bio-gggenome

Ruby client for GGGenome the Ultrafast sequence search, http://gggenome.dbcls.jp/en/

Note: this software is under active development!

Installation

    gem install bio-gggenome

Usage

    require 'bio-gggenome'
    db = "hg19"
    missmatch = 1
    query = "TTCATTGACAACATT"
    hits = Bio::GGGenome.search(db, missmatch, query)
    
    hits['results'].each do |hit|
      hit['name']     #=> 'chr1'
      hit['position'] #=> 83462476
      hit['strand']   #=> "+"
    end

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/nakao/bio-gggenome

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

Cite

If you use this software, please cite one of

• 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-gggenome

Copyright

Copyright (c) 2013 Mitsuteru Nakao. See LICENSE.txt for further details.