cmdline.rb in mspire-0.4.5

- old
+ new

@@ -39,11 +39,11 @@
     },
     :decoy => 
     {
       :hits_together => true,
       :decoy_on_match => true,
-      :decoy_to_target_ratio => 1.0,
+      :pi_zero => 1.0,
     },
     :bad_aa => 
     {
       :false_if_found => true,
       :bkg => 0.0, 
@@ -59,26 +59,23 @@
       :proteins_expected => true,
     },
     :ties => true,
   }
   COMMAND_LINE = {
-    :decoy => ["--decoy /REGEXP/|FILENAME[,DTR,DOM]", Array, "REGEXP for decoy proteins (catenated searches) or a",
+    :decoy => ["--decoy /REGEXP/|FILENAME[,PI0,DOM]", Array, "REGEXP for decoy proteins (catenated searches) or a",
                                                 "FILENAME of separate search on decoys.", 
                                                 "All regular expressions must be surrounded by '/'",
                                                 "(no extended options [trailing modifiers]).",
                                                 "e.g., a run using concatenated reversed proteins that",
                                                 "includes 'REVERSE' in the fasta heading:",
                                                 "    --decoy /REVERSE/",
                                                 "Anything fancier should be quoted:",
                                                 "    --decoy '/^\\s*REVERSE/'",
                                                 "If decoys proteins were searched in a separate file,",
                                                 "then give the FILENAME (e.g., --decoy decoy.srg)",
-                                                "DTR = Decoy to Target Ratio (default: #{DEFAULTS[:decoy][:decoy_to_target_ratio]})",
+                                                "PI0 = Incorrect Targets to Decoy Ratio (default: #{DEFAULTS[:decoy][:pi_zero]})",
                                                 "DOM = *true/false, decoy on match",],
-      :decoy_pi_zero => ["--decoy_pi_zero", "uses sequest Xcorrs to estimate the",
-                                            "percentage of incorrect target hits.",
-                                            "This over-rides any given DTR (above)"],
         :tps => ["--tps <fasta>", "for a completely defined sample, this is the",
                                   "fasta file containing the true protein hits"],
          # may require digestion:
         :fasta => ["--fasta FASTA", "fasta file for phobius transmembrane",
                                     "(needed if PEPS options is not false)"],
@@ -157,10 +154,10 @@
           else
             # assume that it is a filename
             raise ArgumentError, "File does not exist: #{first_arg}\n(was this supposed to be a regular expression? if so, should be given: /#{first_arg}/)" unless File.exist?(first_arg)
             first_arg
           end
-        val_opts[:decoy_to_target_ratio] = (ar[1] || DEFAULTS[:decoy][:decoy_to_target_ratio]).to_f
+        val_opts[:pi_zero] = (ar[1] || DEFAULTS[:decoy][:pi_zero]).to_f
         val_opts[:decoy_on_match] = self.boolean(ar[2], DEFAULTS[:decoy][:decoy_on_match])
         myargs.push(val_opts)
         opts[:validators].push(myargs)
       },
         :fasta => lambda {|arg, opts|