bio-sra

A Sequence Read Archive (SRA) download script and Ruby interface to the SRAdb (SRA metadata) SQLite database.

Installation

gem install bio-sra

Download script usage

Download a single run file to the current directory:

sra_download --runs ERR229501.sra

Download a list of runs

$ cat srr_list.txt
ERR229501
ERR229498
$ sra_download --runs -f srr_list.txt

Download all runs that are a part of the experiment ERP001779 (Microbial biogeography of public restroom surfaces)

$ sra_download ERP001779

This finds ERP001779 and links it to runs through the SRAdb

Ruby interface script

require 'bio-sra'

The API doc is online. For more code examples see the test files in the source tree.

Project home page

Information on the source tree, documentation, examples, issues and how to contribute, see

http://github.com/wwood/bioruby-sra

The BioRuby community is on IRC server: irc.freenode.org, channel: #bioruby.

Cite

This Ruby code is unpublished, but there's a problem with

• BioRuby: bioinformatics software for the Ruby programming language
• Biogem: an effective tool-based approach for scaling up open source software development in bioinformatics

Biogems.info

This Biogem is published at #bio-sra

Copyright

Copyright (c) 2012 Ben J. Woodcroft. See LICENSE.txt for further details.