def get_variants(chromosome, start, end):
"""
Return all variants between [chrom, start) and (chrom, end]
"""
q = db_session.query(orm.Variant)
q = q.filter_by(chromosome=chromosome).filter(and_(start >= start, start <= end))
return [orm.dump(p) for p in q]
def get_variants_by_individual(individual_id):
"""
Return variants that have been called in an individual
"""
ind_id = individual_id
ind = db_session.query(orm.Individual).filter(orm.Individual.id == ind_id).one_or_none()
if not ind:
return NoContent, 404
variants = [call.variant for call in ind.calls if call.variant is not None]
return [orm.dump(v) for v in variants], 200
def get_individuals_by_variant(variant_id):
"""
Return variants that have been called in an individual
"""
var_id = variant_id
var = db_session.query(orm.Variant).filter(orm.Variant.id == var_id).one_or_none()
if not var:
return NoContent, 404
individuals = [call.individual for call in var.calls if call.individual is not None]
return [orm.dump(i) for i in individuals], 200
def get_calls():
"""
Return all calls
"""
q = db_session.query(orm.Call)
return [orm.dump(p) for p in q]
def get_individuals():
"""
Return all individuals
"""
q = db_session.query(orm.Individual)
return [orm.dump(p) for p in q]