def test_load_variants(real_mongo_adapter, het_variant, case_obj):
mongo_adapter = real_mongo_adapter
## GIVEN an adapter and a vcf with one heterozygote variant
db = mongo_adapter.db
vcf = []
vcf.append(het_variant)
mongo_variant = db.variant.find_one()
assert mongo_variant == None
## WHEN loading the variant into the database
load_variants(
adapter=mongo_adapter,
vcf_obj=vcf,
case_obj=case_obj,
)
mongo_variant = db.variant.find_one()
## THEN assert that the variant is loaded correct
assert mongo_variant["families"] == [case_obj["case_id"]]
assert mongo_variant["observations"] == 1
assert mongo_variant["homozygote"] == 0
assert mongo_variant["hemizygote"] == 0
def test_load_same_variant_different_case(real_mongo_adapter, het_variant,
case_obj):
mongo_adapter = real_mongo_adapter
## GIVEN an adapter and a vcf
db = mongo_adapter.db
vcf = []
vcf.append(het_variant)
## WHEN loading the variant into the database
load_variants(
adapter=mongo_adapter,
vcf_obj=vcf,
case_obj=case_obj,
)
case_id = case_obj["case_id"]
case_id2 = "2"
case_obj["case_id"] = case_id2
load_variants(
adapter=mongo_adapter,
vcf_obj=vcf,
case_obj=case_obj,
)
mongo_variant = db.variant.find_one()
assert mongo_variant["observations"] == 2
assert mongo_variant["families"] == [case_id, case_id2]
def test_load_variants_skip_case_id(real_mongo_adapter, het_variant, case_obj):
mongo_adapter = real_mongo_adapter
## GIVEN an adapter and a vcf with tho heterygote variants
db = mongo_adapter.db
vcf = []
vcf.append(het_variant)
## WHEN loading the variants into the database
load_variants(
adapter=mongo_adapter,
vcf_obj=vcf,
case_obj=case_obj,
skip_case_id=True,
)
mongo_variant = db.variant.find_one()
## THEN assert that the variant is loaded correct
assert mongo_variant.get("families") == None
def test_load_two_variants(real_mongo_adapter, het_variant, case_obj):
mongo_adapter = real_mongo_adapter
## GIVEN an adapter and a vcf with tho heterygote variants
db = mongo_adapter.db
vcf = []
vcf.append(het_variant)
vcf.append(het_variant)
## WHEN loading the variants into the database
load_variants(
adapter=mongo_adapter,
vcf_obj=vcf,
case_obj=case_obj,
)
## THEN assert that the variant is loaded correct
mongo_variant = db.variant.find_one()
assert mongo_variant["observations"] == 2
def test_load_homozygote(real_mongo_adapter, hom_variant, case_obj):
mongo_adapter = real_mongo_adapter
## GIVEN an adapter and a vcf with one homozygote variant
db = mongo_adapter.db
vcf = []
vcf.append(hom_variant)
assert db.variant.find_one() == None
## WHEN loading the variant into the database
load_variants(
adapter=mongo_adapter,
vcf_obj=vcf,
case_obj=case_obj,
)
mongo_variant = db.variant.find_one()
## THEN assert that the variant is loaded correct
assert mongo_variant['families'] == [case_obj['case_id']]
assert mongo_variant['observations'] == 1
assert mongo_variant['homozygote'] == 1
assert mongo_variant['hemizygote'] == 0
def test_load_case_variants(real_mongo_adapter, case_obj):
mongo_adapter = real_mongo_adapter
db = mongo_adapter.db
## GIVEN a mongo adatper with snv variant file
vcf_obj = VCF(case_obj["vcf_path"])
## WHEN loading the variants
nr_variants = load_variants(
adapter=mongo_adapter,
vcf_obj=vcf_obj,
case_obj=case_obj,
)
nr_loaded = 0
for nr_loaded, variant in enumerate(db.variant.find(), 1):
pass
## THEN assert that the correct number of variants was loaded
assert nr_loaded > 0
assert nr_loaded == case_obj["nr_variants"]
def test_load_sv_case_variants(mongo_adapter, sv_case_obj):
db = mongo_adapter.db
## GIVEN a mongo adatper with snv variant file
vcf_obj = VCF(sv_case_obj["vcf_sv_path"])
## WHEN loading the variants
nr_variants = load_variants(
adapter=mongo_adapter,
vcf_obj=vcf_obj,
case_obj=sv_case_obj,
variant_type="sv",
)
nr_loaded_svs = 0
for nr_loaded_svs, variant in enumerate(db.structural_variant.find(), 1):
pass
nr_loaded_snvs = 0
for nr_loaded_snvs, variant in enumerate(db.variant.find(), 1):
pass
## THEN assert that the correct number of variants was loaded
assert nr_loaded_svs > 0
assert nr_loaded_snvs == 0
assert nr_loaded_svs == sv_case_obj["nr_sv_variants"]
def update_database(
adapter,
variant_file=None,
sv_file=None,
family_file=None,
family_type="ped",
skip_case_id=False,
gq_treshold=None,
case_id=None,
max_window=3000,
):
"""Update a case in the database
Args:
adapter: Connection to database
variant_file(str): Path to variant file
sv_file(str): Path to sv variant file
family_file(str): Path to family file
family_type(str): Format of family file
skip_case_id(bool): If no case information should be added to variants
gq_treshold(int): If only quality variants should be considered
case_id(str): If different case id than the one in family file should be used
max_window(int): Specify the max size for sv windows
Returns:
nr_inserted(int)
"""
vcf_files = []
nr_variants = None
vcf_individuals = None
if variant_file:
vcf_info = check_vcf(variant_file)
nr_variants = vcf_info["nr_variants"]
variant_type = vcf_info["variant_type"]
vcf_files.append(variant_file)
# Get the indivuduals that are present in vcf file
vcf_individuals = vcf_info["individuals"]
nr_sv_variants = None
sv_individuals = None
if sv_file:
vcf_info = check_vcf(sv_file, "sv")
nr_sv_variants = vcf_info["nr_variants"]
vcf_files.append(sv_file)
sv_individuals = vcf_info["individuals"]
# If a gq treshold is used the variants needs to have GQ
for _vcf_file in vcf_files:
# Get a cyvcf2.VCF object
vcf = get_vcf(_vcf_file)
if gq_treshold:
if not vcf.contains("GQ"):
LOG.warning(
"Set gq-treshold to 0 or add info to vcf {0}".format(
_vcf_file))
raise SyntaxError("GQ is not defined in vcf header")
# Get a ped_parser.Family object from family file
family = None
family_id = None
if family_file:
with open(family_file, "r") as family_lines:
family = get_case(family_lines=family_lines,
family_type=family_type)
family_id = family.family_id
# There has to be a case_id or a family at this stage.
case_id = case_id or family_id
# Convert infromation to a loqusdb Case object
case_obj = build_case(
case=family,
case_id=case_id,
vcf_path=variant_file,
vcf_individuals=vcf_individuals,
nr_variants=nr_variants,
vcf_sv_path=sv_file,
sv_individuals=sv_individuals,
nr_sv_variants=nr_sv_variants,
)
existing_case = adapter.case(case_obj)
if not existing_case:
raise CaseError("Case {} does not exist in database".format(
case_obj["case_id"]))
# Update the existing case in database
case_obj = load_case(
adapter=adapter,
case_obj=case_obj,
update=True,
)
nr_inserted = 0
# If case was succesfully added we can store the variants
for file_type in ["vcf_path", "vcf_sv_path"]:
variant_type = "snv"
if file_type == "vcf_sv_path":
variant_type = "sv"
if case_obj.get(file_type) is None:
continue
vcf_obj = get_vcf(case_obj[file_type])
try:
nr_inserted += load_variants(
adapter=adapter,
vcf_obj=vcf_obj,
case_obj=case_obj,
skip_case_id=skip_case_id,
gq_treshold=gq_treshold,
max_window=max_window,
variant_type=variant_type,
)
except Exception as err:
# If something went wrong do a rollback
LOG.warning(err)
delete(
adapter=adapter,
case_obj=case_obj,
update=True,
existing_case=existing_case,
)
raise err
return nr_inserted
