ms-ident 0.0.21 → 0.0.22
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 +6 -6
- data/VERSION +1 -1
- data/lib/ms/ident/pepxml.rb +7 -13
- data/lib/ms/ident/pepxml/search_hit.rb +3 -0
- metadata +3 -3
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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36
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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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1
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-
0.0.
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1
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+
0.0.22
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data/lib/ms/ident/pepxml.rb
CHANGED
@@ -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
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@@ -22,11 +24,8 @@ class Ms::Ident::Pepxml
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attr_accessor :msms_pipeline_analysis
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-
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-
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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 ...
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@@ -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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-
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+
search_scores = {}
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search_score_nodes.each do |node|
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-
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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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-
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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
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@@ -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']
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@@ -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
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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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-
-
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version: 0.0.
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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
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@@ -14,7 +14,7 @@ autorequire:
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bindir: bin
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cert_chain: []
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-
date: 2011-03-
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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
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