Utilities for UCSC Bioinformatics Genome Browser ( http://genome.ucsc.edu ) including calculation of a BIN index from a genomic interval to speed-up SQL queries, and conversion between 1-based full-closed (for humans) and 0-based half-open (for machienes) intervals
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README.rdoc

UCSCBin

Author

Hiroyuki Mishima (missy at be.to / hmishima at nagasaki-u.ac.jp)

Copyright

Hiroyuki Mishima, 2010

License

the MIT/X11 license. See the LICENSE file.

A library for handling BIN index and 0/1-based coordination of UCSC Bioinformatics Genome Browser ( genome.ucsc.edu/ )

Original program in C by Jim Kent, 2002

See also related materials:

UCSCBin::Util

convert between 0-based half-open interval and 1-based full-close intervals.

UCSCBin::BinRange

Calculate Bin number from genomic physical position according to UCSC's Bin Indexing System. note: Extended bin index for positions >= 512M is not supported yet. Do you need it? Please email the author.

sample/refseqgene.rb

to run the sample (input interval is regular 1-based full-closed cordination)

sudo gem install sequel
sample/refseqgene.rb chr1:234567-456789

output:

chr1:234567-345678      LOC100133331; LOC100132287; LOC100132062

Note on Patches/Pull Requests

  • github repository is git://github.com/misshie/UCSCBin.git

  • Fork the project.

  • Make your feature addition or bug fix.

  • Add tests for it. This is important so I don't break it in a future version unintentionally.

  • Commit, do not mess with rakefile, version, or history. (if you want to have your own version, that is fine but bump version in a commit by itself I can ignore when I pull)

  • Send me a pull request. Bonus points for topic branches.

Copyright

Copyright © 2010 Hiroyuki MISHIMA. See LICENSE for details.