Mercurial > repos > estrain > data_manager_amrfinderplus_database_builder
changeset 16:cac0aa78dad9 draft
Uploaded
author | estrain |
---|---|
date | Tue, 08 Mar 2022 18:07:54 +0000 |
parents | c74ed5f206bd |
children | 6405c5ba71c6 |
files | data_manager_amrfinderplus_database_builder/data_manager/data_manager_amrfinderplus_database_builder.py |
diffstat | 1 files changed, 8 insertions(+), 7 deletions(-) [+] |
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--- a/data_manager_amrfinderplus_database_builder/data_manager/data_manager_amrfinderplus_database_builder.py Tue Mar 08 18:07:30 2022 +0000 +++ b/data_manager_amrfinderplus_database_builder/data_manager/data_manager_amrfinderplus_database_builder.py Tue Mar 08 18:07:54 2022 +0000 @@ -43,7 +43,6 @@ os.system(blastcmd) for f in pointmuts: - print(f) blastcmd = "makeblastdb -in " + f +" -dbtype nucl -logfile /dev/null" os.system(blastcmd) @@ -59,7 +58,7 @@ return version -def print_json (version,argspath): +def print_json (version,argspath,argsname,argsvalue): valueentry="AMRFinderPlus_"+version @@ -67,8 +66,8 @@ 'data_tables' : { 'amrfinder_databases': [ { - "value":valueentry, - "name":version, + "value":argsvalue, + "name":argsname, "path":argspath, } ] @@ -76,12 +75,14 @@ } with open("out_file", 'w') as fh: - json.dump(data_table_entry,fh, sort_keys=True, indent=2) + json.dump(data_table_entry,fh, sort_keys=True) def main(): parser = argparse.ArgumentParser(description='Download NCBI amrFinderPlus Databases') - parser.add_argument('--path', type=str, required=True, nargs=1, help='Absolute Path and database name') + parser.add_argument('--name', type=str, required=True, nargs=1, help='Database name') + parser.add_argument('--path', type=str, required=True, nargs=1, help='Absolute path to new database folder') + parser.add_argument('--value', type=str, required=True, nargs=1, help='Database value') args = parser.parse_args() @@ -92,6 +93,6 @@ os.chdir("..") shutil.copytree("output",args.path[0]) - print_json(version,args.path[0]) + print_json(version,args.path[0],args.name[0],args.value[0]) if __name__ == "__main__": main()