ms-sequest 0.0.11 → 0.0.12

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data/tap.yml ADDED
File without changes
metadata CHANGED
@@ -1,10 +1,10 @@
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  --- !ruby/object:Gem::Specification
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  name: ms-sequest
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  version: !ruby/object:Gem::Version
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- version: 0.0.11
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+ version: 0.0.12
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  platform: ruby
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  authors:
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- - John Prince
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+ - John T. Prince
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  autorequire:
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  bindir: bin
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  cert_chain: []
@@ -52,6 +52,26 @@ dependencies:
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  - !ruby/object:Gem::Version
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  version: 0.2.3
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  version:
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+ - !ruby/object:Gem::Dependency
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+ name: ms-testdata
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+ type: :development
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+ version_requirement:
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+ version_requirements: !ruby/object:Gem::Requirement
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+ requirements:
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+ - - ">="
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+ - !ruby/object:Gem::Version
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+ version: 0.18.0
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+ version:
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+ - !ruby/object:Gem::Dependency
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+ name: spec/more
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+ type: :development
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+ version_requirement:
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+ version_requirements: !ruby/object:Gem::Requirement
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+ requirements:
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+ - - ">="
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+ - !ruby/object:Gem::Version
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+ version: "0"
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+ version:
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  description: reads .SRF, .SQT and supports conversions
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  email: jtprince@gmail.com
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  executables:
@@ -60,32 +80,55 @@ executables:
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  extensions: []
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  extra_rdoc_files:
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- - README
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- - MIT-LICENSE
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- - History
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+ - LICENSE
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+ - README.rdoc
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  files:
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+ - .autotest
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+ - .gitignore
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+ - .gitmodules
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+ - History
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+ - LICENSE
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+ - README.rdoc
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+ - Rakefile
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+ - VERSION
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+ - bin/srf_to_search.rb
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+ - bin/srf_to_sqt.rb
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+ - lib/ms/sequest.rb
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+ - lib/ms/sequest/bioworks.rb
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  - lib/ms/sequest/params.rb
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+ - lib/ms/sequest/pepxml.rb
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+ - lib/ms/sequest/sqt.rb
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+ - lib/ms/sequest/srf.rb
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  - lib/ms/sequest/srf/search.rb
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  - lib/ms/sequest/srf/search/tap.rb
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  - lib/ms/sequest/srf/sqt.rb
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- - lib/ms/sequest/srf.rb
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- - lib/ms/sequest/sqt.rb
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- - lib/ms/sequest.rb
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- - README
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- - MIT-LICENSE
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- - History
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+ - script/fasta_ipi_to_ncbi-ish.rb
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+ - spec/ms/sequest/bioworks_spec.rb
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+ - spec/ms/sequest/params_spec.rb
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+ - spec/ms/sequest/pepxml_spec.rb
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+ - spec/ms/sequest/sqt_spec.rb
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+ - spec/ms/sequest/sqt_spec_helper.rb
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+ - spec/ms/sequest/srf/search_spec.rb
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+ - spec/ms/sequest/srf/search_spec_helper.rb
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+ - spec/ms/sequest/srf/sqt_spec.rb
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+ - spec/ms/sequest/srf_spec.rb
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+ - spec/ms/sequest/srf_spec_helper.rb
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+ - spec/spec_helper.rb
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+ - spec/testfiles/7MIX_STD_110802_1.sequest_params_fragment.srf
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+ - spec/testfiles/bioworks31.params
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+ - spec/testfiles/bioworks32.params
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+ - spec/testfiles/bioworks33.params
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+ - spec/testfiles/corrupted_900.srf
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+ - spec/testfiles/small.sqt
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+ - spec/testfiles/small2.sqt
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+ - tap.yml
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  has_rdoc: true
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- homepage: http://mspire.rubyforge.org/projects/ms-sequest/
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+ homepage: http://jtprince.github.com/ms-sequest
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  licenses: []
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  post_install_message:
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  rdoc_options:
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- - --main
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- - README
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- - -S
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- - -N
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- - --title
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- - Ms-Sequest
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+ - --charset=UTF-8
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  require_paths:
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  - lib
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  required_ruby_version: !ruby/object:Gem::Requirement
@@ -102,10 +145,20 @@ required_rubygems_version: !ruby/object:Gem::Requirement
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  version:
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  requirements: []
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- rubyforge_project:
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+ rubyforge_project: mspire
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  rubygems_version: 1.3.5
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  signing_key:
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  specification_version: 3
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  summary: An mspire library supporting SEQUEST, Bioworks, SQT, etc
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- test_files: []
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-
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+ test_files:
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+ - spec/ms/sequest/srf/search_spec.rb
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+ - spec/ms/sequest/srf/sqt_spec.rb
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+ - spec/ms/sequest/srf/search_spec_helper.rb
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+ - spec/ms/sequest/sqt_spec.rb
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+ - spec/ms/sequest/params_spec.rb
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+ - spec/ms/sequest/bioworks_spec.rb
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+ - spec/ms/sequest/srf_spec.rb
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+ - spec/ms/sequest/srf_spec_helper.rb
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+ - spec/ms/sequest/sqt_spec_helper.rb
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+ - spec/ms/sequest/pepxml_spec.rb
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+ - spec/spec_helper.rb
data/README DELETED
@@ -1,23 +0,0 @@
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- = {Ms-Sequest}[http://mspire.rubyforge.org/projects/ms-sequest]
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-
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- An {Mspire}[http://mspire.rubyforge.org] library supporting SEQUEST, Bioworks, SQT and associated formats.
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-
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- == Description
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-
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- * Lighthouse[http://bahuvrihi.lighthouseapp.com/projects/16692-mspire/tickets]
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- * Github[http://github.com/jtprince/ms-sequest/tree/master]
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- * {Google Group}[http://groups.google.com/group/mspire-forum]
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-
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- == Installation
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-
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- Ms-Sequest is available as a gem on RubyForge[http://rubyforge.org/projects/mspire]. Use:
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-
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- % gem install ms-sequest
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-
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- == Info
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-
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- Copyright (c) 2006 University of Texas at Austin
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- Copyright (c) Regents of the University of Colorado and Howard Hughes Medical Institute.
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- Developer:: {John Prince}, {Edward Marcotte Lab}[http://polaris.icmb.utexas.edu/home.html], {Natalie Ahn Lab}[http://www.colorado.edu/chem/people/ahnn.html], {Howard Hughes Medical Institute}[http://www.hhmi.org/], {BYU Dept. of Chemistry and Biochemistry}[http://www.chem.byu.edu/]
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- Support::
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- Licence:: {MIT-Style}[link:files/MIT-LICENSE.html]