def get_project_variants_in_gene(self,
project_id,
gene_id,
variant_filter=None):
if variant_filter is None:
modified_variant_filter = VariantFilter()
else:
modified_variant_filter = copy.deepcopy(variant_filter)
modified_variant_filter.add_gene(gene_id)
db_query = self._make_db_query(None, modified_variant_filter)
sys.stderr.write("Project Gene Search: " + str(project_id) +
" all variants query: " + str(db_query))
collection = self._get_project_collection(project_id)
# we have to collect list in memory here because mongo can't sort on xpos,
# as result size can get too big.
# need to find a better way to do this.
variants = []
for variant_dict in collection.find(db_query).hint([
('db_gene_ids', pymongo.ASCENDING), ('xpos', pymongo.ASCENDING)
]):
variant = Variant.fromJSON(variant_dict)
self.add_annotations_to_variant(variant, project_id)
if passes_variant_filter(variant, modified_variant_filter):
variants.append(variant)
variants = sorted(variants, key=lambda v: v.unique_tuple())
return variants
def get_variants_in_gene(self,
project_id,
family_id,
gene_id,
genotype_filter=None,
variant_filter=None):
if variant_filter is None:
modified_variant_filter = VariantFilter()
else:
modified_variant_filter = copy.deepcopy(variant_filter)
modified_variant_filter.add_gene(gene_id)
db_query = self._make_db_query(genotype_filter,
modified_variant_filter)
collection = self._get_family_collection(project_id, family_id)
if not collection:
return
# we have to collect list in memory here because mongo can't sort on xpos,
# as result size can get too big.
# need to find a better way to do this.
variants = []
for variant_dict in collection.find(db_query).hint([
('db_gene_ids', pymongo.ASCENDING), ('xpos', pymongo.ASCENDING)
]):
variant = Variant.fromJSON(variant_dict)
self.add_annotations_to_variant(variant, project_id)
if passes_variant_filter(variant, modified_variant_filter):
variants.append(variant)
variants = sorted(variants, key=lambda v: v.unique_tuple())
for v in variants:
yield v
def get_variants_by_family_for_gene(mall,
family_list,
inheritance_mode,
gene_id,
variant_filter=None,
quality_filter=None,
user=None):
if variant_filter is None:
variant_filter = VariantFilter()
variant_filter.add_gene(gene_id)
by_family = {}
for family in family_list:
family_t = (family.project_id, family.family_id)
variants = list(
get_variants_with_inheritance_mode(
mall,
family,
inheritance_mode,
variant_filter,
quality_filter,
user=user,
))
by_family[family_t] = variants
return by_family
def get_project_variants_in_gene(self, project_id, gene_id, variant_filter=None, user=None):
if variant_filter is None:
modified_variant_filter = VariantFilter()
else:
modified_variant_filter = copy.deepcopy(variant_filter)
modified_variant_filter.add_gene(gene_id)
variants = [variant for variant in self.get_elasticsearch_variants(project_id, variant_filter=modified_variant_filter, user=user, max_results_limit=9999)]
return variants
def get_variants_in_gene(self, project_id, family_id, gene_id, genotype_filter=None, variant_filter=None):
if variant_filter is None:
modified_variant_filter = VariantFilter()
else:
modified_variant_filter = copy.deepcopy(variant_filter)
modified_variant_filter.add_gene(gene_id)
#db_query = self._make_db_query(genotype_filter, modified_variant_filter, user=None)
raise ValueError("Not Implemented")
def get_project_variants_in_gene(self, project_id, gene_id, variant_filter=None, user=None):
if variant_filter is None:
modified_variant_filter = VariantFilter()
else:
modified_variant_filter = copy.deepcopy(variant_filter)
modified_variant_filter.add_gene(gene_id)
variants = [variant for variant in self.get_elasticsearch_variants(project_id, variant_filter=modified_variant_filter, user=user, max_results_limit=9999)]
return variants
def get_variants_in_gene(self, project_id, family_id, gene_id, genotype_filter=None, variant_filter=None):
if variant_filter is None:
modified_variant_filter = VariantFilter()
else:
modified_variant_filter = copy.deepcopy(variant_filter)
modified_variant_filter.add_gene(gene_id)
#db_query = self._make_db_query(genotype_filter, modified_variant_filter, user=None)
raise ValueError("Not Implemented")
def get_variants_in_gene(self, project_id, gene_id, variant_filter=None):
if variant_filter is None:
modified_variant_filter = VariantFilter()
else:
modified_variant_filter = copy.deepcopy(variant_filter)
modified_variant_filter.add_gene(gene_id)
db_query = self._make_db_query(None, modified_variant_filter)
collection = self._get_project_collection(project_id)
variants = []
for variant_dict in collection.find(db_query).hint([('gene_ids', pymongo.ASCENDING), ('xpos', pymongo.ASCENDING)]):
variant = Variant.fromJSON(variant_dict)
if passes_variant_filter(variant, modified_variant_filter):
variants.append(variant)
variants = sorted(variants, key=lambda v: v.unique_tuple())
return variants
def get_variants_by_family_for_gene(mall, family_list, inheritance_mode, gene_id, variant_filter=None, quality_filter=None):
if variant_filter is None:
variant_filter = VariantFilter()
variant_filter.add_gene(gene_id)
by_family = {}
for family in family_list:
family_t = (family.project_id, family.family_id)
variants = list(get_variants_with_inheritance_mode(
mall,
family,
inheritance_mode,
variant_filter,
quality_filter
))
by_family[family_t] = variants
return by_family
def get_project_variants_in_gene(self, project_id, gene_id, variant_filter=None):
if variant_filter is None:
modified_variant_filter = VariantFilter()
else:
modified_variant_filter = copy.deepcopy(variant_filter)
modified_variant_filter.add_gene(gene_id)
db_query = self._make_db_query(None, modified_variant_filter)
logger.info("Project Gene Search: " + str(project_id) + " all variants query: " + str(db_query))
collection = self._get_project_collection(project_id)
# we have to collect list in memory here because mongo can't sort on xpos,
# as result size can get too big.
# need to find a better way to do this.
variants = [Variant.fromJSON(variant_dict) for variant_dict in collection.find(db_query).hint([('db_gene_ids', pymongo.ASCENDING), ('xpos', pymongo.ASCENDING)])]
self.add_annotations_to_variants(variants, project_id)
variants = filter(lambda variant: passes_variant_filter(variant, modified_variant_filter), variants)
variants = sorted(variants, key=lambda v: v.unique_tuple())
return variants
def get_variants_in_gene(self, project_id, family_id, gene_id, genotype_filter=None, variant_filter=None):
if variant_filter is None:
modified_variant_filter = VariantFilter()
else:
modified_variant_filter = copy.deepcopy(variant_filter)
modified_variant_filter.add_gene(gene_id)
db_query = _make_db_query(genotype_filter, modified_variant_filter)
collection = self._get_family_collection(project_id, family_id)
# we have to collect list in memory here because mongo can't sort on xpos,
# as result size can get too big.
# need to find a better way to do this.
variants = []
for variant_dict in collection.find(db_query).hint([('gene_ids', pymongo.ASCENDING), ('xpos', pymongo.ASCENDING)]):
variant = Variant.fromJSON(variant_dict)
if passes_variant_filter(variant, modified_variant_filter):
variants.append(variant)
variants = sorted(variants, key=lambda v: v.unique_tuple())
for v in variants:
yield v
