Changeset 159

Timestamp:

03/09/09 00:50:16 (9 months ago)

Author:

cholt

Message:

maker update for all oomycete

Files:

• MPI/mpi_maker (modified) (1 diff)
• bin/fasta_merge (modified) (1 diff)
• bin/gff3_preds2models (added)
• bin/maker (modified) (4 diffs)
• lib/Dumper/GFF/GFFV3.pm (modified) (1 diff)
• lib/File (added)
• lib/File/NFSLock.pm (added)
• lib/GFFDB.pm (modified) (2 diffs)
• lib/GI.pm (modified) (27 diffs)
• lib/Process/MpiChunk.pm (modified) (8 diffs)
• lib/Process/MpiTiers.pm (modified) (1 diff)
• lib/Widget/RepeatMasker.pm (modified) (1 diff)
• lib/Widget/fgenesh.pm (modified) (1 diff)
• lib/cluster.pm (modified) (3 diffs)
• lib/evaluator/evaluate.pm (modified) (2 diffs)
• lib/runlog.pm (modified) (7 diffs)

MPI/mpi_maker

@@ -250 +250 @@
-               "predictor=s" =>\$OPT{predictor},
-               "retry=i" =>\$OPT{retry},
+               "ignore" =>\$OPT{ignore},
-               "quiet" =>\$main::quiet,
-               "CTL" => sub {GI::generate_control_files() if($rank == $root); MPI_Finalize(); exit(0);},

bin/fasta_merge

@@ -79 +79 @@
-    
-    dump_it($trans, "$outfile.all.$source.transcripts.fasta");
-s
+
-}
-

bin/maker

@@ -143 +143 @@
-           "predictor=s" =>\$OPT{predictor},
-           "retry=i" =>\$OPT{retry},
+           "clean_try" =>\$OPT{clean_try},
+           "evaluate" =>\$OPT{evaluate},
-           "quiet" => \$main::quiet,
-           "CTL" => sub {GI::generate_control_files(); exit(0);},
@@ -236 +238 @@
-   #-set up variables that are the result of chunk accumulation
-   my $masked_total_seq;
-
-
-
+
+
-
-   my $GFF3 = Dumper::GFF::GFFV3->new("$out_dir/$safe_seq_id.gff",
@@ -718 +719 @@
-                                                              );
-
+      my $non_over = maker::auto_annotator::get_non_overlaping_abinits($maker_anno,
+                                                                       $annotations->{abinit}
+                                                                       );
+      
-      #==OUTPUT DATA HERE
-      
@@ -734 +739 @@
-      $GFF3->resolved_flag if (not $chunk->is_last); #adds ### between contigs
-            
-
-
-
-
+
+
+
+
+
+
+
-   }
-   #END CONTIG
-   
-   #--- write fastas for ab-initio predictions
-
-
-
-
-
-
-
-
-
-
-
-
-
-
+
+
+
-   
-   #--- write GFF3 file

lib/Dumper/GFF/GFFV3.pm

@@ -485 +485 @@
-            $type = $k eq 'hit' ? 'match' : 'match_part';
-        }
-
+
+
+
+
+
+
+
-            $type = $k eq 'hit' ? 'match' : 'match_part';
-        }

lib/GFFDB.pm

@@ -181 +181 @@
-          
-          my $table;
-mask$
+
-             next if (! $codes{rm_pass});
-             next if ($skip{repeat_maker});
@@ -618 +618 @@
-        $f->{gene_id} = $gene_id unless(! $gene_id);
-        $f->{gene_name} = $gene_name unless(! $gene_name);
+        $f->{_tran_name} = $tran_name unless(! $gene_name);
-        $f->{_tran_id}   = $tran_id unless(! $tran_id);
-        $f->{maker_qi}  = $t->{maker_qi} unless(! $t->{maker_qi});

lib/GI.pm

@@ -39 +39 @@
-use repeat_mask_seq;
-use maker::sens_spec;
+use File::NFSLock;
-
-@ISA = qw(
@@ -46 +47 @@
-#------------------------------------------------------------------------
-#--------------------------- CLASS FUNCTIONS ----------------------------
+#------------------------------------------------------------------------
+sub set_global_temp {
+    my $dir = shift;
+
+    $TMP = $dir;
+}
-#------------------------------------------------------------------------
-sub get_preds_on_chunk {
@@ -414 +421 @@
-# }
-#-----------------------------------------------------------------------------
-sub abinit_p_and_t_fastas {
-   my $preds = shift;
-   my $id = shift;
-   my $seq_ref = shift;
-   my $out_dir = shift;
-
-   my %fhs;
-
-   foreach my $hit (@{$preds}) {
-      my $source = $hit->algorithm;
-      $source = uri_escape($source,
-                           '\*\?\|\\\/\'\"\{\}\<\>\;\,\^\(\)\$\~\:'
-                          );
-      my $t_name = $hit->name(); # note this is being set in GFFV3::pred_data
-      my $t_seq  = maker::auto_annotator::get_transcript_seq($hit, $seq_ref);   
-                
-      my ($p_seq, $offset, $end) = 
-      maker::auto_annotator::get_translation_seq($t_seq);
-                
-      my $score = 0;
-      foreach my $hsp ($hit->hsps) {
-         $score += $hsp->score();
-      }
-      my $t_def = ">$t_name transcript offset:$offset score:$score";
-      my $p_def = ">$t_name protein score:$score";
-      
-      if (! exists $fhs{$source}) {
-         open(my $t_fh, "> $out_dir/$id.maker.$source.transcripts.fasta");
-         open(my $p_fh, "> $out_dir/$id.maker.$source.proteins.fasta");
-         $fhs{$source}{t} = $t_fh;
-         $fhs{$source}{p} = $p_fh;
-      }
-
-      my $t_fh = $fhs{$source}{t};
-      my $p_fh = $fhs{$source}{p};
-
-      print $t_fh Fasta::toFasta($t_def, \$t_seq);
-      print $p_fh Fasta::toFasta($p_def, \$p_seq);
-   }
-}
-#-----------------------------------------------------------------------------
-sub maker_p_and_t_fastas {
-
+
+
+
+
+
-   
-
-
-
-
+
-      foreach my $a (@{$an->{t_structs}}) {
-         my ($p_fasta, $t_fasta) = get_p_and_t_fastas($a);
-
-
-
+
+
+
+
+
+
+
+
+
+
+
-   }
-   
-
+
+
+
+
+
+
+
+
+
-}
-
@@ -488 +471 @@
-        
-   return($p_fasta, $t_fasta);
+}
+#----------------------------------------------------------------------------
+sub write_p_and_t_fastas{
+    my $p_fastas = shift @_;
+    my $t_fastas = shift @_;
+    my $safe_seq_id = shift @_;
+    my $out_dir = shift @_;
+
+    while( my $key = each %$p_fastas){
+        my $name = "$out_dir/$safe_seq_id.maker";
+        $name .= ".$key" unless($key eq 'maker');
+        $name .= "\.proteins.fasta";
+
+        FastaFile::writeFile(\$p_fastas->{$key},
+                             $name,
+                            );
+    }
+
+    while( my $key = each %$t_fastas){
+        my $name = "$out_dir/$safe_seq_id.maker";
+        $name .= ".$key" unless($key eq 'maker');
+        $name .= "\.transcripts.fasta";
+
+        FastaFile::writeFile(\$t_fastas->{$key},
+                             $name,
+                            );
+    }
-}
-#----------------------------------------------------------------------------
@@ -1052 +1062 @@
-#-----------------------------------------------------------------------------
-sub build_all_indexes {
-
-
-
-
+
+
+
+
+
+
+
+
+
+
+
+
-   }
-}
@@ -1136 +1154 @@
-
-   $db =~ /([^\/]+)$/;
-t_dir
+TMP
-
-   $LOG->add_entry("STARTED", $blast_finished, "") if($LOG_FLAG); 
-
-
-
-
-
+
+
+
+
+
+
+
-   }
-   elsif (-e $blast_finished && ! $opt_f) {
@@ -1385 +1406 @@
-    
-   $db =~ /([^\/]+)$/;
-t_dir
+TMP
-
-   $LOG->add_entry("STARTED", $blast_finished, "") if($LOG_FLAG);
-
-   #copy db to local tmp dir and run xdformat or format db 
-
-
-
+
+
+
+
+
+
-   }
-   elsif (-e $blast_finished && ! $opt_f) {
@@ -1646 +1670 @@
-
-   $db =~ /([^\/]+)$/;
-t_dir
+TMP
-
-   $LOG->add_entry("STARTED", $blast_finished, "") if($LOG_FLAG); 
-
-   #copy db to local tmp dir and run xdformat or formatdb
-
-
-
+
+
+
+
+
+
-   }
-   elsif (-e $blast_finished && ! $opt_f) {
@@ -1977 +2004 @@
-      $CTL_OPT{'model_pass'} = 1;
-      $CTL_OPT{'pred_pass'} = 0;
-1
+0
-      $CTL_OPT{'est'} = '';
-      $CTL_OPT{'est_reads'} = '';
@@ -1990 +2017 @@
-      $CTL_OPT{'rm_gff'} = '';
-      $CTL_OPT{'predictor'} = 'est2genome';
+      $CTL_OPT{'predictor'} = 'gff' if($main::eva);
-      $CTL_OPT{'snaphmm'} = 'fly';
-      $CTL_OPT{'augustus_species'} = 'fly';
@@ -1996 +2024 @@
-      $CTL_OPT{'pred_gff'} = '';
-      $CTL_OPT{'other_gff'} = '';
-c
+C
-      $CTL_OPT{'cpus'} = 1;
+      $CTL_OPT{'evaluate'} = 0;
+      $CTL_OPT{'evaluate'} = 1 if($main::eva);
-      $CTL_OPT{'max_dna_len'} = 100000;
-      $CTL_OPT{'min_contig'} = 1;
@@ -2003 +2033 @@
-      $CTL_OPT{'pred_flank'} = 200;
-      $CTL_OPT{'single_exon'} = 0;
+      $CTL_OPT{'single_length'} = 250;
-      $CTL_OPT{'keep_preds'} = 0;
-      $CTL_OPT{'retry'} = 1;
-
+
+
+
+
-      $CTL_OPT{'clean_up'} = 0;
-   }
@@ -2075 +2109 @@
-      $CTL_OPT{'eva_gspmax'} = 100;
-      $CTL_OPT{'enable_fathom'} = 0;
-
+
-   }
-   
@@ -2133 +2167 @@
-   #--load command line options
-   $CTL_OPT{genome} = $OPT{genome} if (defined $OPT{genome});
+   $CTL_OPT{genome_gff} = $OPT{genome_gff} if (defined $OPT{genome_gff});
-   $CTL_OPT{force} = $OPT{force} if (defined $OPT{force});
-   $CTL_OPT{predictor} = $OPT{predictor} if (defined $OPT{predictor});
-   $CTL_OPT{retry} = $OPT{retry} if (defined $OPT{retry});
-   $CTL_OPT{cpus} = $OPT{cpus} if (defined $OPT{cpus});
+   $CTL_OPT{clean_try} = $OPT{clean_try} if (defined $OPT{clean_try});
-
-   #skip repeat masking command line option
@@ -2147 +2183 @@
-   }
-
+   #required for evaluator to work
+   $CTL_OPT{predictor} = 'gff' if($main::eva);
+   $CTL_OPT{model_pass} = 1 if($main::eva);
+
-   #parse predictor and error check
-   $CTL_OPT{predictor} =~ s/\s+//g;
-   my @predictors = split(',', $CTL_OPT{predictor});
- 
+
-
-   foreach my $p (@predictors) {
@@ -2159 +2199 @@
-         "Valid entries are: est2genome, abinit, gff, snap, augustus,\n".
-         "or fgenesh\n\n";
+      }
+   }
+
+   #parse eval_pred and error check
+   $CTL_OPT{eval_pred} =~ s/\s+//g;
+   my @eval_preds = split(',', $CTL_OPT{eval_pred});
+   $CTL_OPT{_eval_pred} = \@eval_preds;
+
+   foreach my $p (@eval_preds) {
+      if ($p !~ /^snap$|^augustus$|^fgenesh$|^twinscan$|^jigsaw$|^gff$/) {
+         $error .= "ERROR: Invalid eval_pred defined: $p\n".
+         "Valid entries are: gff, snap, augustus, or fgenesh\n\n";
-      }
-   }
@@ -2232 +2284 @@
-   push (@infiles, 'rmlib') if ($CTL_OPT{rmlib});
-   push (@infiles, 'snap') if (grep (/snap/, $CTL_OPT{predictor}));
-   push (@infiles, 'snap') if ($CTL_OPT{snap});
-   push (@infiles, 'augustus') if (grep (/augustus/, $CTL_OPT{predictor})); 
-   push (@infiles, 'augustus') if ($CTL_OPT{augustus});
-   push (@infiles, 'fgenesh') if (grep (/fgenesh/, $CTL_OPT{predictor}));
-   push (@infiles, 'fgenesh') if ($CTL_OPT{fgenesh});
-   push (@infiles, 'twinscan') if (grep (/twinscan/, $CTL_OPT{predictor}));
-   push (@infiles, 'twinscan') if ($CTL_OPT{twinscan});
-   push (@infiles, 'jigsaw') if (grep (/jigsaw/, $CTL_OPT{predictor}));
-
-
+
+
+
+
+
+
-   push (@infiles, 'rm_gff') if($CTL_OPT{rm_gff});
-   push (@infiles, 'est_gff') if($CTL_OPT{est_gff});
@@ -2266 +2318 @@
-         next;
-      }
-
-
+
-         $error .= "ERROR: The \'$in\' file $CTL_OPT{$in} does not exist.\n".
-         "Please check your control files: maker_opts.ctl, maker_bopts, or maker_exe.ctl\n\n";
@@ -2279 +2330 @@
-                               
-   #--error check that values are meaningful
-$CTL_OPT{augustus}
+grep (/^augustus$/, @infiles)
-      warn "WARNING: There is no species specified for Augustus in maker_opts.ctl augustus_species.\n".
-      "As a result the default (fly) will be used.\n\n";
-      $CTL_OPT{augustus_species} = "fly";
-   }
-$CTL_OPT{augustus}
+grep (/^augustus$/, @infiles)
-       (! $ENV{AUGUSTUS_CONFIG_PATH} || ! -e "$ENV{AUGUSTUS_CONFIG_PATH}/extrinsic/extrinsic.MPE.cfg")
-      ) {
-      $error .= "ERROR: The environmental variable AUGUSTUS_CONFIG_PATH has not been set\n".
-      "or is not set correctly Please set this in your profile per Augustus\n".
-
-
-($CTL_OPT{snap}||$CTL_OPT{enable_fathom}
-
+ then try again.
+
+grep (/^snaps$|^fathom$/, @infiles
+/Fathom
-      "As a result, the default (fly) will be used.\n\n";
-      $CTL_OPT{snaphmm} = "fly";
-   }
-
-
-
+
-       (! exists $ENV{ZOE} || ! -e $ENV{ZOE}."/HMM/".$CTL_OPT{snaphmm})
-      ) {
-
-
-$CTL_OPT{fgenesh}
+/Fathom
+
+grep (/^fgenesh$/, @infiles)
-      if (! $CTL_OPT{fgenesh_par_file}) {
-         $error .= "ERROR: There is no parameter file secified for for FgenesH in\n".
@@ -2323 +2372 @@
-   }
-   if ($CTL_OPT{retry} < 0) {
-
+
+
-      $CTL_OPT{retry} = 0;
-
-
+
+
+
+
+
-   die $error if ($error);   
-
@@ -2342 +2395 @@
-   if ($iterator->number_of_entries() > 1000 && ! $CTL_OPT{datastore}) {
-      warn "WARNING:  There are more than 1000 fasta entries in the input file.\n".
-D
+A two depth d
-      "the output directory.\n\n";
-      
@@ -2365 +2418 @@
-   }
-
-
+and indexes 
-   create_blastdb(\%CTL_OPT, $mpi_size);
+   build_all_indexes(\%CTL_OPT);
+
+   #--set up optional global TMP
+   if($CTL_OPT{TMP}){
+       $CTL_OPT{_TMP} = tempdir("maker_XXXXXX", CLEANUP => 1, DIR => 1);
+   }
-
-   #--set values for datastructure
@@ -2390 +2449 @@
-   my $dir = shift || Cwd::cwd();
-   my %O = (@_) ? @_ : set_defaults();
-
-
-
-
-
-
-
-
+
+
+
+
+
+
+
+
+
+
+
+
+
-   print OUT "est_pass:$O{est_pass} #use ests in genome_gff: 1 = yes, 0 = no\n";
-   print OUT "altest_pass:$O{altest_pass} #use alternate organism ests in genome_gff: 1 = yes, 0 = no\n";
-   print OUT "protein_pass:$O{protein_pass} #use proteins in genome_gff: 1 = yes, 0 = no\n";
-protein
-protein_pass} #use gene models in genome_gff: 1 = yes, 0 = no\n"
+rm
+model_pass} #use gene models in genome_gff: 1 = yes, 0 = no\n" if(!$ev)
-   print OUT "pred_pass:$O{pred_pass} #use ab-initio predictions in genome_gff: 1 = yes, 0 = no\n";
-protein_pass} #passthrough everything else in genome_gff: 1 = yes, 0 = no\n"
+other_pass} #passthrough everything else in genome_gff: 1 = yes, 0 = no\n" if(!$ev)
-   print OUT "\n";
-
+
+
+
+
+
-   print OUT "est:$O{est} #non-redundant set of assembled ESTs in fasta format (classic EST analysis)\n";
-   print OUT "est_reads:$O{est_reads} #un-assembled EST reads in fasta format (for deep nextgen mRNASeq)\n";
-   print OUT "altest:$O{altest} #EST/cDNA sequence file in fasta format from an alternate organism\n";
- seperate
+n external
-   print OUT "altest_gff:$O{altest_gff} #Alternate organism EST evidence from a seperate gff3 file\n";
-   print OUT "\n";
-must
+should
-   print OUT "protein:$O{protein}  #protein sequence file in fasta format\n";
-
+n external
-   print OUT "\n";
-   print OUT "#-----Repeat Masking (leave values blank to skip)\n";
@@ -2421 +2489 @@
-   print OUT "repeat_protein:$O{repeat_protein} #a database of transposable element proteins in fasta format\n";
-   print OUT "rmlib:$O{rmlib} #an organism specific repeat library in fasta format\n";
-
+n external
-   print OUT "\n";
-
-
+
+
+
+
-   print OUT "snaphmm:$O{snaphmm} #SNAP HMM model\n";
-   print OUT "augustus_species:$O{augustus_species} #Augustus gene prediction model\n";
-   print OUT "fgenesh_par_file:$O{fgenesh_par_file} #Fgenesh parameter file\n";
- gff3 file (annotation passthrough)\n"
-
+n external gff3 file (annotation pass-through)\n" if(!$ev)
+n external
-   print OUT "\n";
-
-through to final output from a gff3 file\n"
-
+ if(!$ev)
+-through to final output from an extenal gff3 file\n" if(!$ev)
+ if(!$ev)
-   print OUT "#-----External Application Specific Options\n";
-   print OUT "alt_peptide:$O{alt_peptide} #amino acid used to replace non standard amino acids in blast databases\n";
@@ -2439 +2509 @@
-   print OUT "\n";
-   print OUT "#-----Maker Specific Options\n";
+   print OUT "evaluate:$O{evaluate} #run Evaluator on all annotations\n" if(!$ev);
-   print OUT "max_dna_len:$O{max_dna_len} #length for dividing up contigs into chunks (larger values increase memory usage)\n";
-   print OUT "min_contig:$O{min_contig} #all contigs from the input genome file below this size will be skipped\n";
-EST and protein
+evidence
-   print OUT "pred_flank:$O{pred_flank} #length of sequence surrounding EST and protein evidence used to extend gene predictions\n";
-
-
+
+
+
-   print OUT "retry:$O{retry} #number of times to retry a contig if annotation fails for some reason\n";
-
+
+
+
-   close (OUT);
-    
-
-
+
+
+
-   print OUT "#-----BLAST and Exonerate Statistics Thresholds\n";
-   print OUT "blast_type:$O{blast_type} #set to 'wublast' or 'ncbi'\n";
@@ -2479 +2554 @@
-    
-   #--build maker_exe.ctl file
-
-
+
+
+
-   print OUT "formatdb:$O{formatdb} #location of NCBI formatdb executable\n";
-   print OUT "blastall:$O{blastall} #location of NCBI blastall executable\n";
@@ -2494 +2570 @@
-   print OUT "augustus:$O{augustus} #location of augustus executable\n";
-   print OUT "fgenesh:$O{fgenesh} #location of fgenesh executable\n";
-
-
+
-   print OUT "\n";
-   print OUT "#-----Other Algorithms\n";
-   print OUT "jigsaw:$O{jigsaw} #location of jigsaw executable (not yet implemented)\n";
-   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";
-   close(OUT);
-    

lib/Process/MpiChunk.pm

@@ -130 +130 @@
-      #-set up variables that are the result of chunk accumulation
-      $VARS->{masked_total_seq} = '';
-''
-''
+{}
+{}
-
-      #--prebuild an index of the databases
@@ -650 +650 @@
-            my $masked_preds = GI::abinits($masked_file,
-                                           $the_void,
-
+.".masked"
-                                           \%CTL_OPT,
-                                           $LOG
@@ -1527 +1527 @@
-                                                                     \%CTL_OPT
-                                                                    );
-
-
-
-
-
+
+
+
+
+
+
+
+
-            #------------------------RESULTS
-         }
@@ -1551 +1554 @@
-            @args = (qw{chunk
-                        maker_anno
+                        non_over
+                        annotations
-                        blastx_data
-                        blastn_data
@@ -1569 +1574 @@
-         elsif ($flag eq 'run') {
-            #-------------------------CODE
-
-
+
+
+
+
-            my $blastx_data = $VARS->{blastx_data};
-            my $blastn_data = $VARS->{blastn_data};
@@ -1601 +1608 @@
-            $GFF3->resolved_flag if (not $chunk->is_last); #adds ### between contigs
-            
-
-
-
-
+
+
+
+
+
+
+
-            #-------------------------CODE
-
@@ -1661 +1671 @@
-
-            #--- write fastas for ab-initio predictions
-
-
-
-
-
-
-
-
-
-
-
-
-
-
+
-            
-            #--- write GFF3 file
@@ -1821 +1818 @@
-   my $tag = shift || 'throw';
-
-= "ERROR: Failed while ".$extra."!!\n\n"
+.= "ERROR: Failed while ".$extra."!!\n\n" if($extra)
-   
-   if($tag eq 'handle'){

lib/Process/MpiTiers.pm

@@ -260 +260 @@
-   if($chunk->failed){
-      my $E = $chunk->exception;
-ERROR: 
+
-   }
-   else{

lib/Widget/RepeatMasker.pm

@@ -250 +250 @@
-        foreach my $key (keys %hsps){
-                 my $f =
-q_name
+key
-                                                                  '-description'  => 'NA',
-                                                                  '-algorithm'    => 'repeat_masker',

lib/Widget/fgenesh.pm

@@ -157 +157 @@
-
-        my $iterator = new Iterator::Fasta($q_file);
-Entry
+Fasta
-
-        my $def     = Fasta::getDef($fasta);
-        my $q_seq   = Fasta::getSeqRef($fasta);
-
-
+
-        
-        my $fh = new FileHandle();

lib/cluster.pm

@@ -14 +14 @@
-use compare;
-use SimpleCluster;
+use Shadower;
+
-@ISA = qw(
-       );
@@ -166 +168 @@
-        my $ref = $hit->algorithm;
-
-
+
+
-        return  1 if $ref =~ /^snap$/i;
-        return  1 if $ref =~ /^augustus$/i;
-        return  1 if $ref =~ /^fgenesh$/i;
-        return  1 if $ref =~ /^twinscan$/i;
+        return  1 if $ref =~ /^jigsaw$/i;
+        return  1 if $ref =~ /^pred_gff\:/i;
-        return  2 if $ref =~ /^blastn$/i;
-        return  2 if $ref =~ /^tblastx$/i;
+        return  2 if $ref =~ /^altest_gff\:/i;
-        return  3 if $ref =~ /^blastx$/i;
+        return  3 if $ref =~ /^protein_gff\:/i;
-        return  4 if $ref =~ /2genome$/i;
+        return  4 if $ref =~ /^est_gff\:/i;
+        return  5 if $ref =~ /^maker$/i;
+        return  5 if $ref =~ /^model_gff\:/i;
-        die "UNKNOWN CLASS(".ref($hit)."), ALGORITHM($ref), in cluster::criteria\n";
-}
@@ -182 +192 @@
-
-        my $score =  $hit->score();
+        $score = '' if(! defined $score);
-        #check if value is numerical ad adjust if not
-        if($score !~ /^[-+]?(?:\d+(?:\.\d*)?|\.\d+)(?:e[-+]?\d+)?$/){
-
+
+
-        }
-        if($score !~ /^[-+]?(?:\d+(?:\.\d*)?|\.\d+)(?:e[-+]?\d+)?$/){
-            $score = $hit->significance;
+            $score = '' if(! defined $score);
-            if($score =~ /^[-+]?(?:\d+(?:\.\d*)?|\.\d+)(?:e[-+]?\d+)?$/){
-                $score = 10000 - (10000 * $score);

lib/evaluator/evaluate.pm

@@ -21 +21 @@
-#--------------------------------- METHODS ------------------------------------
-#------------------------------------------------------------------------------
-
-sub evaluate_in_maker {
-
@@ -114 +113 @@
-        }
-}
-
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
-#-------------------------------------------------------------------------------
-sub power_evaluate {

lib/runlog.pm

@@ -24 +24 @@
-                  'rm_gff',
-                  'predictor',
+                  'eval_pred',
-                  'sort_base',
-                  'snaphmm',
@@ -34 +35 @@
-                  'pred_flank',
-                  'single_exon',
+                  'single_length',
-                  'keep_preds',
-                  'alt_peptide',
+                  'evaluate',
-                  'blast_type',
-                  'pcov_blastn',
@@ -55 +58 @@
-                  'ep_score_limit',
-                  'en_score_limit',
+                  'enable_fathom'
-                 );
-
@@ -155 +159 @@
-         }
-         else{
-2
+($CTL_OPTIONS{clean_try}) ? 2 : 3
-            $continue_flag = -1 if($self->{die_count} > $CTL_OPTIONS{retry}); #only let die up to count
-            $rm_key{retry}++ if ($continue_flag == 2);
@@ -196 +200 @@
-               $continue_flag = 1; #re-run because ctlopts changed
-            
-
-
+
+
+
+
+
-               if (-e $gff_file) {
-                  $rm_key{gff}++; #always rebuild gff when some option has changed
@@ -544 +551 @@
-      print STDERR "#---------------------------------------------------------------------\n",
-                   "Now retrying the contig!!\n",
+                   "All contig related data will be erased before continuing!!\n",
+                   "SeqID: $seq_id\n",
+                   "Length: $length\n",
+                   "Retry: $die_count!!\n",
+                   "#---------------------------------------------------------------------\n\n\n";
+   }
+   elsif($flag == 3){
+      print STDERR "#---------------------------------------------------------------------\n",
+                   "Now retrying the contig!!\n",
-                   "SeqID: $seq_id\n",
-                   "Length: $length\n",
@@ -587 +603 @@
-   }
-   elsif($flag == 2){
-
+
+
+
+
-   }
-   elsif($flag == -1){