def test_xn2vParser_wrong_path(self):
with self.assertRaises(Exception):
xn2vParser(data_dir="tests/dataty", params=params)
with self.assertRaises(Exception):
xn2vParser(data_dir="tests/test_xn2vParser.py", params=params)
with self.assertRaises(Exception):
xn2vParser(data_dir="tests/data")
def test_parse(self):
p = xn2vParser(data_dir="tests/data", params=params)
# TODO: currently testing only execution, in
# the future it will be necessary to also test
# if the return value is correct
p.parse()
p.output_ensembl_gene2gene_id("output.test.txt")
os.remove("output.test.txt")
p.get_gene_disease_count()
p.get_ensembl_gene2gene_map_count()
p.get_unique_string_protein_set()
p.get_string_valid_ppi_count()
p.get_string_raw_ppi_count()
p.get_protein2gene_map_count()
p.output_nodes_and_edges_test_set("output.tsv")
os.remove("output.tsv")
p.output_nodes_and_edges("output.tsv")
os.remove("output.tsv")
p.gene_protein_disease_edges("output.tsv")
os.remove("output.tsv")
d2d_path = os.path.join(data_download_dir,
'pairwise_disease_similarity_9_2017.tsv')
if not os.path.isfile(d2d_path):
log.error(
"You need to run pairdc and put its output file (e.g., pairwise_disease_similarity.tsv) into the data directory."
)
log.error("Could not find {}".format(d2d_path))
sys.exit(1)
parameters = {
'string_threshold': 700,
'gtex_threshold': 0.9,
'gtex_path': gtex_path,
'gene2ensembl_path': gene2ensembl_path,
'string_path': string_path,
'tcrd_path': TCRD_path,
'g2d_train_path': g2d_training_path,
'g2d_test_path': g2d_test_path,
'd2d_path': d2d_path
}
parser = xn2vParser(params=parameters)
parser.parse()
parser.print_summary()
outfilename_training = "edgelist.txt"
parser.gene_protein_disease_edges(outfilename_training)
parser.output_nodes_and_edges(outfilename_training)
outfilename_test = "g2d_test.txt"
parser.output_nodes_and_edges_test_set(outfilename_test)
def test_summary(self):
p = xn2vParser(data_dir="tests/data", params=params)
# TODO: currently testing only execution,
# but the following method currently
# consists only of a "pass"
p.print_summary()
def test_get_number_proteins_found_TCRD(self):
p = xn2vParser(data_dir="tests/data", params=params)
# TODO: currently testing only execution, in
# the future it will be necessary to also test
# if the return value is correct
p.get_number_proteins_found_TCRD()
def test_xn2vParser_init(self):
p = xn2vParser(data_dir="tests/data", params=params)
p.qc_input()