ms-error_rate 0.0.7 → 0.0.8

data/VERSION

@@ -1 +1 @@
-0.0.7
+0.0.8

data/bin/mascot_pepxml_to_peptide_hit_qvalues.rb

@@ -4,7 +4,7 @@ require 'trollop'
 require 'nokogiri'
 require 'set'
 
-require 'ms/error_rate/qvalue'
+require 'ms/error_rate/qvalue/pepxml'
 
 opts = Trollop::Parser.new do
   banner %Q{usage: #{File.basename(__FILE__)} <fwd>.xml <decoy>.xml ...
@@ -12,50 +12,26 @@ outputs: <fwd>.phq.csv
 phq.tsv?: see schema/peptide_hit_qvalues.phq.tsv
 }
   opt :z_together, "do not group by charge state", :default => false
+  opt :verbose, "be verbose", :default => false
 end
 
-DELIMITER = "\t"
-
 opt = opts.parse(ARGV)
 if ARGV.size == 0 || (ARGV.size%2 != 0)
   puts "\n\n!! only even numbers of files accepted (target decoy target decoy ...) !!\n\n" if (ARGV.size%2 != 0)
   opts.educate
   exit 
 end
+$VERBOSE = opt.delete(:verbose)
 
 files = ARGV.to_a
-
-PeptideHit = Struct.new(:aaseq, :charge, :ionscore, :qvalue)
-
-# this is a list of high quality peptide hits associated with each group
-peptide_hits_per_file = files.map do |file|
-  File.open(file) do |io|
-    doc = Nokogiri::XML.parse(io, nil, nil, Nokogiri::XML::ParseOptions::DEFAULT_XML | Nokogiri::XML::ParseOptions::NOBLANKS)
-    # we can work with namespaces, or just remove them ...
-    doc.remove_namespaces!
-    root = doc.root
-    search_hits = root.xpath('//search_hit')
-    search_hits.map do |search_hit| 
-      aaseq = search_hit['peptide']
-      ionscore = search_hit.children.find {|node| node.name == 'search_score' && node['name'] == 'ionscore' }['value'].to_f
-      charge = search_hit.parent.parent['assumed_charge'].to_i
-      PeptideHit.new(aaseq, charge, ionscore)
-    end
+files.each_slice(2).map do |target, decoy|
+  hit_qvalue_pairs = Ms::ErrorRate::Qvalue::Pepxml.target_decoy_qvalues(target, decoy, opt, &:ionscore)
+  hits = [] ; qvals = []
+  hit_qvalue_pairs.each do |hit, qval|
+    hits << hit ; qvals << qval
   end
+  outfile = Ms::Ident::PeptideHit::Qvalue.to_phq(target.chomp(File.ext(target)), hits, qvals)
+  puts "created: #{outfile}" if $VERBOSE
 end
 
-hits_per_target = peptide_hits_per_file.each_slice(2).map do |target_hits, decoy_hits|
-  pairs = Ms::ErrorRate::Qvalue.target_decoy_qvalues(target_hits, decoy_hits, :z_together => opt[:z_together], &:ionscore)
-  target_peptide_hits = pairs.map {|peptide_hit, qvalue| peptide_hit.qvalue = qvalue ; peptide_hit }
-end
-
-files.each_slice(2).map(&:first).zip(hits_per_target) do |file, hits|
-  newfile = file.chomp(File.extname(file)) + ".phq.tsv"
-  File.open(newfile,'w') do |out| 
-    out.puts %w(aaseq charge qvalue).join(DELIMITER)
-    hits.each do |hit|
-      out.puts hit.values_at(0,1,3).join(DELIMITER)
-    end
-  end
-end
 

metadata

@@ -5,8 +5,8 @@ version: !ruby/object:Gem::Version
   segments: 
   - 0
   - 0
-  - 7
-  version: 0.0.7
+  - 8
+  version: 0.0.8
 platform: ruby
 authors: 
 - John T. Prince
@@ -14,7 +14,7 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2011-03-28 00:00:00 -06:00
+date: 2011-03-30 00:00:00 -06:00
 default_executable: 
 dependencies: 
 - !ruby/object:Gem::Dependency