Mercurial > repos > estrain > data_manager_amrfinderplus
changeset 4:f119fb382a21 draft
Uploaded
| author | estrain |
|---|---|
| date | Mon, 23 May 2022 09:55:24 +0000 |
| parents | 2c887282d3ef |
| children | d6c3cee5fe48 |
| files | data_manager_amrfinderplus/data_manager/data_manager_amrfinderplus.py |
| diffstat | 1 files changed, 11 insertions(+), 7 deletions(-) [+] |
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--- a/data_manager_amrfinderplus/data_manager/data_manager_amrfinderplus.py Mon May 23 09:41:15 2022 +0000 +++ b/data_manager_amrfinderplus/data_manager/data_manager_amrfinderplus.py Mon May 23 09:55:24 2022 +0000 @@ -12,13 +12,16 @@ from ftplib import FTP -def download_from_ncbi(): +def download_from_ncbi(output_direcotry): NCBI_FTP_SERVER = 'ftp.ncbi.nlm.nih.gov' FILENAME = 'version.txt' NCBI_DOWNLOAD_PATH = '/pathogen/Antimicrobial_resistance/AMRFinderPlus/database/latest/' email = 'anonymous@example.com' + cwd = os.getcwd() + os.chdir(output_directory) + ftp = FTP( NCBI_FTP_SERVER ) ftp.login( 'anonymous', email) ftp.cwd(NCBI_DOWNLOAD_PATH) @@ -56,6 +59,8 @@ ftp.quit() + os.chdir(cwd) + return version def print_json (version,argspath,argsname,argsout): @@ -83,16 +88,15 @@ args = parser.parse_args() + with open(args.out[0]) as fh: + params = json.load(fh) - with open(args.out[0]) as fh: - config = json.load(fh) - - output_directory = config.get("output_data", [{}])[0].get("extra_files_path", None) - os.mkdir( output_directory ) + output_directory = params['output_data'][0]['extra_files_path'] + os.mkdir(output_directory) data_manager_dict = {} #Fetch the files and build blast databases - version=download_from_ncbi() + version=download_from_ncbi(output_directory) #shutil.copytree("amrdb",args.path[0]) print_json(version,output_directory,args.name[0],args.out[0])