def test_remove_pathway(self):
source = os.path.join(os.path.dirname(__file__), "testfiles")
gene_set = fetch_reactome_geneset(source=source, species="H**o sapiens")
org_count = len(gene_set.gene_sets)
gene_set.remove_pathways(["R-HSA-2029481"])
self.assertEqual(org_count - 1, len(gene_set.gene_sets))
def test_build_from_url(self):
source = "https://reactome.org/download/current"
gene_set = fetch_reactome_geneset(source=source, species="H**o sapiens")
self.assertTrue("R-HSA-1980143" in gene_set.gene_sets)
self.assertEqual(150, len(gene_set.gene_sets["R-HSA-1980143"]))
def test_add_gene_set_interactors(self):
source = os.path.join(os.path.dirname(__file__), "testfiles")
gene_set = fetch_reactome_geneset(source=source, species="H**o sapiens")
filename = os.path.join(os.path.dirname(__file__), "testfiles", "IntAct_Static_100.txt")
interactors = load_reactome_interactors(filename)
org_gene_set = gene_set.copy()
gene_set.add_interactors(interactors)
# no change detectable with test files
self.assertEqual(len(gene_set.gene_sets["R-HSA-2029481"]), len(org_gene_set.gene_sets["R-HSA-2029481"]))
def test_build_from_file(self):
source = os.path.join(os.path.dirname(__file__), "testfiles")
gene_set = fetch_reactome_geneset(source=source, species="H**o sapiens")
self.assertTrue("R-HSA-2029481" in gene_set.gene_sets)
self.assertEqual(4, len(gene_set.gene_sets["R-HSA-2029481"]))
# make sure there is a name for every pathway
for gene_set_id in gene_set.gene_sets:
self.assertIsNotNone(gene_set.gene_set_names[gene_set_id])
def _get_gene_set(self):
# load the gene set
gene_set_file = os.path.join(gettempdir(), "test_gene_set.pkl")
if os.path.isfile(gene_set_file):
gene_set = geneset_builder.GeneSet.create_from_file(gene_set_file)
else:
gene_set = geneset_builder.fetch_reactome_geneset(source="https://reactome.org/download/current/",
species="H**o sapiens")
gene_set.save(gene_set_file)
return gene_set
def test_load_save(self):
source = os.path.join(os.path.dirname(__file__), "testfiles")
gene_set = fetch_reactome_geneset(source=source, species="H**o sapiens")
filename = os.path.join(gettempdir(), "reactome_human.pikl")
if os.path.isfile(filename):
os.unlink(filename)
gene_set.save(filename)
loaded_set = GeneSet.create_from_file(filename)
self.assertEqual(len(gene_set.gene_sets), len(loaded_set.gene_sets))
self.assertEqual(len(gene_set.gene_set_names), len(loaded_set.gene_set_names))