ms-error_rate 0.0.11 → 0.0.12

data/VERSION

@@ -1 +1 @@
-0.0.11
+0.0.12

data/bin/mascot_pepxml_to_peptide_hit_qvalues.rb

@@ -6,6 +6,12 @@ require 'set'
 
 require 'ms/ident/pepxml'
 require 'ms/ident/peptide_hit/qvalue'
+require 'ms/error_rate/qvalue'
+
+def putsv(*args)
+  puts(*args) if $VERBOSE
+  $stdout.flush
+end
 
 EXT = Ms::Ident::PeptideHit::Qvalue::FILE_EXTENSION
 combine_base  = "combined"
@@ -32,33 +38,38 @@ $VERBOSE = opt.delete(:verbose)
 
 files = ARGV.to_a
 
-files.each_slice(2).map!(&:reverse) if opt[:decoy_first]
+(files=files.each_slice(2).map(&:reverse).flatten) if opt[:decoy_first]
 
 groups_of_search_hits = files.map do |file|
-  Ms::Ident::Pepxml.search_hits(file)
+  putsv "reading search hits: #{file}"
+  Ms::Ident::Pepxml.simple_search_hits(file)
 end
 
 to_run = {}
 if opt[:combine]
+  putsv "combining all target hits together and all decoy hits together"
   all_target = [] ; all_decoy = []
   groups_of_search_hits.each_slice(2) do |target_hits,decoy_hits| 
     all_target.push(*target_hits) ; all_decoy.push(*decoy_hits)
   end
-  to_run[combine_base] = [all_target, all_decoy]
+  to_run[combine_base + EXT] = [all_target, all_decoy]
 else
-  groups_of_search_hits.each_slice(2).zip(files) do |target_hits_and_decoy_hits, file|
-    to_run[file.chomp(File.extname(file)) + EXT] = target_hits_and_decoy_hits
+  files.zip(groups_of_search_hits).each_slice(2) do |pair_of_file_and_hit_pairs|
+    (tfile_hits, dfile_hits) = pair_of_file_and_hit_pairs
+    file = tfile_hits.first
+    to_run[file.chomp(File.extname(file)) + EXT] = [tfile_hits.last, dfile_hits.last]
   end
 end
 
 to_run.each do |file, target_decoy_pair|
-  hit_qvalue_pairs = Ms::ErrorRate::Qvalue.target_decoy_qvalues(target_decoy_pair.first, target_decoy_pair.last, :z_together => opt[:z_together])
+  putsv "calculating qvalues for #{file}"
+  hit_qvalue_pairs = Ms::ErrorRate::Qvalue.target_decoy_qvalues(target_decoy_pair.first, target_decoy_pair.last, :z_together => opt[:z_together]) {|hit| hit.search_scores[:ionscore] }
   hits = [] ; qvals = []
   hit_qvalue_pairs.each do |hit, qval|
     hits << hit ; qvals << qval
   end
   outfile = Ms::Ident::PeptideHit::Qvalue.to_file(file, hits, qvals)
-  puts "created: #{outfile}" if $VERBOSE
+  putsv "created: #{outfile}"
 end
 
 

data/lib/ms/error_rate/qvalue.rb

@@ -2,7 +2,6 @@
 require 'set'
 require 'ms/error_rate/decoy'
 
-
 class Array
   def group_by(&block)
     hash = Hash.new {|h,k| h[k] = [] }

metadata

@@ -5,8 +5,8 @@ version: !ruby/object:Gem::Version
   segments: 
   - 0
   - 0
-  - 11
-  version: 0.0.11
+  - 12
+  version: 0.0.12
 platform: ruby
 authors: 
 - John Prince
@@ -14,7 +14,7 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2011-03-30 00:00:00 -06:00
+date: 2011-03-31 00:00:00 -06:00
 default_executable: 
 dependencies: 
 - !ruby/object:Gem::Dependency 
@@ -95,7 +95,6 @@ executables:
 - fasta_to_nuclear.rb
 - fasta_to_peptide_centric_db.rb
 - fasta_to_phobius.rb
-- fasta_to_protein_length.rb
 - generate_sbv_input_hashes.rb
 - mascot_pepxml_to_peptide_hit_qvalues.rb
 - phobius_to_nontransmembrane.rb
@@ -117,7 +116,6 @@ files:
 - bin/fasta_to_nuclear.rb
 - bin/fasta_to_peptide_centric_db.rb
 - bin/fasta_to_phobius.rb
-- bin/fasta_to_protein_length.rb
 - bin/generate_sbv_input_hashes.rb
 - bin/mascot_pepxml_to_peptide_hit_qvalues.rb
 - bin/phobius_to_nontransmembrane.rb

data/bin/fasta_to_protein_length.rb

@@ -1,20 +0,0 @@
-#!/usr/bin/env ruby
-
-if ARGV.size == 0
-  puts "usage: #{File.basename(__FILE__)} <file>.fasta ..."
-  puts "output: <file>.protid_to_size.yml"
-  exit
-end
-
-ARGV.each do |file|
-  base = file.chomp(File.extname(file))
-  outfile = base + ".protid_to_size.yml"
-  cnt = 0
-  File.open(outfile,'w') do |out|
-    Ms::Fasta.foreach(file) do |entry|
-      out.puts "#{entry.entry_id}: #{entry.sequence.size}"
-      cnt += 1
-    end
-  end
-  puts "wrote #{cnt} protein lengths to: #{outfile}"
-end