def test_pdb_mutation_pipeline_have_sequences(pdb_id): """Make sure that we can copy folders with precalculated Provean score(s). """ unique_temp_dir_old = _get_unique_temp_dir(pdb_id) unique_temp_dir = op.join(op.splitext(__file__)[0], pdb_id + '_have_sequences', '.elaspic') os.makedirs(unique_temp_dir, exist_ok=True) try: shutil.copy2( op.join(unique_temp_dir_old, 'sequence.json'), op.join(unique_temp_dir, 'sequence.json')) shutil.copytree( op.join(unique_temp_dir_old, 'sequence'), op.join(unique_temp_dir, 'sequence')) conf.read_configuration_file( DEFAULT={ 'unique_temp_dir': unique_temp_dir }, EXTERNAL_DIRS={ 'pdb_dir': os.environ['PDB_DIR'], 'blast_db_dir': os.environ['BLAST_DB_DIR'], 'archive_dir': os.environ['ARCHIVE_DIR'] } ) os.chdir(unique_temp_dir) helper_fns.run_pdb_mutation_pipeline( pdb_id, pdb_mutatations, have_sequences=True) except: raise finally: shutil.rmtree(unique_temp_dir)
def test_pdb_mutation_pipeline(pdb_id): """Canonical folder. """ unique_temp_dir = _get_unique_temp_dir(pdb_id) os.makedirs(unique_temp_dir, exist_ok=True) conf.read_configuration_file( DEFAULT={ 'unique_temp_dir': unique_temp_dir }, EXTERNAL_DIRS={ 'pdb_dir': os.environ['PDB_DIR'], 'blast_db_dir': os.environ['BLAST_DB_DIR'], 'archive_dir': os.environ['ARCHIVE_DIR'] } ) os.chdir(unique_temp_dir) helper_fns.run_pdb_mutation_pipeline(pdb_id, pdb_mutatations)