def test_multiple_mappings(self):
trait1 = trait.Trait("barrett esophagus/esophageal adenocarcinoma",
"http://www.ebi.ac.uk/efo/EFO_0000478",
"esophageal adenocarcinoma", 1)
trait2 = trait.Trait("barrett esophagus/esophageal adenocarcinoma",
"http://www.ebi.ac.uk/efo/EFO_0000280",
"Barrett's esophagus", 1)
test_trait_list = clinvar_to_evidence_strings.create_trait_list(
["barrett esophagus/esophageal adenocarcinoma"],
MAPPINGS.trait_2_efo, 1)
self.assertEqual([trait1, trait2], test_trait_list)
def create_trait_list(name_list, trait_2_efo_dict, trait_counter):
trait_string, mappings = trait.map_efo(trait_2_efo_dict, name_list)
if mappings is None:
return None
new_trait_list = []
for mapping in mappings:
new_trait_list.append(
trait.Trait(trait_string, mapping[0], mapping[1], trait_counter))
# Only ClinVar records associated to a
# trait with mapped EFO term will generate evidence_strings
if not new_trait_list:
return None
return new_trait_list