def testBuildMimDiseasesDict(self):
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)
gene_tuples_dict = {}
for mimid, mimdisease in mim_diseases.iteritems():
gene_tuples_dict[mimid] = mimdisease.genetuples
desired_gene_tuples = {
'604367': [('5468', 'C')], '125853': [('5468', 'C')],
'609734': [('5443', 'C')], '609338': [('5468', 'C')],
'601665': [('8431', 'P'), ('5443', 'C'), ('51738', 'P'),
('5468', 'C'), ('6492', 'C'), ('4160', 'C')]
}
phetypes_dict = {}
for mimid, mimdisease in mim_diseases.iteritems():
phetypes_dict[mimid] = mimdisease.phe_mm
desired_phenotypes = {'604367': '(3)', '125853': '(3)',
'609734': '(3)', '609338': '(3)',
'601665': '(3)'}
self.assertEqual(gene_tuples_dict, desired_gene_tuples)
self.assertEqual(phetypes_dict, desired_phenotypes)
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 testBuildMim2EntrezDict(self):
mim2gene_file = 'test_files/DO/test_mim2gene.csv'
mim2entrez_dict = process_do.build_mim2entrez_dict(mim2gene_file)
desired_output = {'155541': '4160', '604630': '8431', '601487': '5468',
'605353': '51738', '176830': '5443',
'603128': '6492', '100640': '216', '616919': '22844',
'616923': '388591'}
self.assertEqual(mim2entrez_dict, desired_output)