Mercurial > repos > estrain > data_manager_amrfinderplus
changeset 2:316961434166 draft
Uploaded
| author | estrain |
|---|---|
| date | Mon, 23 May 2022 09:35:13 +0000 |
| parents | 6dfbca41a8c4 |
| children | 2c887282d3ef |
| files | data_manager_amrfinderplus/data_manager/data_manager_amrfinderplus.py |
| diffstat | 1 files changed, 13 insertions(+), 5 deletions(-) [+] |
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--- a/data_manager_amrfinderplus/data_manager/data_manager_amrfinderplus.py Mon May 23 09:10:19 2022 +0000 +++ b/data_manager_amrfinderplus/data_manager/data_manager_amrfinderplus.py Mon May 23 09:35:13 2022 +0000 @@ -82,14 +82,22 @@ parser.add_argument('--out', type=str, required=True, nargs=1, help='output file') args = parser.parse_args() - - os.mkdir("amrdb") - os.chdir("amrdb") + + + with open(args.out[0]) as fh: + config = json.load(fh) + + output_directory = config.get("output_data", [{}])[0].get("extra_files_path", None) + data_manager_dict = {} + data_manager_dict["data_tables"] = config.get("data_tables", {}) + data_manager_dict["data_tables"][args.datatable_name] = data_manager_dict[ + "data_tables" + ].get(args.datatable_name, []) + #Fetch the files and build blast databases version=download_from_ncbi() - os.chdir("..") #shutil.copytree("amrdb",args.path[0]) - print_json(version,os.path.abspath("amrdb"),args.name[0],args.out[0]) + print_json(version,output_directory,args.name[0],args.out[0]) if __name__ == "__main__": main()