def testAddDOTermAnnotations(self):
do_obo_file = 'test_files/DO/test_do_obo_file.obo'
doid_omim_dict = process_do.build_doid_omim_dict(do_obo_file)
mim2gene_file = 'test_files/DO/test_mim2gene.csv'
genemap_file = 'test_files/DO/test_genemap.csv'
mim2entrez_dict = process_do.build_mim2entrez_dict(mim2gene_file)
mim_diseases = process_do.build_mim_diseases_dict(genemap_file,
mim2entrez_dict)
process_do.add_do_term_annotations(
doid_omim_dict, self.disease_ontology, mim_diseases)
# We know from testBuildOmimDict above that this is the only
# one with OMIM xrefs
doid = 'DOID:9970'
do_term = self.disease_ontology.get_term(doid)
annot_dict = {}
for annotation in do_term.annotations:
if annotation.gid not in annot_dict:
annot_dict[annotation.gid] = []
else:
annot_dict[annotation.gid].append(annotation.ref)
desired_annots = {4160: [], 8431: [], 51738: [], 5443: [],
5468: [], 6492: []}
self.assertEqual(annot_dict, desired_annots)
def testBuildOmimDict(self):
do_obo_file = 'test_files/DO/test_do_obo_file.obo'
doid_omim_dict = process_do.build_doid_omim_dict(do_obo_file)
# Only one of the DO terms in the test DO OBO file has an
# OMIM xref
desired_output = {'DOID:9970': set(['601665'])}
self.assertEqual(doid_omim_dict, desired_output)
def testCreateDOAbstractTitle(self):
do_obo_file = 'test_files/DO/test_do_obo_file.obo'
doid_omim_dict = process_do.build_doid_omim_dict(do_obo_file)
# We know from testBuildOmimDict above that this is the only
# one with OMIM xrefs
doid = 'DOID:9970'
do_term = self.disease_ontology.get_term(doid)
abstract = process_do.create_do_term_abstract(do_term, doid_omim_dict)
desired_abstract = ' Annotations from child terms in the disease ' + \
'ontology are propagated through transitive closure. ' + \
'Annotations directly to this term are provided by the OMIM' + \
' disease ID 601665. Only annotations with confidence labeled' + \
' C or P by OMIM have been added.'
self.assertEqual(abstract, desired_abstract)