RubyGems - mspire-sequest - Versions diffs - 0.2.5 - Mend

mspire-sequest 0.2.5

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Files changed (40) hide show

data/.autotest +30 -0
data/.gitmodules +9 -0
data/History +79 -0
data/LICENSE +22 -0
data/README.rdoc +85 -0
data/Rakefile +52 -0
data/VERSION +1 -0
data/bin/srf_to_pepxml.rb +7 -0
data/bin/srf_to_search.rb +7 -0
data/bin/srf_to_sqt.rb +8 -0
data/lib/mspire/sequest/params.rb +331 -0
data/lib/mspire/sequest/pepxml/modifications.rb +247 -0
data/lib/mspire/sequest/pepxml/params.rb +32 -0
data/lib/mspire/sequest/sqt.rb +393 -0
data/lib/mspire/sequest/srf/pepxml/sequest.rb +21 -0
data/lib/mspire/sequest/srf/pepxml.rb +333 -0
data/lib/mspire/sequest/srf/search.rb +158 -0
data/lib/mspire/sequest/srf/sqt.rb +218 -0
data/lib/mspire/sequest/srf.rb +715 -0
data/lib/mspire/sequest.rb +6 -0
data/script/fasta_ipi_to_ncbi-ish.rb +29 -0
data/spec/mspire/sequest/params_spec.rb +135 -0
data/spec/mspire/sequest/pepxml/modifications_spec.rb +50 -0
data/spec/mspire/sequest/pepxml_spec.rb +311 -0
data/spec/mspire/sequest/sqt_spec.rb +51 -0
data/spec/mspire/sequest/sqt_spec_helper.rb +34 -0
data/spec/mspire/sequest/srf/pepxml_spec.rb +89 -0
data/spec/mspire/sequest/srf/search_spec.rb +131 -0
data/spec/mspire/sequest/srf/sqt_spec.rb +228 -0
data/spec/mspire/sequest/srf_spec.rb +113 -0
data/spec/mspire/sequest/srf_spec_helper.rb +172 -0
data/spec/spec_helper.rb +22 -0
data/spec/testfiles/7MIX_STD_110802_1.sequest_params_fragment.srf +0 -0
data/spec/testfiles/bioworks31.params +77 -0
data/spec/testfiles/bioworks32.params +62 -0
data/spec/testfiles/bioworks33.params +63 -0
data/spec/testfiles/corrupted_900.srf +0 -0
data/spec/testfiles/small.sqt +87 -0
data/spec/testfiles/small2.sqt +176 -0
metadata +185 -0

metadata ADDED Viewed

@@ -0,0 +1,185 @@
+--- !ruby/object:Gem::Specification
+name: mspire-sequest
+version: !ruby/object:Gem::Version
+  version: 0.2.5
+  prerelease:
+platform: ruby
+authors:
+- John T. Prince
+autorequire:
+bindir: bin
+cert_chain: []
+date: 2012-03-20 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: mspire
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 0.7.3
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 0.7.3
+- !ruby/object:Gem::Dependency
+  name: trollop
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '1.16'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '1.16'
+- !ruby/object:Gem::Dependency
+  name: jeweler
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 1.5.2
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 1.5.2
+- !ruby/object:Gem::Dependency
+  name: bio
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 1.4.2
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 1.4.2
+- !ruby/object:Gem::Dependency
+  name: ms-testdata
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - '='
+      - !ruby/object:Gem::Version
+        version: 0.2.1
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - '='
+      - !ruby/object:Gem::Version
+        version: 0.2.1
+- !ruby/object:Gem::Dependency
+  name: rspec
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 2.8.0
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 2.8.0
+description: reads .SRF, .SQT and supports conversions
+email: jtprince@gmail.com
+executables:
+- srf_to_pepxml.rb
+- srf_to_search.rb
+- srf_to_sqt.rb
+extensions: []
+extra_rdoc_files:
+- LICENSE
+- README.rdoc
+files:
+- .autotest
+- .gitmodules
+- History
+- LICENSE
+- README.rdoc
+- Rakefile
+- VERSION
+- bin/srf_to_pepxml.rb
+- bin/srf_to_search.rb
+- bin/srf_to_sqt.rb
+- lib/mspire/sequest.rb
+- lib/mspire/sequest/params.rb
+- lib/mspire/sequest/pepxml/modifications.rb
+- lib/mspire/sequest/pepxml/params.rb
+- lib/mspire/sequest/sqt.rb
+- lib/mspire/sequest/srf.rb
+- lib/mspire/sequest/srf/pepxml.rb
+- lib/mspire/sequest/srf/pepxml/sequest.rb
+- lib/mspire/sequest/srf/search.rb
+- lib/mspire/sequest/srf/sqt.rb
+- script/fasta_ipi_to_ncbi-ish.rb
+- spec/mspire/sequest/params_spec.rb
+- spec/mspire/sequest/pepxml/modifications_spec.rb
+- spec/mspire/sequest/pepxml_spec.rb
+- spec/mspire/sequest/sqt_spec.rb
+- spec/mspire/sequest/sqt_spec_helper.rb
+- spec/mspire/sequest/srf/pepxml_spec.rb
+- spec/mspire/sequest/srf/search_spec.rb
+- spec/mspire/sequest/srf/sqt_spec.rb
+- spec/mspire/sequest/srf_spec.rb
+- spec/mspire/sequest/srf_spec_helper.rb
+- spec/spec_helper.rb
+- spec/testfiles/7MIX_STD_110802_1.sequest_params_fragment.srf
+- spec/testfiles/bioworks31.params
+- spec/testfiles/bioworks32.params
+- spec/testfiles/bioworks33.params
+- spec/testfiles/corrupted_900.srf
+- spec/testfiles/small.sqt
+- spec/testfiles/small2.sqt
+homepage: http://github.com/princelab/mspire-sequest
+licenses:
+- MIT
+post_install_message:
+rdoc_options: []
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  none: false
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
+required_rubygems_version: !ruby/object:Gem::Requirement
+  none: false
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
+requirements: []
+rubyforge_project: mspire
+rubygems_version: 1.8.18
+signing_key:
+specification_version: 3
+summary: An mspire library supporting SEQUEST, Bioworks, SQT, etc
+test_files: []