def variant(self, document_id, gene_panels=None, case_id=None):
"""Returns the specified variant.
Arguments:
document_id : A md5 key that represents the variant or "variant_id"
gene_panels(List[GenePanel])
case_id (str): case id (will search with "variant_id")
Returns:
variant_object(Variant): A odm variant object
"""
query = {}
if case_id:
# search for a variant in a case
query['case_id'] = case_id
query['variant_id'] = document_id
else:
# search with a unique id
query['_id'] = document_id
variant_obj = self.variant_collection.find_one(query)
if variant_obj:
variant_obj = self.add_gene_info(variant_obj, gene_panels)
if variant_obj['chromosome'] in ['X', 'Y']:
## TODO add the build here
variant_obj['is_par'] = is_par(variant_obj['chromosome'],
variant_obj['position'])
return variant_obj
def test_is_par_wrong_chromosome():
## GIVEN a position that is in the first par region
chromosome = "1"
position = 60001
build = "37"
## WHEN checking the coordinates for the positions
## THEN assert that there way a hit
assert is_par(chromosome, position, build) is False
def test_is_par():
## GIVEN a position that is in the first par region
chromosome = "X"
position = 60001
build = "37"
## WHEN checking the coordinates for a variant
## THEN assert that there way a hit
assert is_par(chromosome, position, build)
def test_is_par_wrong_chromosome():
## GIVEN a position that is in the first par region
chromosome = '1'
position = 60001
build = '37'
## WHEN checking the coordinates for the positions
## THEN assert that there way a hit
assert is_par(chromosome, position, build) is False
def test_is_par():
## GIVEN a position that is in the first par region
chromosome = 'X'
position = 60001
build = '37'
## WHEN checking the coordinates for a variant
## THEN assert that there way a hit
assert is_par(chromosome, position, build)
def variant(
self,
document_id=None,
gene_panels=None,
case_id=None,
simple_id=None,
variant_type="clinical",
):
"""Returns the specified variant.
Arguments:
document_id : A md5 key that represents the variant or "variant_id"
gene_panels(List[GenePanel])
case_id (str): case id (will search with "variant_id")
simple_id (str): a variant simple_id (example: 1_161184089_G_GTA)
variant_type(str): 'research' or 'clinical' - default 'clinical'
Returns:
variant_object(Variant): A odm variant object
"""
query = {}
if case_id and document_id:
# search for a variant in a case by variant_id
query["case_id"] = case_id
query["variant_id"] = document_id
elif case_id and simple_id:
# search for a variant in a case by its simple_id
query["case_id"] = case_id
query["simple_id"] = simple_id
query["variant_type"] = variant_type
else:
# search with a unique id
query["_id"] = document_id
variant_obj = self.variant_collection.find_one(query)
if not variant_obj:
return variant_obj
case_obj = self.case(case_id=variant_obj["case_id"])
if case_obj:
variant_obj = self.add_gene_info(
variant_obj=variant_obj,
gene_panels=gene_panels,
build=case_obj["genome_build"],
)
else:
variant_obj = self.add_gene_info(variant_obj=variant_obj,
gene_panels=gene_panels)
if variant_obj["chromosome"] in ["X", "Y"]:
# TO DO add the build here
variant_obj["is_par"] = is_par(variant_obj["chromosome"],
variant_obj["position"])
return variant_obj
