seen in a ny affected individual
in the family.
"""
if not family_file:
logger.warning("Please provide a family file")
ctx.abort()
variant_path = os.path.abspath(variant_file)
adapter = ctx.obj['adapter']
try:
variant_handle = get_file_handle(variant_path)
nr_variants = check_vcf(variant_handle)
except VcfError as error:
logger.warning(error)
ctx.abort()
logger.info("Vcf file looks fine")
logger.info("Nr of variants in vcf: {0}".format(nr_variants))
start_inserting = datetime.now()
try:
nr_inserted = load_database(
adapter=adapter,
variant_file=variant_path,
family_file=family_file,
family_type=family_type,
skip_case_id=skip_case_id,
case_id=case_id,
gq_treshold=gq_treshold,
nr_variants=nr_variants,
)
except (SyntaxError, CaseError, IOError) as error:
logger.warning(error)
ctx.abort()
logger.info("Time to insert variants: {0}".format(
datetime.now() - start_inserting))
def load(ctx, variant_file, family_file, family_type, skip_case_id,
gq_treshold, case_id):
"""Load the variants of a case
The loading is based on if the variant is seen in a ny affected individual
in the family.
"""
if not family_file:
logger.warning("Please provide a family file")
ctx.abort()
variant_path = os.path.abspath(variant_file)
adapter = ctx.obj['adapter']
try:
variant_handle = get_file_handle(variant_path)
nr_variants = check_vcf(variant_handle)
except VcfError as error:
logger.warning(error)
ctx.abort()
logger.info("Vcf file looks fine")
logger.info("Nr of variants in vcf: {0}".format(nr_variants))
start_inserting = datetime.now()
try:
nr_inserted = load_database(
adapter=adapter,
variant_file=variant_path,
family_file=family_file,
family_type=family_type,
skip_case_id=skip_case_id,
case_id=case_id,
gq_treshold=gq_treshold,
nr_variants=nr_variants,
)
except (SyntaxError, CaseError, IOError) as error:
logger.warning(error)
ctx.abort()
logger.info("Time to insert variants: {0}".format(datetime.now() -
start_inserting))
adapter.check_indexes()
