ms-error_rate 0.0.8 → 0.0.9

data/VERSION

@@ -1 +1 @@
-0.0.8
+0.0.9

data/bin/fasta_to_protein_length.rb

@@ -0,0 +1,20 @@
+#!/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

data/bin/mascot_pepxml_to_peptide_hit_qvalues.rb

@@ -4,6 +4,7 @@ require 'trollop'
 require 'nokogiri'
 require 'set'
 
+require 'ms/ident/peptide_hit/qvalue'
 require 'ms/error_rate/qvalue/pepxml'
 
 opts = Trollop::Parser.new do
@@ -30,7 +31,7 @@ files.each_slice(2).map do |target, decoy|
   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)
+  outfile = Ms::Ident::PeptideHit::Qvalue.to_phq(target.chomp(File.extname(target)), hits, qvals)
   puts "created: #{outfile}" if $VERBOSE
 end
 

metadata

@@ -5,8 +5,8 @@ version: !ruby/object:Gem::Version
   segments: 
   - 0
   - 0
-  - 8
-  version: 0.0.8
+  - 9
+  version: 0.0.9
 platform: ruby
 authors: 
 - John T. Prince
@@ -67,6 +67,7 @@ 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
@@ -87,6 +88,7 @@ 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