Project

bio-wolf_psort_wrapper

0.0
No commit activity in last 3 years
No release in over 3 years
bio-wolf_psort_wrapperwwood/bioruby-wolf_psort_wrapperHomepageDocumentationSource CodeBug TrackerWiki
Enables the localisation predictor WoLF PSORT to be run locally. The algorithm is available at http://wolfpsort.org/
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 Popularity
Downloads
9,495
Stars
1
Forks
0
Watchers
3
 Releases
Current version
0.0.3
Total releases
2
First release
2012-01-20
Latest release
2012-01-20
 Development
Primary Language
Ruby
Average date of last 50 commits
2012-01-19
Reverse Dependencies
0

 Dependencies

Development

bio
>= 1.4.2
bundler
~> 1.0.0
jeweler
~> 1.6.4
rcov
>= 0
shoulda
>= 0
 Project Readme

The biogem bio-wolf_psort_wrapper

A wrapper around the protein sub-cellular localisation program WoLF PSORT, so that it can be run locally. More information is about the underlying program is available from http://wolfpsort.org/aboutWoLF_PSORT.html.en and on the same site the executables required for this package to run are provided.

    require 'bio-wolf_psort_wrapper'
    wolf_psort_result = Bio::PSORT::WoLF_PSORT::Wrapper.new.run(
      'MTQVPPVTFQQYGPVITTSAGNPVDDNQNSVTAGPYGPAILSNFHLIDKLAHFDRERIPE
       RVVHAKGGGAFGYFEVTHDITRFCKAKLFEKIGKRTPVFARFSTVAGESGSADTRRDPRG
       FALKFYTEEGNWDMVGNNTPIFFVRDAIKFPDFIHTQKRHPQTHLHDPNMVWDFFSLVPE
       SVHQVTFLYTDRGTPDGFRHMNGYGSHTFKFINKDNEAFYVKWHFKTNQGIKNLNRQRAK
       ELESEDPDYAVRDLFNAIAKREFPSWTFCIQVMPLKDAETYKWNVFDVTKVWPHGDYPLI
       PVGRLVLDRNPENYFQDVEQAAFAPAHMVPGIEPSEDRMLQGRMFSYIDTHRHRLGANYH
       QIPVNRPWNARGGDYSVRDGPMCVDGNKGSQLNYEPNSVDGFPKEDRNAAVSGTTTVSGT
       VACHPQEHPNSDFEQPGNFYRTVLSEPEREALIGNIAEHLRQARRDIQERQVKIFYKCDP
       EYGERVARAIGLPTAACYPAKM*'.gsub(/\s/,''),
      'plant'
    ) #=> Bio::PSORT::WoLF_PSORT::Report object
    wolf_psort_result.score_hash #=> {'pero' => 8.0, 'nucl' => 2.0, 'mito' => 1.5, 'mito_plas' => 1.5, 'cyto_nucl' => 1.5}

Contributing to bio-wolf_psort_wrapper

  • 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.

Copyright

Copyright (c) 2012 Ben J Woodcroft. See LICENSE.txt for further details.