mspire-lipidomics 0.1.5 → 0.1.8

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", ">= 0.7.8"
+  gem.add_dependency "mspire", "~> 0.7.17"
   gem.add_development_dependency "rubabel", ">= 0.1.0"
   gem.add_development_dependency "rspec", "~> 2.3.0"
   gem.add_development_dependency "jeweler", "~> 1.6.4"

data/VERSION

@@ -1 +1 @@
-0.1.5
+0.1.8

data/bin/lipidomic-search.rb

@@ -1,5 +1,8 @@
 #!/usr/bin/env ruby
 
+puts "under development"
+
+=begin
 require 'trollop'
 require 'ms/mzml'
 require 'ms/lipid/search'
@@ -197,3 +200,4 @@ files.each do |file|
     end
   end
 end
+=end

data/lib/mspire/lipid/ion.rb

@@ -1,4 +1,5 @@
 require 'mspire/lipid/ion/fragment'
+require 'mspire/molecular_formula'
 
 module Mspire
   class Lipid
@@ -20,20 +21,27 @@ module Mspire
       def charge
         z = 0
         @modifications.each do |mod|
-          z -= mod.charge
+          z += mod.charge
         end
         z
       end
 
+      # a MolecularFormula object
       def formula
-        formula = lipid.formula.dup
+        _formula = @lipid.formula
+        _formula = Mspire::MolecularFormula.from_any(_formula) unless _formula.is_a?(Mspire::MolecularFormula)
         modifications.each do |mod|
-          formula += mod.formula
+          if mod.gain?
+            _formula += mod.formula 
+          else
+            _formula -= mod.formula
+          end
         end
-        formula
+        _formula
       end
 
-      def mz
+      # value is cached
+      def mz_signed
         return @mz if @mz
         mass = @lipid.mass
         charge = 0
@@ -48,6 +56,12 @@ module Mspire
         end
       end
 
+      # the unsigned m/z value
+      def mz
+        _mz_signed = mz_signed
+        _mz_signed >= 0 ? _mz_signed : -_mz_signed
+      end
+
       def inspect
         "<|| Ion mz=#{mz} #{lipid.inspect} + #{modifications.map(&:inspect).join(', ')} ||>"
       end

data/lib/mspire/lipid/modification.rb

@@ -59,7 +59,7 @@ module Mspire
 
       # as a symbol
       attr_accessor :name
-      # as a MolecularFormula object
+      # a MolecularFormula object
       attr_accessor :formula
       # negative indicates a loss
       attr_accessor :massdiff
@@ -73,7 +73,7 @@ module Mspire
       #
       #     attributes:
       #     :formula = the chemical formula, lipidmaps style ("C2H4BrO") or
-      #                any valid argument to MolecularFormula.new
+      #                any valid argument to MolecularFormula.from_any
       #     :massdiff = +/-Float
       #     :charge = +/- Integer
       #
@@ -89,7 +89,7 @@ module Mspire
         @name = name
         @formula = 
           if ( form_string = (opts[:formula] || FORMULAS[name]) )
-            Mspire::MolecularFormula.new( form_string )
+            Mspire::MolecularFormula.from_any( form_string )
           end
         @massdiff = opts[:massdiff] || MASSDIFFS[name]
         @charge = opts[:charge] || CHARGE[name]
@@ -102,10 +102,12 @@ module Mspire
         end
       end
 
-      def charged_formula
+      def charged_formula_string
         @formula.to_s + @charge.abs.times.map { (@charge > 0) ? '+' : '-' }.join
       end
 
+      alias_method :to_s, :charged_formula_string
+
       def gain?
         massdiff > 0
       end
@@ -115,7 +117,7 @@ module Mspire
       end
 
       def inspect
-        "<Mod: #{charged_formula}>"
+        "<Mod: #{to_s}>"
       end
 
     end

data/lib/mspire/lipid_maps.rb

@@ -69,7 +69,7 @@ module Mspire
       if opts.values_at(:molecular_formula_objects, :rubabel_molecules).any? || (opts[:high_res_mass] && lm_ft == :programmatic)
         lipids.each do |lipid|
           if opts[:molecular_formula_objects]
-            lipid.formula = Mspire::MolecularFormula.new(lipid.formula)
+            lipid.formula = Mspire::MolecularFormula.from_string(lipid.formula)
           end
           if lm_ft == :programmatic && opts[:high_res_mass]
             lipid.mass = Mspire::Mass.formula_to_exact_mass(lipid.formula)

data/mspire-lipidomics.gemspec

@@ -5,11 +5,11 @@
 
 Gem::Specification.new do |s|
   s.name = "mspire-lipidomics"
-  s.version = "0.1.5"
+  s.version = "0.1.8"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["John T. Prince"]
-  s.date = "2012-05-10"
+  s.date = "2012-07-10"
   s.description = "does lipidomics"
   s.email = "jtprince@gmail.com"
   s.executables = ["lipidomic-search.rb"]
@@ -56,27 +56,27 @@ Gem::Specification.new do |s|
   s.homepage = "http://github.com/princelab/mspire-lipidomics"
   s.licenses = ["MIT"]
   s.require_paths = ["lib"]
-  s.rubygems_version = "1.8.18"
+  s.rubygems_version = "1.8.24"
   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>, [">= 0.7.8"])
+      s.add_runtime_dependency(%q<mspire>, ["~> 0.7.17"])
       s.add_development_dependency(%q<rubabel>, [">= 0.1.0"])
       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>, [">= 0.7.8"])
+      s.add_dependency(%q<mspire>, ["~> 0.7.17"])
       s.add_dependency(%q<rubabel>, [">= 0.1.0"])
       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>, [">= 0.7.8"])
+    s.add_dependency(%q<mspire>, ["~> 0.7.17"])
     s.add_dependency(%q<rubabel>, [">= 0.1.0"])
     s.add_dependency(%q<rspec>, ["~> 2.3.0"])
     s.add_dependency(%q<jeweler>, ["~> 1.6.4"])

data/script/find_nearest_lipid.rb

@@ -14,11 +14,11 @@ 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 :lithium, "search for lithium adducts"
-  opt :ammonium, "search for ammonium adducts"
-  opt :proton_gain, "search for proton gain"
-  opt :proton_loss, "search for proton loss"
-  opt :water_loss, "if used, *all* mods are also considered with water loss"
+  opt :lithium, "search for i down to 1 lithium adducts", :default => 0
+  opt :ammonium, "search for i down to 1 ammonium adducts", :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
   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"
@@ -33,7 +33,7 @@ end
 
 CHARGED_MODS = [:lithium, :ammonium, :proton_gain, :proton_loss]
 
-unless CHARGED_MODS.any? {|key| opts[key] }
+unless CHARGED_MODS.any? {|key| opts[key] > 0 }
   puts "*" * 78
   puts "ArgumentError: need at least one charged mod!"
   puts "*" * 78
@@ -44,9 +44,11 @@ end
 (lipidmaps, *actual_mzs) = ARGV
 
 if f=opts[:textfile]
-  actual_mzs = IO.readlines(f).map(&:chomp).map(&:to_f)
+  actual_mzs = IO.readlines(f).map(&:chomp)
 end
 
+actual_mzs.map!(&:to_f)
+
 unless actual_mzs.size > 0
   STDERR.puts "NO m/z values given!!!"
   parser.educate
@@ -55,14 +57,14 @@ end
 
 $VERBOSE = opts[:verbose]
 
-MSLM = Mspire::Lipid::Modification
+LipidMod = Mspire::Lipid::Modification
 
 mods = {
-  proton_gain: MSLM.new(:proton),
-  water_loss: MSLM.new(:water, :loss => true),
-  lithium: MSLM.new(:lithium),
-  ammonium: MSLM.new(:ammonium),
-  proton_loss: MSLM.new(:proton, :loss => true)
+  proton_gain: LipidMod.new(:proton),
+  water_loss: LipidMod.new(:water, :loss => true),
+  lithium: LipidMod.new(:lithium),
+  ammonium: LipidMod.new(:ammonium),
+  proton_loss: LipidMod.new(:proton, :loss => true)
 }
 
 lipids = Mspire::LipidMaps.parse_file(lipidmaps)
@@ -70,10 +72,12 @@ lipids = Mspire::LipidMaps.parse_file(lipidmaps)
 ions = []
 lipids.each do |lipid| 
   CHARGED_MODS.each do |key|
-    if opts[key]
-      ions << Mspire::Lipid::Ion.new(lipid, [mods[key]])
-      if opts[:water_loss]
-        ions << Mspire::Lipid::Ion.new(lipid, [mods[key], mods[:water_loss]]) 
+    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)) 
+        end
       end
     end
   end
@@ -110,7 +114,7 @@ actual_mzs.each do |exp_mz|
     rank = i + 1
     ppm = ((exp_mz - ion.mz) / ion.mz) * 1e6
     lipid = ion.lipid
-    row.push( rank, ppm, ppm.abs, lipid.category, lipid.lm_id, lipid.common_name, ion.modifications.map(&:charged_formula).join(", ") )
+    row.push( rank, ppm, ppm.abs, lipid.category, lipid.lm_id, lipid.common_name, ion.modifications.map(&:charged_formula_string).join(", ") )
   end
   puts row.join("\t")
 end

data/spec/mspire/lipid/ion_spec.rb

@@ -1,6 +1,5 @@
 require 'spec_helper'
 
-
 require 'mspire/lipid'
 require 'mspire/lipid/modification'
 require 'mspire/lipid/ion'
@@ -15,17 +14,29 @@ end
 describe Mspire::Lipid::Ion do
 
   before do
-    lipid = Mspire::Lipid.new
-    lipid.mass = 300.2
+    lipid = Mspire::Lipid.new("LMGP02010009", "PE(16:0/18:1(9Z))", "1-hexadecanoyl-2-(9Z-octadecenoyl)-sn-glycero-3-phosphoethanolamine", 'C39H76NO8P', 717.5308, 'Glycerophospholipids [GP]', 'Glycerophosphoethanolamines [GP02]', 'Diacylglycerophosphoethanolamines [GP0201]', '7850611', 'FHQVHHIBKUMWTI-OTMQOFQLSA-N')
     proton = Mspire::Lipid::Modification.new(:proton)
+    proton_loss = Mspire::Lipid::Modification.new(:proton, :loss => true)
     h2o_loss = Mspire::Lipid::Modification.new(:water, :loss => true)
-    @plus1 = Mspire::Lipid::Ion.new(lipid, [proton, h2o_loss])
-    @plus2 = Mspire::Lipid::Ion.new(lipid, [proton, proton, h2o_loss])
+    @plus1_less_h20 = Mspire::Lipid::Ion.new(lipid, [proton, h2o_loss])
+    @plus2_less_h20 = Mspire::Lipid::Ion.new(lipid, [proton, proton, h2o_loss])
+    @minus1_less_h20 = Mspire::Lipid::Ion.new(lipid, [proton_loss, h2o_loss])
   end
 
   it 'calculates the correct m/z' do
-    @plus1.mz.should be_within(1e5).of(283.196711735)
-    @plus2.mz.should be_within(1e5).of(142.101994085)
+    @plus1_less_h20.mz.should be_within(1e-5).of(700.52751178307)
+    @plus2_less_h20.mz.should be_within(1e-5).of(350.76739412492003)
+    @minus1_less_h20.mz.should be_within(1e-5).of(698.5129588842301)
+  end
+
+  it 'calculates the correct formula' do
+    @plus1_less_h20.formula.to_s.should == "C39H75NO7P"
+    @plus1_less_h20.charge.should == 1
+
+    @plus2_less_h20.formula.to_s.should == "C39H76NO7P"
+    @plus2_less_h20.charge.should == 2
+    @minus1_less_h20.formula.to_s.should == "C39H73NO7P"
+    @minus1_less_h20.charge.should == -1
   end
 
   describe 'predicting ms/ms fragments' do
@@ -43,7 +54,8 @@ describe Mspire::Lipid::Ion do
         mzs.sort.should == frags.sort
       end
 
-      it '11-methyl-9S-hydroxy-13E-hexadecenoic acid' do
+      # WORKING THIS GUY OUT!!!!!!
+      xit '11-methyl-9S-hydroxy-13E-hexadecenoic acid' do
         lipid = Mspire::Lipid.new(nil, 'Made Up', '11-methyl-9S-hydroxy-13E-hexadecenoic acid',	'C17H32O3', 284.23514488492003, 'Fatty Acyls [FA]', 'Fatty Acids and Conjugates [FA01]', 'Branched fatty acids [FA0102]')
         ion = Mspire::Lipid::Ion.new(lipid, [MSS::PROTON_LOSS])
 
@@ -69,7 +81,6 @@ describe Mspire::Lipid::Ion do
         frags << frag1 - (MSS::H2O + MSS::CO2)
 
         mzs = ion.predict_fragment_mzs
-        p mzs
         #mzs.sort.should == frags.sort
       end
 

data/spec/mspire/lipid/modification_spec.rb

@@ -1,30 +1,46 @@
 require 'spec_helper'
 
 require 'mspire/lipid/modification'
+require 'mspire/lipid'
+require 'mspire/lipid/ion'
 
 describe Mspire::Lipid::Modification do
   Mod = Mspire::Lipid::Modification
 
-  it 'can create common mods easily' do
-    # water loss
-    water_loss = Mod.new(:water, :loss => true)
-    water_loss.loss?.should be_true
-    water_loss.massdiff.<(0).should be_true
-    water_loss.charge.should == 0
-    water_loss.charged_formula.should == 'H2O'
-
-    # proton gain
-    prot = Mod.new(:proton)
-    prot.gain?.should be_true
-    prot.massdiff.>(0).should be_true
-    prot.charge.should == 1
-    prot.charged_formula.should == 'H+'
-
-    ammon = Mod.new(:ammonium)
-    ammon.gain?.should be_true
-    ammon.massdiff.>(0).should be_true
-    ammon.charge.should == 1
-    ammon.charged_formula.should == 'H4N+'
+  describe 'creates common mods easily' do
+
+    it 'water loss' do
+      water_loss = Mod.new(:water, :loss => true)
+      water_loss.loss?.should be_true
+      water_loss.massdiff.<(0).should be_true
+      water_loss.charge.should == 0
+      water_loss.charged_formula_string.should == 'H2O'
+    end
+
+    it 'proton gain' do
+      prot = Mod.new(:proton)
+      prot.gain?.should be_true
+      prot.massdiff.>(0).should be_true
+      prot.charge.should == 1
+      prot.charged_formula_string.should == 'H+'
+    end
+
+    it 'proton loss' do
+      prot_loss = Mod.new(:proton, :loss => true)
+      prot_loss.gain?.should be_false
+      prot_loss.loss?.should be_true
+      prot_loss.massdiff.<(0).should be_true
+      prot_loss.charge.should == -1
+      prot_loss.charged_formula_string.should == 'H-'
+    end
+
+    it 'ammonium gain' do
+      ammon = Mod.new(:ammonium)
+      ammon.gain?.should be_true
+      ammon.massdiff.>(0).should be_true
+      ammon.charge.should == 1
+      ammon.charged_formula_string.should == 'H4N+'
+    end
   end
 
   it 'can create custom mods' do

data/spec/mspire/lipid/search_spec.rb

@@ -1,3 +1,5 @@
+
+=begin
 require 'spec_helper'
 
 require 'mspire/lipid_maps'
@@ -77,3 +79,4 @@ describe Mspire::Lipid::Search do
   end
 
 end
+=end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: mspire-lipidomics
 version: !ruby/object:Gem::Version
-  version: 0.1.5
+  version: 0.1.8
   prerelease: 
 platform: ruby
 authors:
@@ -9,24 +9,24 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2012-05-10 00:00:00.000000000 Z
+date: 2012-07-10 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: 0.7.8
+        version: 0.7.17
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     none: false
     requirements:
-    - - ! '>='
+    - - ~>
       - !ruby/object:Gem::Version
-        version: 0.7.8
+        version: 0.7.17
 - !ruby/object:Gem::Dependency
   name: rubabel
   requirement: !ruby/object:Gem::Requirement
@@ -155,7 +155,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 1.8.18
+rubygems_version: 1.8.24
 signing_key: 
 specification_version: 3
 summary: mass spectrometry based lipidomics - especially shotgun lipidomics