ncbi-genome-download 0.2.0

Download genome files from the NCBI FTP server.

# NCBI Genome Downloading Scripts

[](http://github.drone.secondarymetabolites.org/kblin/ncbi-genome-download)
[](https://landscape.io/github/kblin/ncbi-genome-download/master)

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 .
```
If this fails on older versions of Python, try updating your `pip` tool first:
```
pip install --upgrade pip
```
and then rerun the `ncbi-genome-download` install.

`ncbi-genome-download` is only developed and tested on Python releases still under active
support by the Python project. At the moment, this means versions 2.7, 3.3, 3.4, 3.5 and 3.6.
Specifically, no attempt at testing under Python versions older than 2.7 or 3.3 is being made.

If your system is stuck on an older version of Python, consider using a tool like
[Homebrew](http://brew.sh) or [Linuxbrew](http://linuxbrew.sh) to obtain a more up-to-date
version.


## Usage

To download all bacterial RefSeq genomes in GenBank format from NCBI, run the following:
```
ncbi-genome-download bacteria
```

If you're on a reasonably fast connection, you might want to try running multiple downloads in parallel:
```
ncbi-genome-download bacteria --parallel 4
```


To download all fungal GenBank genomes from NCBI in GenBank format, run:
```
ncbi-genome-download --section genbank fungi
```

To download all viral RefSeq genomes in FASTA format, run:
```
ncbi-genome-download --format fasta viral
```

To download only completed bacterial RefSeq genomes in GenBank format, run:
```
ncbi-genome-download --assembly-level complete bacteria
```

To download bacterial RefSeq genomes of the genus _Streptomyces_, run:
```
ncbi-genome-download --genus Streptomyces bacteria
```
**Note**: This is a simple string match on the organism name provided by NCBI only.

You can also use this with a slight trick to download genomes of a certain species as well:
```
ncbi-genome-download --genus "Streptomyces coelicolor" bacteria
```
**Note**: The quotes are important. Again, this is a simple string match on the organism
name provided by the NCBI.

To download bacterial RefSeq genomes based on their NCBI species taxonomy ID, run:
```
ncbi-genome-download --species-taxid 562 bacteria
```
**Note**: The above command will download all RefSeq genomes belonging to _Escherichia coli_.

To download a specific bacterial RefSeq genomes based on its NCBI taxonomy ID, run:
```
ncbi-genome-download --taxid 511145 bacteria
```
**Note**: The above command will download the RefSeq genome belonging to _Escherichia coli str. K-12 substr. MG1655_.


It is possible to also create a human-readable directory structure in parallel to mirroring
the layout used by NCBI:
```
ncbo-genome-download --human-readable bacteria
```
This will use links to point to the appropriate files in the NCBI directory structure,
so it saves file space. Note that links are not supported on some Windows file systems and some
older versions of Windows.


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.