bio-liftover

A Ruby solution for UCSC LiftOver tool.

Suggestions and help from Pjotr Prins.

Note: this software is under active development!

Installation

gem install bio-liftover

Usage

Inside script:

require 'bio-liftover'

As bin file:

bio-liftover

Usage: bio-liftover ([-v] -c ) bio-liftover ([-v] -f -c ) bio-liftover -h | --help bio-liftover -v | --verbose

Options: -h --help Show this screen. -v --verbose Increase information during run. -c --coord Coordinate as input i.e. hg19,hg18,chr2,55000. -f --file Load local chain file.

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/andreirozanski/bioruby-liftover

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 (http://biogems.info/index.html#bio-liftover)

Copyright

Copyright (c) 2014 Andrei Rozanski. See LICENSE.txt for further details.