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 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 affected_individuals(ped_path):
"""Extract affected individuals from a PED file.
Args:
ped_path (path): path to the PED file
Returns:
list: list of affected individuals
"""
with open(ped_path, 'r') as ped_stream:
locus_fam = get_family(family_lines=ped_stream, family_type='alt')
if not locus_fam.affected_individuals:
logger.warn('no affected individuals in ped file')
return None
return locus_fam.affected_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 affected_individuals(ped_path):
"""Extract affected individuals from a PED file.
Args:
ped_path (path): path to the PED file
Returns:
list: list of affected individuals
Raises:
mip2scout.exc.FrequencyError: if no affected individals in PED
"""
with open(ped_path, 'r') as ped_stream:
locus_fam = get_family(family_lines=ped_stream, family_type='alt')
if not locus_fam.affected_individuals:
message = "no affected individuals in ped file"
logger.error(message)
raise FrequencyError(message)
return locus_fam.affected_individuals
def load(ctx, variant_file, family_file, family_type, bulk_insert):
"""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.error("Please provide a family file")
ctx.abort()
if variant_file == '-':
logger.info("Parsing variants from stdin")
variant_file = get_vcf_handle(fsock=sys.stdin)
else:
logger.info("Start parsing variants from stdin")
variant_path = os.path.abspath(variant_file)
variant_file = get_vcf_handle(infile=variant_file)
try:
family = get_family(family_lines=family_file, family_type=family_type)
except SyntaxError as error:
logger.warning(error.message)
ctx.abort()
if not family.affected_individuals:
logger.error("No affected individuals could be found in ped file")
ctx.abort()
logger.info("Found affected individuals in ped file: {0}"
.format(', '.join(family.affected_individuals)))
adapter = ctx.obj['adapter']
try:
load_variants(adapter, family.family_id, family.affected_individuals,
variant_file, bulk_insert=bulk_insert,
vcf_path=variant_path)
except CaseError as error:
logger.error(error.message)
ctx.abort()
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
def test_get_family(case_lines):
family = get_family(case_lines)
assert family.family_id == 'recessive_trio'
def test_get_multiple_families(two_cases):
with pytest.raises(CaseError):
family = get_family(two_cases)
def test_get_multiple_families(two_cases):
with pytest.raises(CaseError):
family = get_family(two_cases)
def test_get_family(case_lines):
family = get_family(case_lines)
assert family.family_id == 'recessive_trio'
