genome_update

genome_update is a package that downloads genomes from NCBI and saves information about them in a yaml file. It can also use a local yaml file to update and download new genomes.

Sequence statistics is also calculated for each genome and added to the yaml file.

Getting Started

These instructions will provide information how to install and use the software.

Prerequisites

Python Pandas PyYaml

How to install

To install Genome_update you can either download source code directly from github and build it your self, an easier alternative is to use pip.

Installing by pip:

pip install genome_update

Pip will also install all prerequisities. It is also recommended to update all prerequisities.

Installing genome_update and upgrading prerequisities:

pip install genome_update --upgrade

Usage

Download all genomes from a specific genus:

genome_update -g <Genus>

Download all genomes from a specific genus, but much faster:

genome_update -g <Genus> -p <threads>

Download all genomes from a specific genus, but much faster, to a specific directory (default is /genomes):

genome_update -g <Genus> -p <threads> -o <directory>

Download all genomes from a specific species:

genome_update -g <Genus> -s <species_taxid>

To update a local yaml file:

genome_update -u -i <yamlfile>

To download missing genomes from a local yaml file:

genome_update -d -i <yamlfile>

To download genomes from another domain than bacteria:

genome_update -domain <domain> -g <Genus> 

Authors

• Emil Samuelsson - Initial work - Emisam

License

This project is licensed under the MIT License - see the LICENSE file for details