ms-core 0.0.9 → 0.0.10

data/Gemfile

@@ -0,0 +1,13 @@
+source "http://rubygems.org"
+# Add dependencies required to use your gem here.
+# Example:
+#   gem "activesupport", ">= 2.3.5"
+
+# Add dependencies to develop your gem here.
+# Include everything needed to run rake, tests, features, etc.
+group :development do
+  gem "spec-more", ">= 0"
+  gem "bundler", "~> 1.0.0"
+  gem "jeweler", "~> 1.5.2"
+  gem "rcov", ">= 0"
+end

data/Gemfile.lock

@@ -0,0 +1,22 @@
+GEM
+  remote: http://rubygems.org/
+  specs:
+    bacon (1.1.0)
+    git (1.2.5)
+    jeweler (1.5.2)
+      bundler (~> 1.0.0)
+      git (>= 1.2.5)
+      rake
+    rake (0.8.7)
+    rcov (0.9.9)
+    spec-more (0.0.4)
+      bacon
+
+PLATFORMS
+  ruby
+
+DEPENDENCIES
+  bundler (~> 1.0.0)
+  jeweler (~> 1.5.2)
+  rcov
+  spec-more

data/Rakefile

@@ -1,30 +1,36 @@
 require 'rubygems'
+require 'bundler'
+begin
+  Bundler.setup(:default, :development)
+rescue Bundler::BundlerError => e
+  $stderr.puts e.message
+  $stderr.puts "Run `bundle install` to install missing gems"
+  exit e.status_code
+end
 require 'rake'
-require 'jeweler'
-require 'rcov/rcovtask'
-require 'rake/rdoctask'
-require 'rake/testtask'
 
+require 'jeweler'
 Jeweler::Tasks.new do |gem|
+  # gem is a Gem::Specification... see http://docs.rubygems.org/read/chapter/20 for more options
   gem.name = "ms-core"
-  gem.summary = "basic, shared functionality for mspire libraries"
-  gem.description = "basic, shared functionality for mspire libraries"
- gem.email = "jtprince@gmail.com"
-  gem.homepage = "http://github.com/jtprince/ms-core/rdoc"
-  gem.authors = ["Simon Chiang", "John Prince"]
-  # dependencies:
-  gem.add_dependency("molecules", ">= 0.2.0")
-
-  # dev dependencies:
-  gem.add_development_dependency "spec-more", ">= 0"
+  gem.homepage = "http://github.com/jtprince/ms-core"
+  gem.license = "MIT"
+  gem.summary = %Q{basic, shared functionality for mspire libraries}
+  gem.description = %Q{basic, shared functionality for mspire libraries}
+  gem.email = "jtprince@gmail.com"
+  gem.authors = ["John T. Prince", "Simon Chiang"]
+  # Dependencies in Gemfile
 end
+Jeweler::RubygemsDotOrgTasks.new
 
+require 'rake/testtask'
 Rake::TestTask.new(:spec) do |spec|
   spec.libs << 'lib' << 'spec'
   spec.pattern = 'spec/**/*_spec.rb'
   spec.verbose = true
 end
 
+require 'rcov/rcovtask'
 Rcov::RcovTask.new do |spec|
   spec.libs << 'spec'
   spec.pattern = 'spec/**/*_spec.rb'
@@ -33,6 +39,7 @@ end
 
 task :default => :spec
 
+require 'rake/rdoctask'
 Rake::RDocTask.new do |rdoc|
   version = File.exist?('VERSION') ? File.read('VERSION') : ""
 

data/VERSION

@@ -1 +1 @@
-0.0.9
+0.0.10

data/lib/ms/mass/aa.rb

@@ -1,9 +1,11 @@
-require 'molecules'
+require 'yaml'
+
 require 'ms/mass'
 
 module Ms
   module Mass
 
+   
     # A module for working with commonly used residue masses in proteomics.
     #
     #     require 'ms/mass/aa'
@@ -15,10 +17,96 @@ module Ms
     #     # or use symbols
     #     MONO[:A]  # => 71.0371137878
     #
-    # This module is built on the excellent {'molecules'
+    # molecules is built on constants and constants on ruby-units and it seems
+    # impossible to get ruby-units 1.9 compatible.  Until that point, values
+    # will remain hard coded and these values are free of dependencies.
+    #
+    # The values are built using the excellent {'molecules'
     # library}[http://github.com/bahuvrihi/molecules/tree/master].  See that
     # library for more serious work with masses.
     module AA
+
+      yaml = <<-END
+        --- 
+        avg: 
+          "*": 118.88603
+          A: 71.0779
+          B: 172.1405
+          C: 103.1429
+          D: 115.0874
+          E: 129.11398
+          F: 147.17386
+          G: 57.05132
+          H: 137.13928
+          I: 113.15764
+          K: 128.17228
+          L: 113.15764
+          M: 131.19606
+          N: 114.10264
+          O: 211.28076
+          P: 97.11518
+          Q: 128.12922
+          R: 156.18568
+          S: 87.0773
+          T: 101.10388
+          U: 150.0379
+          V: 99.13106
+          W: 186.2099
+          X: 118.88603
+          Y: 163.17326
+          Z: 128.6231
+        mono: 
+          "*": 118.805716
+          A: 71.0371137878
+          B: 172.048405
+          C: 103.0091844778
+          D: 115.026943032
+          E: 129.0425930962
+          F: 147.0684139162
+          G: 57.0214637236
+          H: 137.0589118624
+          I: 113.0840639804
+          K: 128.0949630177
+          L: 113.0840639804
+          M: 131.0404846062
+          N: 114.0429274472
+          O: 211.1446528645
+          P: 97.052763852
+          Q: 128.0585775114
+          R: 156.1011110281
+          S: 87.0320284099
+          T: 101.0476784741
+          U: 150.9536355878
+          V: 99.0684139162
+          W: 186.0793129535
+          X: 118.805716
+          Y: 163.0633285383
+          Z: 128.550585
+      END
+
+    
+      embedded_mass_hashes = YAML.load(yaml)
+      # amino_acids keys as strings, monoisotopic masses
+      MONO_STRING = embedded_mass_hashes['mono']
+      # amino_acids keys as symbols, monoisotopic masses
+      MONO_SYM = Hash[MONO_STRING.map {|aa,mass| [aa.to_sym, mass] } ]
+
+      # amino_acids keys as strings, average masses
+      AVG_STRING = embedded_mass_hashes['avg']
+      # amino_acids keys as symbols, average masses
+      AVG_SYM = Hash[AVG_STRING.map {|aa,mass| [aa.to_sym, mass] } ]
+
+      # amino_acids keys as symbols and also strings, monoisotopic masses
+      MONO = MONO_SYM.merge(MONO_STRING)
+      # amino_acids keys as symbols and also strings, average masses
+      AVG = AVG_SYM.merge(AVG_STRING)
+
+      ###########################################################################
+      # This section is broken in 1.9 (ruby-units fault), so we generate the
+      # data and include it.
+      ###########################################################################
+
+=begin
       # These are included here to offer maximum functionality
       MOLECULES_MONO_UNSUPPORTED = {
         :B => 172.048405, # average of aspartic acid and asparagine
@@ -39,10 +127,11 @@ module Ms
       # returns a hash based on the molecules library of amino acid residues.
       # type is :mono or :avg
       def self.mass_index(type=:mono)
+        require 'molecules'
         hash = {}
         ('A'..'Z').each do |letter|
           if res = Molecules::Libraries::Residue[letter]
-            hash[letter] =
+            hash[letter.to_sym] =
               if type == :mono
                 res.mass
               elsif type == :avg
@@ -55,13 +144,38 @@ module Ms
         hash
       end
 
+      # Returns mono and avg tables as yaml with all keys as strings.
+      # The top level keys are 'avg' and 'mono'
+      def self.indices_to_yaml
+        # this only works with ruby1.8 currently, so we use it to generate the
+        # data we need
+        require 'molecules'
+        [AVG, MONO].each do |hash|
+          hash.each {|k,v| hash[k.to_s] = hash.delete(k) }
+        end
+        {'avg' => AVG, 'mono' => MONO}.to_yaml
+      end
+
       MONO = MOLECULES_MONO_UNSUPPORTED.merge( self.mass_index(:mono) )
       AVG = MOLECULES_AVG_UNSUPPORTED.merge( self.mass_index(:avg) )
-      [AVG, MONO].each do |hash|
-        hash.each {|k,v| hash[k.to_s] = v }
+
+      # the script to sort it nicely using ruby 1.9:
+      require 'yaml'
+      h = YAML.load_file(ARGV.shift)
+      new_hash = {}
+      h.sort.each do |key, aahash|
+        new_hash[key] = Hash[aahash.sort]
       end
+      puts new_hash.to_yaml
+
+=end
+
+      ###########################################################################
+      # End fudge
+      ###########################################################################
 
     end
   end
 end
 
+

data/spec/ms/mass/aa_spec.rb

@@ -0,0 +1,14 @@
+require 'spec_helper'
+
+require 'ms/mass/aa'
+
+describe 'using a mass table' do
+  it 'has monoisotopic masses by string or symbol' do
+    Ms::Mass::AA::MONO['A'].is 71.0371137878
+    Ms::Mass::AA::MONO[:A].is 71.0371137878
+  end
+  it 'has average masses by string or symbol' do
+    Ms::Mass::AA::AVG['A'].is 71.0779
+    Ms::Mass::AA::AVG[:A].is 71.0779
+  end
+end

data/spec/spec_helper.rb

@@ -1,5 +1,16 @@
 require 'rubygems'
-require 'spec/more'
+require 'bundler'
+begin
+  Bundler.setup(:default, :development)
+rescue Bundler::BundlerError => e
+  $stderr.puts e.message
+  $stderr.puts "Run `bundle install` to install missing gems"
+  exit e.status_code
+end
 require 'benchmark'
+require 'spec/more'
+
+$LOAD_PATH.unshift(File.dirname(__FILE__))
+$LOAD_PATH.unshift(File.join(File.dirname(__FILE__), '..', 'lib'))
 
 Bacon.summary_on_exit

metadata

@@ -5,22 +5,21 @@ version: !ruby/object:Gem::Version
   segments: 
   - 0
   - 0
-  - 9
-  version: 0.0.9
+  - 10
+  version: 0.0.10
 platform: ruby
 authors: 
+- John T. Prince
 - Simon Chiang
-- John Prince
 autorequire: 
 bindir: bin
 cert_chain: []
 
-date: 2011-02-21 00:00:00 -07:00
+date: 2011-02-24 00:00:00 -07:00
 default_executable: 
 dependencies: 
 - !ruby/object:Gem::Dependency 
-  name: molecules
-  prerelease: false
+  name: spec-more
   requirement: &id001 !ruby/object:Gem::Requirement 
     none: false
     requirements: 
@@ -28,15 +27,43 @@ dependencies:
       - !ruby/object:Gem::Version 
         segments: 
         - 0
-        - 2
-        - 0
-        version: 0.2.0
-  type: :runtime
+        version: "0"
+  type: :development
+  prerelease: false
   version_requirements: *id001
 - !ruby/object:Gem::Dependency 
-  name: spec-more
-  prerelease: false
+  name: bundler
   requirement: &id002 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ~>
+      - !ruby/object:Gem::Version 
+        segments: 
+        - 1
+        - 0
+        - 0
+        version: 1.0.0
+  type: :development
+  prerelease: false
+  version_requirements: *id002
+- !ruby/object:Gem::Dependency 
+  name: jeweler
+  requirement: &id003 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ~>
+      - !ruby/object:Gem::Version 
+        segments: 
+        - 1
+        - 5
+        - 2
+        version: 1.5.2
+  type: :development
+  prerelease: false
+  version_requirements: *id003
+- !ruby/object:Gem::Dependency 
+  name: rcov
+  requirement: &id004 !ruby/object:Gem::Requirement 
     none: false
     requirements: 
     - - ">="
@@ -45,7 +72,8 @@ dependencies:
         - 0
         version: "0"
   type: :development
-  version_requirements: *id002
+  prerelease: false
+  version_requirements: *id004
 description: basic, shared functionality for mspire libraries
 email: jtprince@gmail.com
 executables: []
@@ -55,6 +83,8 @@ extensions: []
 extra_rdoc_files: 
 - README.rdoc
 files: 
+- Gemfile
+- Gemfile.lock
 - History
 - MIT-LICENSE
 - README.rdoc
@@ -82,12 +112,13 @@ files:
 - lib/openany.rb
 - spec/ms/calc_spec.rb
 - spec/ms/data_spec.rb
+- spec/ms/mass/aa_spec.rb
 - spec/ms/support/binary_search_spec.rb
 - spec/spec_helper.rb
 has_rdoc: true
-homepage: http://github.com/jtprince/ms-core/rdoc
-licenses: []
-
+homepage: http://github.com/jtprince/ms-core
+licenses: 
+- MIT
 post_install_message: 
 rdoc_options: []
 
@@ -98,6 +129,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
   requirements: 
   - - ">="
     - !ruby/object:Gem::Version 
+      hash: -2752488455848385314
       segments: 
       - 0
       version: "0"
@@ -119,5 +151,6 @@ summary: basic, shared functionality for mspire libraries
 test_files: 
 - spec/ms/calc_spec.rb
 - spec/ms/data_spec.rb
+- spec/ms/mass/aa_spec.rb
 - spec/ms/support/binary_search_spec.rb
 - spec/spec_helper.rb