bio-ucsc-util

Ruby FFI binding and implementation of the ucsc utilities. The C source can be found here: hgdownload.cse.ucsc.edu/admin/

More information about the ucsc genome browser data formats can be found here: genome.ucsc.edu/FAQ/FAQformat.html

The following utilities are available

  • bedGraphToBigWig

  • wigToBigWig

  • bigWigInfo

  • bigWigSummary

Usage

The Util class is used for the base conversion utilities:

Bio::Ucsc::Util.wigToBigWig('my.wig','chrom.sizes','out.bw')

The BigWig class can be used to open and interact with the binary files:

bw = Bio::Ucsc::BigWig.open('out.bw') bw.info bw.summary('chr1',1,10,10,'mean')

For more details see the Bio::Ucsc::Util and Bio::Ucsc::BigWig classes

Contributing to bio-ucsc-util

  • Check out the latest master to make sure the feature hasn't been implemented or the bug hasn't been fixed yet.

  • Check out the issue tracker to make sure someone already hasn't requested it and/or contributed it.

  • Fork the project.

  • Start a feature/bugfix branch.

  • Commit and push until you are happy with your contribution.

  • Make sure to add tests for it. This is important so I don't break it in a future version unintentionally.

  • Please try not to mess with the Rakefile, version, or history. If you want to have your own version, or is otherwise necessary, that is fine, but please isolate to its own commit so I can cherry-pick around it.

Dependencies

  • FFI (github.com/ffi/ffi)

Copyright

Copyright © 2012 Nicholas A. Thrower. See LICENSE.txt for further details.