Mercurial > repos > yating-l > data_manager_fetch_reference_data
comparison data_manager/fetch_reference_data.py @ 10:f2e535e1b45c draft
planemo upload
| author | yating-l |
|---|---|
| date | Wed, 03 May 2017 18:24:19 -0400 |
| parents | 877e61138c9c |
| children | 85e817cdf4bd |
comparison
equal
deleted
inserted
replaced
| 9:877e61138c9c | 10:f2e535e1b45c |
|---|---|
| 48 ] | 48 ] |
| 49 tar.extractall(path=downloadpath, members=subdir) | 49 tar.extractall(path=downloadpath, members=subdir) |
| 50 glimmerhmm_trained_dir = os.path.join(downloadpath, 'GlimmerHMM', 'trained_dir', sequence_id) | 50 glimmerhmm_trained_dir = os.path.join(downloadpath, 'GlimmerHMM', 'trained_dir', sequence_id) |
| 51 glimmerhmm_trained_target_dir = os.path.join(target_directory, sequence_id) | 51 glimmerhmm_trained_target_dir = os.path.join(target_directory, sequence_id) |
| 52 shutil.copytree(glimmerhmm_trained_dir, glimmerhmm_trained_target_dir) | 52 shutil.copytree(glimmerhmm_trained_dir, glimmerhmm_trained_target_dir) |
| 53 data_table_entry = dict(value=sequence_id, name=sequence_name, path=glimmerhmm_trained_target_dir) | 53 data_table_entry = dict(value=sequence_id, name=sequence_name, path=glimmerhmm_trained_target_dir.strip('/')) |
| 54 _add_data_table_entry(data_manager_dict, data_table_entry) | 54 _add_data_table_entry(data_manager_dict, data_table_entry) |
| 55 | 55 |
| 56 cleanup_before_exit('tmp') | 56 cleanup_before_exit('tmp') |
| 57 | 57 |
| 58 def _add_data_table_entry(data_manager_dict, data_table_entry): | 58 def _add_data_table_entry(data_manager_dict, data_table_entry): |
| 68 args = parser.parse_args() | 68 args = parser.parse_args() |
| 69 | 69 |
| 70 filename = args.out | 70 filename = args.out |
| 71 | 71 |
| 72 params = from_json_string(open(filename).read()) | 72 params = from_json_string(open(filename).read()) |
| 73 target_directory = params['output_data'][0]['extra_files_path'].strip('/') | 73 target_directory = params['output_data'][0]['extra_files_path'] |
| 74 os.mkdir(target_directory) | 74 os.mkdir(target_directory) |
| 75 data_manager_dict = {} | 75 data_manager_dict = {} |
| 76 | 76 |
| 77 sequence_id, sequence_name = get_reference_id_name(params) | 77 sequence_id, sequence_name = get_reference_id_name(params) |
| 78 trained_dir = get_url(params) | 78 trained_dir = get_url(params) |