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Download genome files from NCBI by accession.

Project description

# NCBI accession download script

A partner script to the popular [ncbi-genome-download](https://github.com/kblin/ncbi-genome-download) script, ncbi-acc-download allows you to download sequences from GenBank/RefSeq by accession through the NCBI [ENTREZ API](https://www.ncbi.nlm.nih.gov/books/NBK184582/).

## 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](http://brew.sh) or [Linuxbrew](http://linuxbrew.sh) 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 `

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 get more detailed information on the download progress by using the –verbose or -v flag.

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](LICENSE) file for details.

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