def test_delete_variants(mongo_adapter, het_variant, case_obj, ind_positions):
"""docstring for test_load_variants"""
db = mongo_adapter.db
vcf = []
vcf.append(het_variant)
family_id = case_obj.family_id
individuals = case_obj.individuals
load_variants(
adapter=mongo_adapter,
family_id=family_id,
individuals=individuals,
ind_positions=ind_positions,
vcf=vcf,
gq_treshold=20,
)
mongo_variant = db.variant.find_one()
assert mongo_variant['families'] == [family_id]
delete_variants(adapter=mongo_adapter,
family_id=family_id,
ind_positions=ind_positions,
individuals=individuals,
vcf=vcf)
mongo_variant = db.variant.find_one()
assert mongo_variant == None
def test_delete_variants(mongo_adapter, het_variant, case_obj):
"""docstring for test_load_variants"""
db = mongo_adapter.db
vcf = []
vcf.append(het_variant)
family_id = case_obj.family_id
individuals = case_obj.individuals
load_variants(
adapter=mongo_adapter,
family_id=family_id,
individuals=individuals,
vcf=vcf,
gq_treshold=20,
)
mongo_variant = db.variant.find_one()
assert mongo_variant['families'] == [family_id]
delete_variants(
adapter=mongo_adapter,
family_id=family_id,
individuals=individuals,
vcf=vcf
)
mongo_variant = db.variant.find_one()
assert mongo_variant == None
def delete(ctx, variant_file, family_file, family_type, family_id):
"""Delete the variants of a case."""
if not family_file or family_id:
logger.error("Please provide a family file or a case id")
logger.info("Exiting")
ctx.abort()
family = get_family(
family_lines=family_file,
family_type=family_type
)
family_id = family.family_id
affected_individuals = family.affected_individuals
adapter = ctx.obj['adapter']
if variant_file == '-':
logger.info("Start parsing variants from stdin")
variant_stream = get_vcf_handle(fsock=sys.stdin)
else:
logger.info("Start parsing variants from stdin")
variant_stream = get_vcf_handle(infile=variant_file)
start_deleting = datetime.now()
try:
count = delete_variants(adapter, variant_stream, family_id,
affected_individuals)
except CaseError as error:
logger.warning(error.message)
ctx.abort()
logger.info("Nr of variants deleted: {0}".format(count))
logger.info("Time to delete variants: {0}"
.format(datetime.now() - start_deleting))
def frequency(context, bulk, remove):
"""Upload or remove variants to/from frequency database."""
loqusdb_auth = context.obj.get("loqusdb", {})
adapter = LoqusdbAdapter()
adapter.connect(**loqusdb_auth)
mip_case = context.obj["case"]
if mip_case.is_old:
logger.warn("unsupported MIP version for frequency: %s", mip_case.version)
else:
vcf_path = mip_case.research_vcf
case_group_id = group_id(mip_case)
# we only care about "rare" variants
ped_path = mip_case.configs.pedigree
try:
affected_inds = affected_individuals(ped_path)
except FrequencyError as error:
logger.warn("LOQUSDB: {}".format(error.message))
if "affected_inds" in locals():
with open(vcf_path, "r") as vcf_stream:
try:
if remove:
count = delete_variants(adapter, vcf_stream, case_group_id, affected_inds)
logger.info("removed {} variants".format(count))
else:
load_variants(
adapter, case_group_id, affected_inds, vcf_stream, bulk_insert=bulk, vcf_path=vcf_path
)
except CaseError as error:
logger.warn("LOQUSDB: {}".format(error.message))
def test_delete_non_existing_variant(mongo_adapter, het_variant, case_obj):
"""docstring for test_load_variants"""
db = mongo_adapter.db
vcf = []
vcf.append(het_variant)
family_id = case_obj.family_id
individuals = case_obj.individuals
delete_variants(adapter=mongo_adapter,
family_id=family_id,
individuals=individuals,
vcf=vcf)
mongo_variant = db.variant.find_one()
assert mongo_variant == None
def test_delete_variant(mongo_adapter, het_variant, case_obj):
"""docstring for test_load_variants"""
db = mongo_adapter.db
vcf = []
vcf.append(het_variant)
family_id_1 = case_obj.family_id
individuals = case_obj.individuals
load_variants(
adapter=mongo_adapter,
family_id=family_id_1,
individuals=individuals,
vcf=vcf,
gq_treshold=20,
)
mongo_variant = db.variant.find_one()
assert mongo_variant['families'] == [family_id_1]
family_id_2 = '2'
load_variants(
adapter=mongo_adapter,
family_id=family_id_2,
individuals=individuals,
vcf=vcf,
gq_treshold=20,
)
mongo_variant = db.variant.find_one()
assert mongo_variant['families'] == [family_id_1, family_id_2]
assert mongo_variant['observations'] == 2
delete_variants(adapter=mongo_adapter,
family_id=family_id_2,
individuals=individuals,
vcf=vcf)
mongo_variant = db.variant.find_one()
assert mongo_variant['families'] == [family_id_1]
assert mongo_variant['observations'] == 1
def test_delete_non_existing_variant(mongo_adapter, het_variant, case_obj):
"""docstring for test_load_variants"""
db = mongo_adapter.db
vcf = []
vcf.append(het_variant)
family_id = case_obj.family_id
individuals = case_obj.individuals
delete_variants(
adapter=mongo_adapter,
family_id=family_id,
individuals=individuals,
vcf=vcf
)
mongo_variant = db.variant.find_one()
assert mongo_variant == None
def upload(adapter, vcf_path, affected, case_id, force=False, bulk=True):
with open(vcf_path, 'r') as vcf_stream:
try:
if force:
count = delete_variants(adapter, vcf_stream,
case_id, affected)
logger.info("removed {} variants".format(count))
load_variants(adapter, case_id, affected, vcf_stream,
bulk_insert=bulk, vcf_path=vcf_path)
except CaseError as error:
logger.warn("LOQUSDB: {}".format(error.message))
def delete(ctx, variant_file, family_file, family_type, case_id):
"""Delete the variants of a case."""
if not family_file:
logger.error("Please provide a family file")
ctx.abort()
adapter = ctx.obj['adapter']
start_deleting = datetime.now()
try:
delete_variants(adapter=adapter,
variant_file=variant_file,
family_file=family_file,
family_type=family_type,
case_id=case_id)
except (CaseError, IOError) as error:
logger.warning(error)
ctx.abort()
logger.info("Time to delete variants: {0}".format(datetime.now() -
start_deleting))
def delete(ctx, variant_file, family_file, family_type, case_id):
"""Delete the variants of a case."""
if not family_file:
logger.error("Please provide a family file")
ctx.abort()
adapter = ctx.obj['adapter']
start_deleting = datetime.now()
try:
delete_variants(
adapter=adapter,
variant_file=variant_file,
family_file=family_file,
family_type=family_type,
case_id=case_id
)
except (CaseError, IOError) as error:
logger.warning(error)
ctx.abort()
logger.info("Time to delete variants: {0}"
.format(datetime.now() - start_deleting))