def test_check_vcf_wrong_type(sv_vcf_path):
## GIVEN a sv vcf file
## WHEN collecting the VCF info with wrong variant type
## THEN assert that a VcfError is raised
with pytest.raises(VcfError):
vcf_info = check_vcf(sv_vcf_path, 'snv')
def test_check_sv_vcf(sv_vcf_path):
## GIVEN a vcf file and a counter that checks the number of variants
true_nr = 0
with open(sv_vcf_path, "r") as f:
for line in f:
if not line.startswith("#"):
true_nr += 1
## WHEN collecting the VCF info
vcf_info = check_vcf(sv_vcf_path, "sv")
## THEN assert that the number of variants collected is correct
assert vcf_info["nr_variants"] == true_nr
## THEN assert that the variant type is correct
assert vcf_info["variant_type"] == "sv"
def test_check_vcf_correct(vcf_path):
## GIVEN a vcf file and a counter that checks the number of variants
true_nr = 0
with open(vcf_path, 'r') as f:
for line in f:
if not line.startswith('#'):
true_nr += 1
## WHEN collecting the VCF info
vcf_info = check_vcf(vcf_path)
## THEN assert that the number of variants collected is correct
assert vcf_info['nr_variants'] == true_nr
## THEN assert that the variant type is correct
assert vcf_info['variant_type'] == 'snv'
def test_get_profiles(real_mongo_adapter, profile_vcf_path, zipped_vcf_path):
# Load profile variants
load_profile_variants(real_mongo_adapter, profile_vcf_path)
vcf_info = check_vcf(zipped_vcf_path)
# Get profiles from vcf
profiles = get_profiles(real_mongo_adapter, zipped_vcf_path)
# Assert that all individuals are included
assert list(profiles.keys()) == vcf_info["individuals"]
# Assert that profile strings are of same lengths
for i, individual in enumerate(profiles.keys()):
if i == 0:
length = len(profiles[individual])
assert len(profiles[individual]) == length
def test_check_vcf(vcf_path):
## GIVEN the path to a vcf
nr_variants = 0
vcf = VCF(vcf_path)
inds = vcf.samples
for var in vcf:
nr_variants += 1
## WHEN checking the vcf
vcf_info = check_vcf(vcf_path)
## THEN assert that the number of variants is correct
assert vcf_info['nr_variants'] == nr_variants
## THEN assert that the individuals are returned
assert vcf_info['individuals'] == inds
## THEN assert that the variant type is correct
assert vcf_info['variant_type'] == 'snv'
def load_profile_variants(adapter, variant_file):
"""
Loads variants used for profiling
Args:
adapter (loqusdb.plugins.Adapter): initialized plugin
variant_file(str): Path to variant file
"""
vcf_info = check_vcf(variant_file)
nr_variants = vcf_info["nr_variants"]
variant_type = vcf_info["variant_type"]
if variant_type != "snv":
LOG.critical("Variants used for profiling must be SNVs only")
raise VcfError
vcf = get_vcf(variant_file)
profile_variants = [build_profile_variant(variant) for variant in vcf]
adapter.add_profile_variants(profile_variants)
def test_check_vcf_unsorted(unsorted_vcf_path):
## GIVEN a vcf file with unsorted variants
## WHEN checking the vcf
## THEN assert that the function raises a VcfError
with pytest.raises(VcfError):
check_vcf(unsorted_vcf_path)
def test_check_vcf_double_variant(double_vcf_path):
## GIVEN a variant file where a variant is duplicated
## WHEN checking the vcf
## THEN assert that the function raises a VcfError
with pytest.raises(VcfError):
check_vcf(double_vcf_path)
def load_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,
profile_file=None,
hard_threshold=0.95,
soft_threshold=0.9,
genome_build=None,
):
"""Load the database with a case and its variants
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
check_profile(bool): Does profile check if True
hard_threshold(float): Rejects load if hamming distance above this is found
soft_threshold(float): Stores similar samples if hamming distance above this is found
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"]
profiles = None
matches = None
if profile_file:
profiles = get_profiles(adapter, profile_file)
###Check if any profile already exists
matches = profile_match(adapter,
profiles,
hard_threshold=hard_threshold,
soft_threshold=soft_threshold)
# 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 and 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:
LOG.info("Loading family from %s", 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,
profiles=profiles,
matches=matches,
profile_path=profile_file,
)
# Build and load a new case, or update an existing one
load_case(
adapter=adapter,
case_obj=case_obj,
)
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,
genome_build=genome_build,
)
except Exception as err:
# If something went wrong do a rollback
LOG.warning(err)
delete(
adapter=adapter,
case_obj=case_obj,
)
raise err
return nr_inserted
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
