Download genome files from NCBI by accession.
Project description
NCBI accession download script
A partner script to the popular ncbi-genome-download
script, ncbi-acc-download
allows you to download sequences from GenBank/RefSeq by accession through
the NCBI ENTREZ API.
Installation
pip install ncbi-acc-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-acc-download
install.
ncbi-acc-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, 3.4, 3.5, 3.6 and 3.7.
Specifically, no attempt at testing under Python versions older than 2.7 or 3.4 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 a nucleotide record AB_12345 in GenBank format, run
ncbi-acc-download AB_12345
To download a nucleotide record AB_12345 in FASTA format, run
ncbi-acc-download --format fasta AB_12345
To download a protein record WP_12345 in FASTA format, run
ncbi-acc-download --molecule protein WP_12345
To just generate a list of download URLs to run the actual download elsewhere, run
ncbi-acc-download --url AB_12345
To get an overview of all options, run
ncbi-acc-download --help
License
All code is available under the Apache License version 2, see the
LICENSE
file for details.
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