genome-update 0.1.3.5

A script for updating a local directory with genomes, from NCBI assembly files

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]



optional 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 {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


Example: To download all genomes from brucella with 10 processes to the folder Brucella-genomes
genome_update -g Brucella -p 10 -o Brucella-genomes