bin/srf_to_search.rb in ms-sequest-0.0.9 vs bin/srf_to_search.rb in ms-sequest-0.0.10

@@ -1,33 +1,78 @@
-#!/usr/bin/env ruby
+#!/usr/bin/ruby
 
 require 'rubygems'
-require 'tap/task'
+require 'optparse'
 require 'ms/sequest/srf/search'
 
+opt = {
+  :format => 'mgf'
+}
+
+opts = OptionParser.new do |op|
+  op.banner = "usage: #{File.basename(__FILE__)} <file>.srf"
+  op.separator "outputs: <file>.mgf"
+  op.on("-f", "--format <mgf|dat>", "the output format (default: #{opt[:format]})") {|v| opt[:format] = v }
+end
+
 if ARGV.size == 0
-  ARGV << "--help"
+  puts opts
+  exit
 end
 
+format = opt[:format]
+
+ARGV.each do |srf_file|
+  base = srf_file.sub(/\.srf$/i, '')
+  newfile = 
+    case format
+    when 'dta'
+      base
+    when 'mgf'
+      base << '.' << format
+    end
+  srf = Ms::Sequest::Srf.new(srf_file, :link_protein_hits => false, :filter_by_precursor_mass_tolerance => false, :read_pephits => false )
+  # options just speed up reading since we don't need .out info anyway
+  case format
+  when 'mgf'
+    srf.to_mgf(newfile)
+  when 'dta'
+    srf.to_dta_files(newfile)
+  end
+end
+
+
+
+
+
+
+
+
+
+
+
+=begin
+
+#require 'tap/task'
 task_class = Ms::Sequest::Srf::SrfToSearch
 
 parser = ConfigParser.new do |opts|
   opts.separator "configurations"
   opts.add task_class.configurations
- 
+
   opts.on "--help", "Print this help" do
     puts "usage: #{File.basename(__FILE__)} <file>.srf ..."
     puts
     puts opts
     exit(0)
   end
 end
 
 parser.parse!(ARGV)
- 
+
 task = task_class.new(parser.config)
 
 ARGV.each do |file|
   task.execute(file)
 end
 
-
+=end