def main(): user_home = find_home_dir() project_dp = os.path.join(user_home, 'pdb') uni_dp = os.path.join(project_dp, 'uni_data') tsv_dp = os.path.join(project_dp, 'tsv_data') working_dp = os.path.join(project_dp, 'working') dirs = ProjectFolders( user_home=user_home, project_home=project_dp, uni_data=uni_dp, tsv_data=tsv_dp, working=working_dp ) create_folders(dirs) fetch_and_write_files(dirs) initial_filtering(dirs) fetcher = UniProtFetcher(dirs) fetcher.fetch_fasta_files() second_filtering(dirs) final_filtering(dirs) uniprot_composite(dirs) print("Processing finished successfully.") return None
def setUp(self): self.temp_dir = mkdtemp(prefix='pdb-tests_') self._create_dirs() self.tsv_test_fp = os.path.join( self.dirs.working, 'pdb_seq.tsv' ) create_folders(self.dirs) return None
def test_tsv_folder_success(self): """create_folders()""" create_folders(self.dirs) expected_path = self.dirs.tsv_data self.assertTrue(isdir(expected_path))
def test_working_folder_success(self): """create_folders()""" create_folders(self.dirs) expected_path = self.dirs.working self.assertTrue(isdir(expected_path))