ms-lipidomics 0.1.1 → 0.1.2

data/Rakefile

@@ -13,7 +13,7 @@ Jeweler::Tasks.new do |gem|
   gem.description = %Q{does ms lipidomics}
   gem.email = "jtprince@gmail.com"
   gem.authors = ["John T. Prince"]
-  gem.add_dependency "mspire", ">= 0.6.18"
+  gem.add_dependency "mspire", ">= 0.6.19"
   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 @@
-0.1.1
+0.1.2

data/bin/lipidomic-search.rb

@@ -27,11 +27,7 @@ class Sample
   # returns a single spectrum object
   def merge_ms1_spectra(file, opts)
     spectra = []
-    warn "using number of peaks as proxy for ms level right now"
-    MS::Mzml.foreach(file) do |spectrum|
-      spectra << spectrum if spectrum.mzs.size > 1000  # <<<<<<------ kludge for ms_level == 1
-    end
-    spectra.each {|spectrum| spectrum.sort! }
+    spectra = MS::Mzml.foreach(file).select {|spec| spec.ms_level == 1 }.map(&:sort!)
 
     MS::Spectrum.merge(spectra, opts)
   end
@@ -52,6 +48,7 @@ parser = Trollop::Parser.new do
   opt :search_unit, "unit for searching nearest hit (ppm or amu)", :default => DEFAULTS[:search_unit].to_s
   opt :top_n_peaks, "the number of highest intensity peaks to query the DB with", :default => 1000
   opt :display_n, "the number of best hits to display", :default => 20
+  opt :lithium, "also search for lithium adducts"
   opt :verbose, "talk about it"
 end
 
@@ -70,11 +67,16 @@ $VERBOSE = opts[:verbose]
 
 proton = MS::Lipid::Modification.new(:proton)
 h2o_loss = MS::Lipid::Modification.new(:water, :loss => true)
+lithium = MS::Lipid::Modification.new(:lithium)
 
 lipids = MS::LipidMaps.parse_file(lipidmaps)
 
 ions = lipids.map do |lipid| 
-  [[proton], [proton, h2o_loss]].map do |mods|
+  mod_groups = [[proton], [proton, h2o_loss]]
+  if opt[:lithium]
+    mod_groups.push( [lithium], [lithium, h2o_loss] )
+  end
+  mod_groups.map do |mods|
     MS::Lipid::Ion.new(lipid, mods)
   end
 end.flatten(1)

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: ms-lipidomics
 version: !ruby/object:Gem::Version
-  version: 0.1.1
+  version: 0.1.2
   prerelease: 
 platform: ruby
 authors:
@@ -13,18 +13,18 @@ date: 2012-02-24 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: mspire
-  requirement: &18073100 !ruby/object:Gem::Requirement
+  requirement: &16132440 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
       - !ruby/object:Gem::Version
-        version: 0.6.18
+        version: 0.6.19
   type: :runtime
   prerelease: false
-  version_requirements: *18073100
+  version_requirements: *16132440
 - !ruby/object:Gem::Dependency
   name: rspec
-  requirement: &18072580 !ruby/object:Gem::Requirement
+  requirement: &16131900 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -32,10 +32,10 @@ dependencies:
         version: 2.3.0
   type: :development
   prerelease: false
-  version_requirements: *18072580
+  version_requirements: *16131900
 - !ruby/object:Gem::Dependency
   name: jeweler
-  requirement: &18072100 !ruby/object:Gem::Requirement
+  requirement: &16147680 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -43,10 +43,10 @@ dependencies:
         version: 1.6.4
   type: :development
   prerelease: false
-  version_requirements: *18072100
+  version_requirements: *16147680
 - !ruby/object:Gem::Dependency
   name: rcov
-  requirement: &18071620 !ruby/object:Gem::Requirement
+  requirement: &16147160 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -54,7 +54,7 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *18071620
+  version_requirements: *16147160
 description: does ms lipidomics
 email: jtprince@gmail.com
 executables: