Mercurial > repos > estrain > data_manager_amrfinderplus_database_builder
changeset 1:cc677cf77613 draft
Uploaded
| author | estrain |
|---|---|
| date | Tue, 08 Mar 2022 02:50:00 +0000 |
| parents | 6ee125deee97 |
| children | d4f61a2a359d |
| files | data_manager_amrfinderplus_database_builder/data_manager/data_manager_amrfinderplus_database_builder.py |
| diffstat | 1 files changed, 12 insertions(+), 2 deletions(-) [+] |
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--- a/data_manager_amrfinderplus_database_builder/data_manager/data_manager_amrfinderplus_database_builder.py Tue Mar 01 03:11:12 2022 +0000 +++ b/data_manager_amrfinderplus_database_builder/data_manager/data_manager_amrfinderplus_database_builder.py Tue Mar 08 02:50:00 2022 +0000 @@ -8,10 +8,11 @@ import shutil import json import re +import argparse from ftplib import FTP -def download_from_ncbi( ): +def download_from_ncbi(): NCBI_FTP_SERVER = 'ftp.ncbi.nlm.nih.gov' FILENAME = 'version.txt' NCBI_DOWNLOAD_PATH = '/pathogen/Antimicrobial_resistance/AMRFinderPlus/database/latest/' @@ -64,13 +65,22 @@ with open("out_file", 'w') as out: out.write(json.dumps(data_tables, sort_keys=True, indent=2)) + + 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') + + args = parser.parse_args() + os.mkdir("output") os.chdir("output") #Fetch the files and build blast databases version=download_from_ncbi() os.chdir("..") + + shutil.copytree("output",args.path[0]) print_json(version) if __name__ == "__main__": main()