Download genome files from the NCBI FTP server.
Project description
# NCBI Genome Downloading Scripts
Some script to download bacterial and fungal genomes from NCBI after they restructured their FTP a while ago.
Idea shamelessly stolen from [Mick Watson’s Kraken downloader scripts](http://www.opiniomics.org/building-a-kraken-database-with-new-ftp-structure-and-no-gi-numbers/) that can also be found in [Mick’s GitHub repo](https://github.com/mw55309/Kraken_db_install_scripts). However, Mick’s scripts are ~~written in Perl~~ specific to actually building a Kraken database (as advertised).
So this is a set of scripts that focuses on the actual genome downloading.
## Installation
` pip install ncbi-genome-download `
Alternatively, clone this repository from GitHub, then run (in a python virtual environment) ` pip install . `
## Usage
To download all bacterial RefSeq genomes from NCBI, run the following:
` ncbi-genome-download bacteria `
To download all fungal GenBank genomes from NCBI, run: ` ncbi-genome-download --section genbank fungi `
To get an overview of all options, run ` ncbi-genome-download --help `
## License All code is available under the Apache License version 2, see the [LICENSE](LICENSE) file for details.
Project details
Release history Release notifications | RSS feed
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
Source Distribution
Hashes for ncbi-genome-download-0.1.3.tar.gz
Algorithm | Hash digest | |
---|---|---|
SHA256 | aa7fd2f2d22e083c1f8df518d9379d894800cd2ac2b53f60d93a7562c2aff088 |
|
MD5 | 9a71b7da7019b75f2b62a2641d2badbb |
|
BLAKE2b-256 | a9345d700b23e9323b5004b285380e3cdc0a9d7c395f4c89057b43eac7d4b8db |