Metadata-Version: 1.1
Name: genome-update
Version: 0.1.5.2
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 Bacteria] [-g GENUS] [-s SPECIES_TAXID] [-t TAXID] [-d] [-u]
        
        
        arguments:
          -h, --help            show this help message and exit
          -o OUTPUT, folder, --output FOLDER 
        The folder which files will be downloaded to 
        
        -name NEWNAME, --newname NEWNAME
        What the yaml file should be named
        
        -p N, --parallel N
        Use N processes to download files (default = 1)
         
        -i INPUT, --input-file-path INPUT
        Local yaml file to update
        
        -domain, --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 a yaml file
        
        -u, --update-yaml
        Use to only update local yaml file
        
        
        Example: To download all genomes from brucella with 10 processes to the folder Brucella-genomes
        genome_update -g Brucella -p 10 -o Brucella-genomes
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
