mspire-lipidomics 0.1.8 → 0.1.9

data/Rakefile

@@ -13,8 +13,8 @@ Jeweler::Tasks.new do |gem|
   gem.description = %Q{does lipidomics}
   gem.email = "jtprince@gmail.com"
   gem.authors = ["John T. Prince"]
-  gem.add_dependency "mspire", "~> 0.7.17"
-  gem.add_development_dependency "rubabel", ">= 0.1.0"
+  gem.add_dependency "mspire", "~> 0.8.3"
+  gem.add_development_dependency "rubabel", ">= 0.1.6"
   gem.add_development_dependency "rspec", "~> 2.3.0"
   gem.add_development_dependency "jeweler", "~> 1.6.4"
   gem.add_development_dependency "rcov", ">= 0"

data/VERSION

@@ -1 +1 @@
-0.1.8
+0.1.9

data/lib/mspire/lipid/modification.rb

@@ -42,13 +42,19 @@ module Mspire
         :proton => 'H',
         :ammonium => 'NH4',
         :lithium => 'Li',
+        :sodium => 'Na',
         :water => 'H2O',
+        :ammonia => 'NH3',
+        :carbon_dioxide => 'CO2',
       }
       CHARGE = {
         :proton => 1,
         :ammonium => 1,
         :lithium => 1,
+        :sodium=> 1,
         :water => 0,
+        :ammonia => 0,
+        :carbon_dioxide => 0,
       }
 
       # determined by running formulas through Mspire::Mass.massdiff

data/mspire-lipidomics.gemspec

@@ -5,11 +5,11 @@
 
 Gem::Specification.new do |s|
   s.name = "mspire-lipidomics"
-  s.version = "0.1.8"
+  s.version = "0.1.9"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["John T. Prince"]
-  s.date = "2012-07-10"
+  s.date = "2012-09-20"
   s.description = "does lipidomics"
   s.email = "jtprince@gmail.com"
   s.executables = ["lipidomic-search.rb"]
@@ -56,28 +56,28 @@ Gem::Specification.new do |s|
   s.homepage = "http://github.com/princelab/mspire-lipidomics"
   s.licenses = ["MIT"]
   s.require_paths = ["lib"]
-  s.rubygems_version = "1.8.24"
+  s.rubygems_version = "1.8.23"
   s.summary = "mass spectrometry based lipidomics - especially shotgun lipidomics"
 
   if s.respond_to? :specification_version then
     s.specification_version = 3
 
     if Gem::Version.new(Gem::VERSION) >= Gem::Version.new('1.2.0') then
-      s.add_runtime_dependency(%q<mspire>, ["~> 0.7.17"])
-      s.add_development_dependency(%q<rubabel>, [">= 0.1.0"])
+      s.add_runtime_dependency(%q<mspire>, ["~> 0.8.3"])
+      s.add_development_dependency(%q<rubabel>, [">= 0.1.6"])
       s.add_development_dependency(%q<rspec>, ["~> 2.3.0"])
       s.add_development_dependency(%q<jeweler>, ["~> 1.6.4"])
       s.add_development_dependency(%q<rcov>, [">= 0"])
     else
-      s.add_dependency(%q<mspire>, ["~> 0.7.17"])
-      s.add_dependency(%q<rubabel>, [">= 0.1.0"])
+      s.add_dependency(%q<mspire>, ["~> 0.8.3"])
+      s.add_dependency(%q<rubabel>, [">= 0.1.6"])
       s.add_dependency(%q<rspec>, ["~> 2.3.0"])
       s.add_dependency(%q<jeweler>, ["~> 1.6.4"])
       s.add_dependency(%q<rcov>, [">= 0"])
     end
   else
-    s.add_dependency(%q<mspire>, ["~> 0.7.17"])
-    s.add_dependency(%q<rubabel>, [">= 0.1.0"])
+    s.add_dependency(%q<mspire>, ["~> 0.8.3"])
+    s.add_dependency(%q<rubabel>, [">= 0.1.6"])
     s.add_dependency(%q<rspec>, ["~> 2.3.0"])
     s.add_dependency(%q<jeweler>, ["~> 1.6.4"])
     s.add_dependency(%q<rcov>, [">= 0"])

data/script/find_nearest_lipid.rb

@@ -15,7 +15,10 @@ parser = Trollop::Parser.new do
   banner ""
   text "modifications: (at least 1 charged mod is required)"
   opt :lithium, "search for i down to 1 lithium adducts", :default => 0
+  opt :sodium, "search for i down to 1 sodium adducts", :default => 0
   opt :ammonium, "search for i down to 1 ammonium adducts", :default => 0
+  opt :ammonia_loss, "search for i down to 1 ammonia losses", :default => 0
+  opt :carbon_dioxide_loss, "search for i down to 1 CO2 losses", :default => 0
   opt :proton_gain, "search for i down to 1 proton additions", :default => 0
   opt :proton_loss, "search for i down to 1 proton losses", :default => 0
   opt :water_loss, "if used, *all* mods are also considered with i down to 0 water losses", :default => 0
@@ -31,7 +34,7 @@ if ARGV.size == 0
   exit
 end
 
-CHARGED_MODS = [:lithium, :ammonium, :proton_gain, :proton_loss]
+CHARGED_MODS = [:lithium, :sodium, :ammonium, :proton_gain, :proton_loss]
 
 unless CHARGED_MODS.any? {|key| opts[key] > 0 }
   puts "*" * 78
@@ -63,8 +66,11 @@ mods = {
   proton_gain: LipidMod.new(:proton),
   water_loss: LipidMod.new(:water, :loss => true),
   lithium: LipidMod.new(:lithium),
+  sodium: LipidMod.new(:sodium),
   ammonium: LipidMod.new(:ammonium),
-  proton_loss: LipidMod.new(:proton, :loss => true)
+  proton_loss: LipidMod.new(:proton, :loss => true),
+  ammonia_loss: LipidMod.new(:ammonium, :loss => true),
+  carbon_dioxide_loss: LipidMod.new(:carbon_dioxide, :loss => true),
 }
 
 lipids = Mspire::LipidMaps.parse_file(lipidmaps)

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: mspire-lipidomics
 version: !ruby/object:Gem::Version
-  version: 0.1.8
+  version: 0.1.9
   prerelease: 
 platform: ruby
 authors:
@@ -9,7 +9,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2012-07-10 00:00:00.000000000 Z
+date: 2012-09-20 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: mspire
@@ -18,7 +18,7 @@ dependencies:
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
-        version: 0.7.17
+        version: 0.8.3
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
@@ -26,7 +26,7 @@ dependencies:
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
-        version: 0.7.17
+        version: 0.8.3
 - !ruby/object:Gem::Dependency
   name: rubabel
   requirement: !ruby/object:Gem::Requirement
@@ -34,7 +34,7 @@ dependencies:
     requirements:
     - - ! '>='
       - !ruby/object:Gem::Version
-        version: 0.1.0
+        version: 0.1.6
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
@@ -42,7 +42,7 @@ dependencies:
     requirements:
     - - ! '>='
       - !ruby/object:Gem::Version
-        version: 0.1.0
+        version: 0.1.6
 - !ruby/object:Gem::Dependency
   name: rspec
   requirement: !ruby/object:Gem::Requirement
@@ -155,7 +155,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 1.8.24
+rubygems_version: 1.8.23
 signing_key: 
 specification_version: 3
 summary: mass spectrometry based lipidomics - especially shotgun lipidomics