ms-lipidomics 0.1.1 → 0.1.2
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- data/Rakefile +1 -1
- data/VERSION +1 -1
- data/bin/lipidomic-search.rb +8 -6
- metadata +10 -10
data/Rakefile
CHANGED
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@@ -13,7 +13,7 @@ Jeweler::Tasks.new do |gem|
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gem.description = %Q{does ms lipidomics}
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gem.email = "jtprince@gmail.com"
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gem.authors = ["John T. Prince"]
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-
gem.add_dependency "mspire", ">= 0.6.
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gem.add_dependency "mspire", ">= 0.6.19"
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gem.add_development_dependency "rspec", "~> 2.3.0"
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gem.add_development_dependency "jeweler", "~> 1.6.4"
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gem.add_development_dependency "rcov", ">= 0"
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data/VERSION
CHANGED
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@@ -1 +1 @@
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1
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-
0.1.
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1
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+
0.1.2
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data/bin/lipidomic-search.rb
CHANGED
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@@ -27,11 +27,7 @@ class Sample
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# returns a single spectrum object
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def merge_ms1_spectra(file, opts)
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spectra = []
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-
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MS::Mzml.foreach(file) do |spectrum|
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spectra << spectrum if spectrum.mzs.size > 1000 # <<<<<<------ kludge for ms_level == 1
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end
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spectra.each {|spectrum| spectrum.sort! }
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spectra = MS::Mzml.foreach(file).select {|spec| spec.ms_level == 1 }.map(&:sort!)
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MS::Spectrum.merge(spectra, opts)
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end
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@@ -52,6 +48,7 @@ parser = Trollop::Parser.new do
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opt :search_unit, "unit for searching nearest hit (ppm or amu)", :default => DEFAULTS[:search_unit].to_s
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opt :top_n_peaks, "the number of highest intensity peaks to query the DB with", :default => 1000
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opt :display_n, "the number of best hits to display", :default => 20
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opt :lithium, "also search for lithium adducts"
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opt :verbose, "talk about it"
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end
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@@ -70,11 +67,16 @@ $VERBOSE = opts[:verbose]
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proton = MS::Lipid::Modification.new(:proton)
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h2o_loss = MS::Lipid::Modification.new(:water, :loss => true)
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lithium = MS::Lipid::Modification.new(:lithium)
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lipids = MS::LipidMaps.parse_file(lipidmaps)
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ions = lipids.map do |lipid|
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-
[[proton], [proton, h2o_loss]]
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mod_groups = [[proton], [proton, h2o_loss]]
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if opt[:lithium]
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mod_groups.push( [lithium], [lithium, h2o_loss] )
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end
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mod_groups.map do |mods|
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MS::Lipid::Ion.new(lipid, mods)
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end
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end.flatten(1)
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metadata
CHANGED
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@@ -1,7 +1,7 @@
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--- !ruby/object:Gem::Specification
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name: ms-lipidomics
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version: !ruby/object:Gem::Version
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version: 0.1.
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version: 0.1.2
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prerelease:
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platform: ruby
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authors:
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@@ -13,18 +13,18 @@ date: 2012-02-24 00:00:00.000000000 Z
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dependencies:
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- !ruby/object:Gem::Dependency
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name: mspire
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requirement: &
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requirement: &16132440 !ruby/object:Gem::Requirement
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none: false
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requirements:
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- - ! '>='
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- !ruby/object:Gem::Version
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version: 0.6.
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version: 0.6.19
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type: :runtime
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prerelease: false
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version_requirements: *
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version_requirements: *16132440
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- !ruby/object:Gem::Dependency
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name: rspec
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requirement: &
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requirement: &16131900 !ruby/object:Gem::Requirement
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none: false
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requirements:
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- - ~>
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@@ -32,10 +32,10 @@ dependencies:
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version: 2.3.0
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type: :development
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prerelease: false
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version_requirements: *
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version_requirements: *16131900
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- !ruby/object:Gem::Dependency
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name: jeweler
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requirement: &
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requirement: &16147680 !ruby/object:Gem::Requirement
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none: false
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requirements:
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- - ~>
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@@ -43,10 +43,10 @@ dependencies:
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version: 1.6.4
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type: :development
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prerelease: false
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version_requirements: *
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version_requirements: *16147680
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- !ruby/object:Gem::Dependency
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name: rcov
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requirement: &
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requirement: &16147160 !ruby/object:Gem::Requirement
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none: false
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requirements:
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- - ! '>='
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@@ -54,7 +54,7 @@ dependencies:
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version: '0'
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type: :development
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prerelease: false
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version_requirements: *
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version_requirements: *16147160
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description: does ms lipidomics
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email: jtprince@gmail.com
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executables:
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