BioRuby BLAST XMLParser Plugin

bio-blast-xmlparser is a plugin of BioRuby, providing fast BLAST XML result parser by using XMLParser native extension. The code was formerly a part of the BioRuby core ("bio" gem), and because of the dependency to the native XMLParser extension, it was moved to this gem.

This gem is also developed as part of an effort to modularize BioRuby. Many more plugins are available at biogems.info.

bio-blast-xmlparser uses xmplarser gem that needs [expat XML Parser Toolkit]{http://www.jclark.com/xml/expat.html} installed on the system.

On Debian/Ubuntu:

# apt-get install libexpat-dev

On RedHat/CentOS:

# yum install expat-devel

Add this line to your application's Gemfile:

gem 'bio-blast-xmlparser'

And then execute:

$ bundle

Or install it yourself as:

$ gem install bio-blast-xmlparser

The existance of the gem is automatically detected by BioRuby core components.

To install this gem onto your local machine, run bundle exec rake install. To release a new version, update the version number in version.rb, and then run bundle exec rake release, which will create a git tag for the version, push git commits and tags, and push the .gem file to rubygems.org.

Bug reports and pull requests are welcome on GitHub at https://github.com/bioruby/bioruby-blast-xmlparser

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