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

Project description

# 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

## License

This project is licensed under the MIT License - see the [LICENSE](LICENSE) file for details

## Acknowledgments

  • Would like to thank kblin for his amazing work with the ncbi_genome_download which provided lots of inspiration when writing genome_update.

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