Changeset 198

Timestamp:

04/08/09 14:42:34 (8 months ago)

Author:

cholt

Message:

Changed back to three control files, and added mpi_evaluator

Files:

• MPI/Install.PL (modified) (1 diff)
• MPI/mpi_evaluator (added)
• MPI/mpi_maker (modified) (2 diffs)
• bin/evaluator (modified) (2 diffs)
• bin/maker (modified) (2 diffs)
• lib/GI.pm (modified) (12 diffs)

MPI/Install.PL

@@ -19 +19 @@
-
-system("cp $FindBin::Bin/mpi_maker $FindBin::Bin/../bin/");
+system("cp $FindBin::Bin/mpi_evaluator $FindBin::Bin/../bin/");

MPI/mpi_maker

@@ -113 +113 @@
-Usage:
-
- <evaluator>
+
-
-     Maker is a program that produces gene annotations in GFF3 file format using
@@ -291 +291 @@
-         if (-e "maker_opts.ctl" &&
-             -e "maker_bopts.ctl" &&
-
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-            ) {
-            
-            @ctlfiles = ("maker_opts.ctl",
-                         "maker_bopts.ctl",
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-                        );
-         }

bin/evaluator

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-use strict "vars";
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-use FindBin;
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-#-----------------------------------------------------------------------------
-#----------------------------------- SUBS ------------------------------------

bin/maker

@@ -82 +82 @@
-Usage:
-
- <evaluator>
+
-
-     Maker is a program that produces gene annotations in GFF3 file format using
@@ -195 +195 @@
-        if (-e "maker_opts.ctl" &&
-            -e "maker_bopts.ctl" &&
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-            ) {
-            
-            @ctlfiles = ("maker_opts.ctl",
-                         "maker_bopts.ctl",
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-                         );
-        }

lib/GI.pm

@@ -2126 +2126 @@
-      $CTL_OPT{'unmask'} = 1;
-      $CTL_OPT{'clean_up'} = 0;
+      #evaluator below here
+      $CTL_OPT{'side_thre'} = 5;
+      $CTL_OPT{'eva_window_size'} = 70;
+      $CTL_OPT{'eva_split_hit'} = 1;
+      $CTL_OPT{'eva_hspmax'} = 100;
+      $CTL_OPT{'eva_gspmax'} = 100;
+      $CTL_OPT{'enable_fathom'} = 0;
+      $CTL_OPT{'enable_fathom'} = 1 if($main::eva);
-   }
-
@@ -2149 +2157 @@
-      $CTL_OPT{'en_score_limit'} = 20;
-      $CTL_OPT{'ep_score_limit'} = 20;
+      #evaluator below here
+      $CTL_OPT{'eva_pcov_blastn'} = 0.80;
+      $CTL_OPT{'eva_pid_blastn'} = 0.85;
+      $CTL_OPT{'eva_eval_blastn'} = 1e-10;
+      $CTL_OPT{'eva_bit_blastn'} = 40;
-   }
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@@ -2185 +2198 @@
-   #evaluator
-   if ($type eq 'all' || $type eq 'eva') {
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-   }
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@@ -2254 +2258 @@
-   $CTL_OPT{genome} = $OPT{genome} if (defined $OPT{genome});
-   $CTL_OPT{genome_gff} = $OPT{genome_gff} if (defined $OPT{genome_gff});
+   $CTL_OPT{model_gff} = $OPT{model_gff} if (defined $OPT{model_gff});
-   $CTL_OPT{force} = $OPT{force} if (defined $OPT{force});
-   $CTL_OPT{predictor} = $OPT{predictor} if (defined $OPT{predictor});
@@ -2380 +2385 @@
-   push (@infiles, '_tblastx', '_formater') if($CTL_OPT{altest});
-   push (@infiles, 'genome') if($CTL_OPT{genome});
-
+ && !$main::eva
-   push (@infiles, 'exonerate') if($CTL_OPT{est}); 
-   push (@infiles, 'exonerate') if($CTL_OPT{protein}); 
@@ -2397 +2402 @@
-   push (@infiles, 'twinscan') if (grep (/twinscan/, @{$CTL_OPT{_run}}));
-   push (@infiles, 'jigsaw') if (grep (/jigsaw/, @{$CTL_OPT{_run}}));
-
+ && $CTL_OPT{evaluate}
-   push (@infiles, 'rm_gff') if($CTL_OPT{rm_gff});
-   push (@infiles, 'est_gff') if($CTL_OPT{est_gff});
-   push (@infiles, 'protein_gff') if($CTL_OPT{protein_gff});
-   push (@infiles, 'genome_gff') if($CTL_OPT{genome_gff});
+   push (@infiles, 'genome_gff') if($main::eva && ! $CTL_OPT{model_gff});
-   push (@infiles, 'pred_gff') if($CTL_OPT{pred_gff});
-   push (@infiles, 'model_gff') if ($CTL_OPT{model_gff});
+   push (@infiles, 'model_gff') if ($main::eva && ! $CTL_OPT{genome_gff});
-   push (@infiles, 'model_gff') if (grep (/gff/, $CTL_OPT{predictor}) &&
-                                    (!$CTL_OPT{genome_gff} ||
@@ -2494 +2501 @@
-       $error .= "The TMP value \'$CTL_OPT{TMP}\' is not a directory or does not exist\n";
-   }
+   if($main::eva && $CTL_OPT{genome_gff} && $CTL_OPT{model_gff}){ #only for evaluator
+       $error .= "You can only specify a GFF3 file for genome_gff or model_gff no both!!\n";
+   }
-   
-   die $error if ($error);   
-
-   #--check genome fasta file
+   my $fasta_gff = ($CTL_OPT{genome_gff}) ? $CTL_OPT{genome_gff} : $CTL_OPT{model_gff};
-   my $iterator = new Iterator::Any( -fasta => $CTL_OPT{genome},
-CTL_OPT{genome_gff}
+fasta_gff
-                                   );
-
-   if ($iterator->number_of_entries() == 0) {
-CTL_OPT{genome_gff}
+fasta_gff
-      die "ERROR:  The file $genome contains no fasta entries\n";
-   }
@@ -2570 +2581 @@
-   open (OUT, "> $dir/maker_opts.ctl") if(!$ev);
-   print OUT "#-----Genome (Required for De-Novo Annotation)\n" if(!$ev);
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-   print OUT "#-----Re-annotation Options (Only Maker derived GFF3)\n" if(!$ev);
-   print OUT "#-----Maker Derived GFF3 Annotations to Evaluate (genome fasta is internal to GFF3)\n" if($ev);
@@ -2586 +2598 @@
-   print OUT "#-----External GFF3 Annotations to Evaluate\n" if($ev);
-   print OUT "model_gff:$O{model_gff} #gene models from an external gff3 file\n" if($ev);
-   print OUT "genome:$O{genome} #genome sequence file in fasta format for GFF3\n"if($ev);
-   print OUT "\n"if($ev);
-   print OUT "#-----EST Evidence (you should provide a value for at least one)\n";
@@ -2639 +2650 @@
-   print OUT "clean_up:$O{clean_up} #removes theVoid directory with individual analysis files, 1 = yes, 0 = no\n";
-   print OUT "TMP:$O{TMP} #specify a directory other than the system default temporary directory for temporary files\n";
+   print OUT "\n";
+   print OUT "#-----EVALUATOR Control Options\n";
+   print OUT "side_thre:$O{side_thre}\n";
+   print OUT "eva_window_size:$O{eva_window_size}\n";
+   print OUT "eva_split_hit:$O{eva_split_hit}\n";
+   print OUT "eva_hspmax:$O{eva_hspmax}\n";
+   print OUT "eva_gspmax:$O{eva_gspmax}\n";
+   print OUT "enable_fathom:$O{enable_fathom}\n";
-   close (OUT);
-    
@@ -2666 +2685 @@
-   print OUT "eval_tblastx:$O{eval_tblastx} #tBlastx eval cutoff\n";
-   print OUT "bit_tblastx:$O{bit_tblastx} #tBlastx bit cutoff\n";
+   print OUT "\n";
+   print OUT "eva_pcov_blastn:$O{eva_pcov_blastn} #Evaluator Blastn Percent Coverage Threshold EST-Genome Alignments\n";
+   print OUT "eva_pid_blastn:$O{eva_pid_blastn} #Evaluator Blastn Percent Identity Threshold EST-Genome Alignments\n";
+   print OUT "eva_eval_blastn:$O{eva_eval_blastn} #Evaluator Blastn eval cutoff\n";
+   print OUT "eva_bit_blastn:$O{eva_bit_blastn} #Evaluator Blastn bit cutoff\n";
-   print OUT "\n";
-   print OUT "ep_score_limit:$O{ep_score_limit} #exonerate protein percent of maximal score threshold\n";
@@ -2695 +2719 @@
-   print OUT "qrna:$O{qrna} #location of qrna executable (not yet implemented)\n";
-   print OUT "fathom:$O{fathom} #location of fathom executable (not yet implemented)\n";
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-}
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