diff --git a/indra/databases/mirbase_client.py b/indra/databases/mirbase_client.py index 4e07f7ce9e..2c2ce6aa98 100644 --- a/indra/databases/mirbase_client.py +++ b/indra/databases/mirbase_client.py @@ -109,7 +109,8 @@ def _read(): next(file) for line in file: try: - mirbase_id, mirbase_name, db, identifier, name = line.strip().split('\t') + mirbase_id, mirbase_name, db, identifier, name = \ + line.strip().split('\t') except ValueError: # fails on WORMBASE since no names continue diff --git a/indra/resources/update_resources.py b/indra/resources/update_resources.py index d281eeee35..087ffd1701 100644 --- a/indra/resources/update_resources.py +++ b/indra/resources/update_resources.py @@ -638,8 +638,10 @@ def update_mirbase(): urlretrieve(url, mirbase_gz_path) mirbase_json_path = os.path.join(path, 'mirbase.tsv') - with gzip.open(mirbase_gz_path, 'rt') as in_file, open(mirbase_json_path, 'w') as out_file: - print('mirbase_id', 'mirbase_name', 'database', 'identifier', 'label', sep='\t', file=out_file) + with gzip.open(mirbase_gz_path, 'rt') as in_file, \ + open(mirbase_json_path, 'w') as out_file: + print('mirbase_id', 'mirbase_name', 'database', 'identifier', 'label', + sep='\t', file=out_file) for line in _process_mirbase_file(in_file): print(*line, sep='\t', file=out_file) @@ -662,11 +664,13 @@ def _process_mirbase_file(lines): for element in group: if not element.startswith('DR'): continue - db, identifier, name = [e.strip() for e in element[len('DR'):].lstrip().split(';')] + db, identifier, name = [e.strip() for e in \ + element[len('DR'):].lstrip().split(';')] yield mirbase_id, mirbase_name, db, identifier, name.rstrip('.') if __name__ == '__main__': + """ update_go_id_mappings() update_cellular_component_hierarchy() update_famplex() @@ -686,5 +690,6 @@ def _process_mirbase_file(lines): update_ncit_map() update_lincs_small_molecules() update_lincs_proteins() - update_mesh_names() + update_mesh_names()a + """ update_mirbase() diff --git a/indra/tests/test_mirbase_client.py b/indra/tests/test_mirbase_client.py index 8569712fc4..b78852e88c 100644 --- a/indra/tests/test_mirbase_client.py +++ b/indra/tests/test_mirbase_client.py @@ -2,23 +2,29 @@ def test_mirbase_id_to_name(): - assert 'hsa-mir-19b-2' == mirbase_client.get_mirbase_name_from_mirbase_id('MI0000075') + assert 'hsa-mir-19b-2' == \ + mirbase_client.get_mirbase_name_from_mirbase_id('MI0000075') def test_mirbase_name_to_id(): - assert 'MI0000075' == mirbase_client.get_mirbase_id_from_mirbase_name('hsa-mir-19b-2') + assert 'MI0000075' == \ + mirbase_client.get_mirbase_id_from_mirbase_name('hsa-mir-19b-2') def test_mirbase_hgnc_mappings(): assert '31476' == mirbase_client.get_hgnc_id_from_mirbase_id('MI0000060') - assert mirbase_client.get_hgnc_id_from_mirbase_id('MI0000056') is None, 'This one is from C. elegans' + assert mirbase_client.get_hgnc_id_from_mirbase_id('MI0000056') is None, \ + 'This one is from C. elegans' def test_hgnc_mirbase_mappings(): assert 'MI0000060' == mirbase_client.get_mirbase_id_from_hgnc_id('31476') - assert mirbase_client.get_mirbase_id_from_hgnc_id('6893') is None, 'HGNC:6893!MAPT is a protein' + assert mirbase_client.get_mirbase_id_from_hgnc_id('6893') is None, \ + 'HGNC:6893!MAPT is a protein' def test_hgnc_symbol_mirbase_mappings(): - assert 'MI0000075' == mirbase_client.get_mirbase_id_from_hgnc_symbol('MIR19B2') - assert mirbase_client.get_mirbase_id_from_hgnc_symbol('MAPT') is None, 'HGNC:6893!MAPT is a protein' + assert 'MI0000075' == \ + mirbase_client.get_mirbase_id_from_hgnc_symbol('MIR19B2') + assert mirbase_client.get_mirbase_id_from_hgnc_symbol('MAPT') is None, \ + 'HGNC:6893!MAPT is a protein'