def delete(adapter,
variant_file,
family_file,
family_type='ped',
case_id=None):
"""Delete a case and all of it's variants from the database"""
vcf = get_vcf(variant_file)
with open(family_file, 'r') as family_lines:
family = get_family(family_lines=family_lines, family_type=family_type)
family_id = family.family_id
if case_id:
family_id = case_id
individuals = family.individuals
vcf_individuals = vcf.samples
ind_positions = {}
for i, ind_id in enumerate(vcf_individuals):
ind_positions[ind_id] = i
delete_family(adapter=adapter, family_id=family_id)
delete_variants(adapter=adapter,
vcf=vcf,
ind_positions=ind_positions,
family_id=family_id,
individuals=individuals)
def load_database(adapter, variant_file, family_file, nr_variants=None,
family_type='ped', skip_case_id=False, gq_treshold=None,
case_id=None):
"""Load the database with a case and its variants
Args:
adapter
variant_file(str)
family_file(str)
family_type(str)
skip_case_id(bool)
"""
vcf = get_vcf(variant_file)
with open(family_file, 'r') as family_lines:
family = get_family(
family_lines=family_lines,
family_type=family_type
)
family_id = family.family_id
if case_id:
family_id = case_id
if not family.affected_individuals:
logger.warning("No affected individuals could be found in ped file")
logger.info("Found affected individuals in ped file: {0}"
.format(', '.join(family.affected_individuals)))
load_family(
adapter=adapter,
case_id=family_id,
vcf_path=variant_file
)
load_variants(
adapter=adapter,
family_id=family_id,
individuals=family.individuals,
vcf=vcf,
nr_variants=nr_variants,
skip_case_id=skip_case_id,
gq_treshold=gq_treshold,
)
def load_database(
adapter,
variant_file,
family_file,
nr_variants=None,
family_type="ped",
skip_case_id=False,
gq_treshold=None,
case_id=None,
):
"""Load the database with a case and its variants
Args:
adapter
variant_file(str)
family_file(str)
family_type(str)
skip_case_id(bool)
"""
vcf = get_vcf(variant_file)
with open(family_file, "r") as family_lines:
family = get_family(family_lines=family_lines, family_type=family_type)
family_id = family.family_id
if case_id:
family_id = case_id
if not family.affected_individuals:
logger.warning("No affected individuals could be found in ped file")
logger.info("Found affected individuals in ped file: {0}".format(", ".join(family.affected_individuals)))
load_family(adapter=adapter, case_id=family_id, vcf_path=variant_file)
load_variants(
adapter=adapter,
family_id=family_id,
individuals=family.individuals,
vcf=vcf,
nr_variants=nr_variants,
skip_case_id=skip_case_id,
gq_treshold=gq_treshold,
)
def delete(adapter, variant_file, family_file, family_type="ped", case_id=None):
"""Delete a case and all of it's variants from the database"""
vcf = get_vcf(variant_file)
with open(family_file, "r") as family_lines:
family = get_family(family_lines=family_lines, family_type=family_type)
family_id = family.family_id
if case_id:
family_id = case_id
individuals = family.individuals
delete_family(adapter=adapter, family_id=family_id)
delete_variants(adapter=adapter, vcf=vcf, family_id=family_id, individuals=individuals)
def delete(adapter,
variant_file,
family_file,
family_type='ped',
case_id=None):
"""Delete a case and all of it's variants from the database"""
vcf = get_vcf(variant_file)
with open(family_file, 'r') as family_lines:
family = get_family(family_lines=family_lines, family_type=family_type)
family_id = family.family_id
if case_id:
family_id = case_id
individuals = family.individuals
delete_family(adapter=adapter, family_id=family_id)
delete_variants(adapter=adapter,
vcf=vcf,
family_id=family_id,
individuals=individuals)
def load_database(adapter,
variant_file,
family_file,
nr_variants=None,
family_type='ped',
skip_case_id=False,
gq_treshold=None,
case_id=None):
"""Load the database with a case and its variants
Args:
adapter
variant_file(str)
family_file(str)
family_type(str)
skip_case_id(bool)
"""
vcf = get_vcf(variant_file)
if gq_treshold:
if not vcf.contains('GQ'):
logger.warning('Set gq-treshold to 0 or add info to vcf')
raise SyntaxError('GQ is not defined in vcf header')
with open(family_file, 'r') as family_lines:
family = get_family(family_lines=family_lines, family_type=family_type)
family_id = family.family_id
if case_id:
family_id = case_id
if not family.affected_individuals:
logger.warning("No affected individuals could be found in ped file")
logger.debug("Found affected individuals in ped file: {0}".format(
', '.join(family.affected_individuals)))
vcf_individuals = vcf.samples
ind_positions = {}
for i, ind_id in enumerate(vcf_individuals):
ind_positions[ind_id] = i
for ind_id in family.individuals:
if ind_id not in ind_positions:
raise CaseError(
"Ind {0} in ped file does not exist in VCF".format(ind_id))
load_family(adapter=adapter, case_id=family_id, vcf_path=variant_file)
try:
load_variants(
adapter=adapter,
family_id=family_id,
individuals=family.individuals,
vcf=vcf,
ind_positions=ind_positions,
nr_variants=nr_variants,
skip_case_id=skip_case_id,
gq_treshold=gq_treshold,
)
except Exception as err:
logger.warning(err)
##TODO Delete inserted information here
raise err