Mercurial > repos > galaxyp > data_manager_eggnog_mapper_abspath
diff data_manager/data_manager_eggnog.py @ 1:269f0970d762 draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
| author | galaxyp |
|---|---|
| date | Sat, 05 Sep 2020 07:24:42 +0000 |
| parents | 9d5f039c637f |
| children | b711f5b6bd44 |
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--- a/data_manager/data_manager_eggnog.py Mon Nov 11 11:49:47 2019 -0500 +++ b/data_manager/data_manager_eggnog.py Sat Sep 05 07:24:42 2020 +0000 @@ -11,7 +11,7 @@ def _get_db_version(sqlitedb_path): - version = '4.5' + version = '5.0' try: query = 'select version from version' conn = sqlite3.connect(sqlitedb_path) @@ -28,7 +28,6 @@ parser = argparse.ArgumentParser() parser.add_argument('--config_file') parser.add_argument('--install_path') - parser.add_argument('--dbs', default='') args = parser.parse_args() eggnog_db_path = os.path.join(args.install_path, 'eggnog.db') @@ -46,19 +45,9 @@ data_table_entry = dict(value=db_version, name=db_version, path=args.install_path) dm_dict['data_tables'][data_table].append(data_table_entry) - data_table = 'eggnog_mapper_hmm_dbs' - dm_dict['data_tables'][data_table]\ - = dm_dict['data_tables'].get(data_table, []) - if args.dbs: - dbs = [x.strip() for x in args.dbs.split(',')] - for db in dbs: - key = '%s_%s' % (db_version, db) - data_table_entry = dict(key=key, db_version=db_version, - value=db, name=db, path=db) - dm_dict['data_tables'][data_table].append(data_table_entry) # save info to json file - open(args.config_file, 'wb').write(json.dumps(dm_dict)) + open(args.config_file, 'w').write(json.dumps(dm_dict)) if __name__ == "__main__":