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:

• genomewiki.ucsc.edu/index.php/Bin_indexing_system,

• Kent, et. al. Genome Research 2002.12:996-1006, www.ncbi.nlm.nih.gov/pmc/articles/PMC186604/

• src/lib/binRange.c in the kent source tree. hgdownload.cse.ucsc.edu/admin/jksrc.zip

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.