Metadata-Version: 1.1
Name: genome-update
Version: 0.1.1
Summary: A script for updating a local directory with genomes, from NCBI assembly files
Home-page: https://github.com/Emisam/genome_update.git
Author: Emil Samuelsson
Author-email: Emil@Samuelsson.pp.se
License: MIT
Description: A script that downloads genomes for a selected genus/species/subspecies from NCBI assembly file.
        Can also be used to update a local directory with a specified yaml file.  
        
        
        usage: genome_downloader.py [-h] [-f FOLDER] [-o OUTPUT] [-p N] [-i INPUT]
                       [-domain {archaea,bacteria,fungi,invertebrate,plant,protozoa,vertebrate_mammalian,vertebrate_other,viral}]
                       [-g GENUS] [-s SPECIES_TAXID] [-t TAXID] [-d] [-u]
        
        
        
        optional arguments:
          -h, --help            show this help message and exit
          -f FOLDER, --folder-output FOLDER 
                                The folder which files will be downloaded to
          -o OUTPUT, --output-file OUTPUT
                                The folder which files will be downloaded to
          -p N, --parallel N    Use N processes to download files (default = 1)
          -i INPUT, --input-file-path INPUT
                                Local yaml file to update
          -domain {archaea,bacteria,fungi,invertebrate,plant,protozoa,vertebrate_mammalian,vertebrate_other,viral}, 
          --domain {archaea,bacteria,fungi,invertebrate,plant,protozoa,vertebrate_mammalian,vertebrate_other,viral}
                                The domain to download from
          -g GENUS, --genus GENUS
                                Specify the target genus
          -s SPECIES_TAXID, --species-taxid SPECIES_TAXID
                                Used to specify a target species_taxid
          -t TAXID, --taxid TAXID
                                Used to specify a target taxid
          -d, --download        Use to only download files for all unique isolates in
                                a yaml file
          -u, --update-yaml     Use to only update local yaml file
        
Platform: UNKNOWN
Classifier: Development Status :: 3 - Alpha
Classifier: Intended Audience :: Science/Research
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python :: 3
