ms-ident 0.0.21 → 0.0.22

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data/Rakefile CHANGED
@@ -29,12 +29,12 @@ Rake::TestTask.new(:spec) do |spec|
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  spec.verbose = true
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  end
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- require 'rcov/rcovtask'
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- Rcov::RcovTask.new do |spec|
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- spec.libs << 'spec'
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- spec.pattern = 'spec/**/*_spec.rb'
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- spec.verbose = true
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- end
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+ #require 'rcov/rcovtask'
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+ #Rcov::RcovTask.new do |spec|
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+ # spec.libs << 'spec'
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+ # spec.pattern = 'spec/**/*_spec.rb'
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+ # spec.verbose = true
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+ #end
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  task :default => :spec
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data/VERSION CHANGED
@@ -1 +1 @@
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- 0.0.21
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+ 0.0.22
@@ -2,6 +2,8 @@ require 'nokogiri'
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  require 'ms/ident'
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  require 'ms/ident/pepxml/msms_pipeline_analysis'
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+ require 'ostruct'
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+
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  module Ms ; module Ident ; end ; end
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  class Numeric
@@ -22,11 +24,8 @@ class Ms::Ident::Pepxml
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  attr_accessor :msms_pipeline_analysis
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- def self.search_hits(file)
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- fields = [:aaseq, :charge]
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- ss_names = []
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- have_ss_names = false
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- # begin with aaseq, charge
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+ # returns an array of Ms::Ident::Pepxml::SearchHit::Simple structs
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+ def self.simple_search_hits(file)
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  hit_values = File.open(file) do |io|
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  doc = Nokogiri::XML.parse(io, nil, nil, Nokogiri::XML::ParseOptions::DEFAULT_XML | Nokogiri::XML::ParseOptions::NOBLANKS)
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  # we can work with namespaces, or just remove them ...
@@ -37,18 +36,13 @@ class Ms::Ident::Pepxml
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  aaseq = search_hit['peptide']
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  charge = search_hit.parent.parent['assumed_charge'].to_i
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  search_score_nodes = search_hit.children.select {|node| node.name == 'search_score' }
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- ss_values = []
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+ search_scores = {}
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  search_score_nodes.each do |node|
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- ss_names << node['name'].to_sym unless have_ss_names
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- ss_values << node['value'].to_f
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+ search_scores[node['name'].to_sym] = node['value'].to_f
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  end
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- have_ss_names = true
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- [aaseq, charge, *ss_values]
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+ Ms::Ident::Pepxml::SearchHit::Simple.new(aaseq, charge, search_scores)
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  end
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  end
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- fields.push(*ss_names)
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- peptide_hit_class = Struct.new(*fields)
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- hit_values.map {|ar| peptide_hit_class.new(*ar) }
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  end
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  def pepxml_version
@@ -120,6 +120,7 @@ class Ms::Ident::Pepxml
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  end
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  def from_pepxml_node(node)
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+ node.attributes
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  self[0] = node['hit_rank'].to_i
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  self[1] = node['peptide']
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  self[2] = node['peptide_prev_aa']
@@ -135,6 +136,8 @@ class Ms::Ident::Pepxml
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  self[12] = node['is_rejected'].to_i
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  self
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  end
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+
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+ Simple = Struct.new(:aaseq, :charge, :search_scores)
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  end
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  end
metadata CHANGED
@@ -5,8 +5,8 @@ version: !ruby/object:Gem::Version
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  segments:
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  - 0
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  - 0
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- - 21
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- version: 0.0.21
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+ - 22
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+ version: 0.0.22
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  platform: ruby
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  authors:
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  - John T. Prince
@@ -14,7 +14,7 @@ autorequire:
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  bindir: bin
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  cert_chain: []
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- date: 2011-03-30 00:00:00 -06:00
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+ date: 2011-03-31 00:00:00 -06:00
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  default_executable:
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  dependencies:
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  - !ruby/object:Gem::Dependency