Download genome files from NCBI by accession.
NCBI accession download script
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 is only developed and tested on Python releases still under active
support by the Python project. At the moment, this means versions 3.6, 3.7, 3.8, and 3.9.
Specifically, no attempt at testing under Python versions older than 3.6 is being made.
ncbi-acc-download 0.2.6 was the last version to support Python 2.7.
To download a nucleotide record AB_12345 in GenBank format, run
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
If you want to concatenate multiple sequences into a single file, run
ncbi-acc-download --out two_genomes.gbk AB_12345 AB_23456
You can use this with
/dev/stdout as the filename to print the downloaded data to
standard output instead of writing to a file if you want to chain
ncbi-acc-download with other
command line tools, like so:
ncbi-genome-download --out /dev/stdout --format fasta AB_12345 AB_23456 | gzip > two_genomes.fa.gz
If you want to download all records covered by a WGS master record instead of the master record itself, run
ncbi-acc-download --recursive NZ_EXMP01000000
You can supply a genomic range to the accession download using
ncbi-acc-download NC_007194 --range 1001:9000
As cutting a record up with a range operator like that can leave partial features at both ends of the
record, you can combine the range download with the new
correct extended validator to remove the
ncbi-acc-download NC_007194 --range 1001:9000 --extended-validation correct
You can get more detailed information on the download progress by using the
To get an overview of all options, run
All code is available under the Apache License version 2, see the
LICENSE file for details.
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