def get_cases(variant_source, case_lines=None, case_type='ped',
variant_type='snv', variant_mode='vcf'):
"""Create a cases and populate it with individuals
Args:
variant_source (str): Path to vcf files
case_lines (Iterable): Ped like lines
case_type (str): Format of case lines
Returns:
case_objs (list(puzzle.models.Case))
"""
individuals = get_individuals(
variant_source=variant_source,
case_lines=case_lines,
case_type=case_type,
variant_mode=variant_mode
)
case_objs = []
case_ids = set()
compressed = False
tabix_index = False
#If no individuals we still need to have a case id
if variant_source.endswith('.gz'):
logger.debug("Found compressed variant source")
compressed = True
tabix_file = '.'.join([variant_source, 'tbi'])
if os.path.exists(tabix_file):
logger.debug("Found index file")
tabix_index = True
for individual in individuals:
case_ids.add(individual.case_id)
for case_id in case_ids:
logger.info("Found case {0}".format(case_id))
case = Case(
case_id=case_id,
name=case_id,
variant_source=variant_source,
variant_type=variant_type,
variant_mode=variant_mode,
compressed=compressed,
tabix_index=tabix_index
)
# Add the individuals to the correct case
for individual in individuals:
if individual.case_id == case_id:
logger.info("Adding ind {0} to case {1}".format(
individual.name, individual.case_id
))
case.add_individual(individual)
case_objs.append(case)
return case_objs
def _get_cases(self, individuals):
"""Return the cases found in the database
Args:
individuals(list): List of Individuals
Returns:
case_objs(list): List of Cases
"""
case_objs = []
case_ids = set()
logger.info("Looking for cases in {0}".format(
self.db
))
for individual in individuals:
case_ids.add(individual.case_id)
for case_id in case_ids:
logger.info("Found case {0}".format(case_id))
case = Case(
case_id=case_id,
name=case_id,
variant_source=self.db,
variant_type=self.variant_type,
variant_mode='gemini',
)
# Add the individuals to the correct case
for individual in individuals:
if individual.case_id == case_id:
logger.info("Adding ind {0} to case {1}".format(
individual.name, individual.case_id
))
case.add_individual(individual)
case_objs.append(case)
return case_objs
def get_case(variant_source, case_lines=None, case_type='ped', variant_type='snv',
variant_mode='vcf'):
"""Create a cases and populate it with individuals
Args:
variant_source (str): Path to vcf files
case_lines (Iterable): Ped like lines
case_type (str): Format of case lines
Returns:
case_objs (list): List with Case objects
"""
individuals = get_individuals(
vcf=variant_source,
case_lines=case_lines,
case_type=case_type,
)
#If no individuals we still need to have a case id
case_id = os.path.basename(variant_source)
for individual in individuals:
case_id = individual.case_id
case = Case(case_id=case_id, variant_source=variant_source,
name=case_id, variant_type=variant_type,
variant_mode=variant_mode,
)
logger.debug("Found case with case_id: {0} and name: {1}".format(
case.case_id, case.name))
for individual in individuals:
case.add_individual(individual)
return case
def get_cases(variant_source, case_lines=None, case_type='ped',
variant_type='snv', variant_mode='vcf'):
"""Create a cases and populate it with individuals
Args:
variant_source (str): Path to vcf files
case_lines (Iterable): Ped like lines
case_type (str): Format of case lines
Returns:
case_objs (list(puzzle.models.Case))
"""
individuals = get_individuals(
variant_source=variant_source,
case_lines=case_lines,
case_type=case_type,
variant_mode=variant_mode
)
case_objs = []
case_ids = set()
compressed = False
tabix_index = False
#If no individuals we still need to have a case id
if variant_source.endswith('.gz'):
logger.debug("Found compressed variant source")
compressed = True
tabix_file = '.'.join([variant_source, 'tbi'])
if os.path.exists(tabix_file):
logger.debug("Found index file")
tabix_index = True
if len(individuals) > 0:
for individual in individuals:
case_ids.add(individual.case_id)
else:
case_ids = [os.path.basename(variant_source)]
for case_id in case_ids:
logger.info("Found case {0}".format(case_id))
case = Case(
case_id=case_id,
name=case_id,
variant_source=variant_source,
variant_type=variant_type,
variant_mode=variant_mode,
compressed=compressed,
tabix_index=tabix_index
)
# Add the individuals to the correct case
for individual in individuals:
if individual.case_id == case_id:
logger.info("Adding ind {0} to case {1}".format(
individual.name, individual.case_id
))
case.add_individual(individual)
case_objs.append(case)
return case_objs
Args:
case_id (str): A case id
Returns:
A Case object
"""
if case_id:
for case in self.case_objs:
if case.case_id == case_id:
return case
else:
if self.cases:
return list(self.case_objs)[0]
return Case(case_id='unknown')
def individual(self, ind_id=None):
"""Return a individual object
Args:
ind_id (str): A individual id
Returns:
individual (puzzle.models.individual)
"""
for ind_obj in self.individual_objs:
if ind_obj.ind_id == ind_id:
return ind_obj
return None
