mspire-lipidomics 0.1.9 → 0.1.10

data/Rakefile

@@ -13,7 +13,7 @@ Jeweler::Tasks.new do |gem|
   gem.description = %Q{does lipidomics}
   gem.email = "jtprince@gmail.com"
   gem.authors = ["John T. Prince"]
-  gem.add_dependency "mspire", "~> 0.8.3"
+  gem.add_dependency "mspire", "~> 0.8.4"
   gem.add_development_dependency "rubabel", ">= 0.1.6"
   gem.add_development_dependency "rspec", "~> 2.3.0"
   gem.add_development_dependency "jeweler", "~> 1.6.4"

data/VERSION

@@ -1 +1 @@
-0.1.9
+0.1.10

data/lib/mspire/lipid/modification.rb

@@ -75,7 +75,8 @@ module Mspire
       # if no mass or formula is given then it searches command mods for the name
       # @param [Symbol] name the name of the mod
       # A number of opts are expected if they are not found in the FORMULAS,
-      # CHARGE, or MASSDIFFS hashes:
+      # CHARGE, or MASSDIFFS hashes.  However, the massdiff will be inferred
+      # from the formula if it is not given:
       #
       #     attributes:
       #     :formula = the chemical formula, lipidmaps style ("C2H4BrO") or

data/mspire-lipidomics.gemspec

@@ -5,7 +5,7 @@
 
 Gem::Specification.new do |s|
   s.name = "mspire-lipidomics"
-  s.version = "0.1.9"
+  s.version = "0.1.10"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["John T. Prince"]
@@ -63,20 +63,20 @@ Gem::Specification.new do |s|
     s.specification_version = 3
 
     if Gem::Version.new(Gem::VERSION) >= Gem::Version.new('1.2.0') then
-      s.add_runtime_dependency(%q<mspire>, ["~> 0.8.3"])
+      s.add_runtime_dependency(%q<mspire>, ["~> 0.8.4"])
       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>, ["~> 0.8.3"])
+      s.add_dependency(%q<mspire>, ["~> 0.8.4"])
       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>, ["~> 0.8.3"])
+    s.add_dependency(%q<mspire>, ["~> 0.8.4"])
     s.add_dependency(%q<rubabel>, [">= 0.1.6"])
     s.add_dependency(%q<rspec>, ["~> 2.3.0"])
     s.add_dependency(%q<jeweler>, ["~> 1.6.4"])

data/script/find_nearest_lipid.rb

@@ -14,6 +14,7 @@ parser = Trollop::Parser.new do
   opt :top_n, "how many closest ions to print", :default => 3
   banner ""
   text "modifications: (at least 1 charged mod is required)"
+  #opt :newmod, "<name>:<formula>:<charge>:<L/G>:<#occurences>  L/G=loss or gain", :type => :string, :multi => true
   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
@@ -22,6 +23,8 @@ parser = Trollop::Parser.new do
   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
+  text ""
+  text "other:"
   opt :textfile, "a text file with m/z values, one per line", :type => String
   opt :lower_bound, "use lower bound searching (requires m/z's to be in sorted order)"
   opt :sort, "sorts the m/z's"
@@ -35,6 +38,7 @@ if ARGV.size == 0
 end
 
 CHARGED_MODS = [:lithium, :sodium, :ammonium, :proton_gain, :proton_loss]
+UNCHARGED_MODS = [:water_loss, :carbon_dioxide_loss, :ammonia_loss]
 
 unless CHARGED_MODS.any? {|key| opts[key] > 0 }
   puts "*" * 78
@@ -81,8 +85,10 @@ lipids.each do |lipid|
     if opts[key] > 0
       opts[key].downto(1) do |num_charge_mod|
         mods_to_use = [mods[key]] * num_charge_mod
-        opts[:water_loss].downto(0) do |i|
-          ions << Mspire::Lipid::Ion.new(lipid, mods_to_use + ([mods[:water_loss]]*i)) 
+        UNCHARGED_MODS.each do |umod|
+          opts[umod].downto(0) do |i|
+            ions << Mspire::Lipid::Ion.new(lipid, mods_to_use + ([mods[:umod]]*i)) 
+          end
         end
       end
     end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: mspire-lipidomics
 version: !ruby/object:Gem::Version
-  version: 0.1.9
+  version: 0.1.10
   prerelease: 
 platform: ruby
 authors:
@@ -18,7 +18,7 @@ dependencies:
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
-        version: 0.8.3
+        version: 0.8.4
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
@@ -26,7 +26,7 @@ dependencies:
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
-        version: 0.8.3
+        version: 0.8.4
 - !ruby/object:Gem::Dependency
   name: rubabel
   requirement: !ruby/object:Gem::Requirement