def testFakeDataSet1(self):
string_db = StringDB('rdf_graph', True)
string_db.graph = RDFGraph(True)
self.assertEqual(len(string_db.graph), 0)
ensembl = Ensembl('rdf_graph', True)
prot_map = ensembl.fetch_protein_gene_map('9606')
[prot_map.update({k: ['ENSEMBL:' + prot_map[k]]}) for k in prot_map.keys()]
print("Finished fetching ENSP IDs, fetched {} proteins".format(len(prot_map)))
# just looking
# for key in prot_map:
# if string_db.graph.curie_regexp.match(prot_map[key]) is None:
# print("INVALID curie for %s from %s", prot_map[key], key)
dataframe = pd.DataFrame(data=self.test_set_1, columns=self.columns)
string_db._process_protein_links(dataframe, prot_map, '9606')
# g1 <interacts with> g2
triples = """
ENSEMBL:ENSG00000001626 RO:0002434 ENSEMBL:ENSG00000004059 .
"""
self.assertTrue(self.test_util.test_graph_equality(triples, string_db.graph))
def testFakeDataSet2(self):
"""
Dataset contains a deprecated protein ID
that we expect if filtered out by ensembl biomart
We test that this returns an empty graph
:return:
"""
string_db = StringDB('rdf_graph', True)
string_db.graph = RDFGraph()
self.assertEqual(len(string_db.graph), 0)
dataframe = pd.DataFrame(data=self.test_set_2, columns=self.columns)
string_db._process_protein_links(dataframe, self.protein_list, '9606')
self.assertEqual(len(string_db.graph), 0)
def testFakeDataSet2(self):
"""
Dataset contains a deprecated protein ID
that we expect if filtered out by ensembl biomart
We test that this returns an empty graph
:return:
"""
string_db = StringDB('rdf_graph', True)
string_db.graph = RDFGraph()
self.assertEqual(len(string_db.graph), 0)
dataframe = pd.DataFrame(data=self.test_set_2, columns=self.columns)
string_db._process_protein_links(dataframe, self.protein_list, 9606)
self.assertEqual(len(string_db.graph), 0)
def testFakeDataSet1(self):
string_db = StringDB('rdf_graph', True)
string_db.graph = RDFGraph(True)
self.assertEqual(len(string_db.graph), 0)
ensembl = Ensembl('rdf_graph', True)
prot_map = ensembl.fetch_protein_gene_map(9606)
for key in prot_map.keys():
prot_map[key] = "ENSEMBL:{}".format(prot_map[key])
print("Finished fetching ENSP IDs, "
"fetched {} proteins".format(len(prot_map.keys())))
dataframe = pd.DataFrame(data=self.test_set_1, columns=self.columns)
string_db._process_protein_links(dataframe, prot_map, 9606)
triples = """
ENSEMBL:ENSG00000001626 RO:0002434 ENSEMBL:ENSG00000004059 .
"""
self.assertTrue(self.test_util.test_graph_equality(
triples, string_db.graph))
def testFakeDataSet1(self):
string_db = StringDB('rdf_graph', True)
string_db.graph = RDFGraph(True)
self.assertEqual(len(string_db.graph), 0)
ensembl = Ensembl('rdf_graph', True)
prot_map = ensembl.fetch_protein_gene_map(9606)
for key in prot_map.keys():
prot_map[key] = "ENSEMBL:{}".format(prot_map[key])
print("Finished fetching ENSP IDs, fetched {} proteins".format(
len(prot_map.keys())))
dataframe = pd.DataFrame(data=self.test_set_1, columns=self.columns)
string_db._process_protein_links(dataframe, prot_map, 9606)
triples = """
ENSEMBL:ENSG00000001626 RO:0002434 ENSEMBL:ENSG00000004059 .
"""
self.assertTrue(
self.test_util.test_graph_equality(triples, string_db.graph))