Mercurial > repos > estrain > data_manager_amrfinderplus
changeset 8:2ec5dcc42c63 draft
Uploaded
| author | estrain |
|---|---|
| date | Sun, 22 May 2022 18:42:43 +0000 |
| parents | 8072c9795674 |
| children | 949480e9f6a3 |
| files | data_manager_amrfinderplus/data_manager/data_manager_amrfinderplus.py |
| diffstat | 1 files changed, 5 insertions(+), 7 deletions(-) [+] |
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--- a/data_manager_amrfinderplus/data_manager/data_manager_amrfinderplus.py Sun May 22 18:24:09 2022 +0000 +++ b/data_manager_amrfinderplus/data_manager/data_manager_amrfinderplus.py Sun May 22 18:42:43 2022 +0000 @@ -58,7 +58,7 @@ return version -def print_json (version,argskey,argspath,argsname,argsvalue,argsout): +def print_json (version,argspath,argsname,argsout): valueentry="AMRFinderPlus_"+version @@ -66,8 +66,7 @@ 'data_tables' : { 'amrfinder_databases': [ { - "dbkey":argskey, - "value":argsvalue, + "value":version, "name":argsname, "path":argspath, } @@ -76,14 +75,13 @@ } with open(argsout, 'w') as fh: - json.dump(data_table_entry,fh, sort_keys=True) + ##json.dump(data_table_entry,fh, sort_keys=True) + json.dump(data_table_entry, fh, indent=2, sort_keys=True) def main(): parser = argparse.ArgumentParser(description='Download NCBI amrFinderPlus Databases') parser.add_argument('--name', type=str, required=True, nargs=1, help='Database name') - parser.add_argument('--value', type=str, required=True, nargs=1, help='Database value') - parser.add_argument('--key', type=str, required=True, nargs=1, help='Database value') parser.add_argument('--out', type=str, required=True, nargs=1, help='output file') args = parser.parse_args() @@ -95,6 +93,6 @@ os.chdir("..") #shutil.copytree("output",args.path[0]) - print_json(version,args.key[0],os.path.abspath("output"),args.name[0],args.value[0],args.out[0]) + print_json(version,os.path.abspath("output"),args.name[0],args.out[0]) if __name__ == "__main__": main()