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
that can also be found in Mick's GitHub
repo. 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 or Linuxbrew 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 only bacterial reference genomes from RefSeq in GenBank format, run:
ncbi-genome-download --refseq-category reference 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:
ncbi-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.
It is also possible to re-run a previous download with the --human-readable option.
In this case, ncbi-genome-download will not download any new genome files, and just create
human-readable directory structure. Note that if any files have been changed on the NCBI side,
a file download will be triggered.
To get an overview of all options, run
ncbi-genome-download --help
As a method
You can also use it as a method call. Pass the pythonised keyword arguments (_ instead of -)
as described above or in the --help:
import ncbi_genome_download as ngd
ngd.download()
Note: To specify a taxonomic group, like bacteria, use the group keyword.
License
All code is available under the Apache License version 2, see the
LICENSE file for details.