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revision 1.1, Wed Oct 3 20:55:54 2007 UTC revision 1.2, Fri Oct 5 17:25:53 2007 UTC
# Line 49  Line 49 
49  &FIG::verify_dir($work);  &FIG::verify_dir($work);
50  chdir $work or &fatal("chdir $work failed: $!");  chdir $work or &fatal("chdir $work failed: $!");
51    
52    my $code = $meta->get_metadata("genome.genetic_code");
53    $code = 11 unless $code;
54    
55  if (0 or (not -s "$work/orfs3.cds"))  if (0 or (not -s "$work/orfs3.cds"))
56  {  {
57      &run("$crit_scripts/blast-contigs $contigs > $work/contigs.blast");      &run("$crit_scripts/blast-contigs $contigs > $work/contigs.blast");
58    
59      &run("$crit_scripts/make-blastpairs $work/contigs.blast > $work/contigs.blast.pairs");      &run("$crit_scripts/make-blastpairs $work/contigs.blast > $work/contigs.blast.pairs");
60      &run("$crit_bin/scanblastpairs $contigs $work/contigs.blast.pairs $work/contigs.triplets");      &run("$crit_bin/scanblastpairs $contigs $work/contigs.blast.pairs $work/contigs.triplets");
61      &run("$crit_scripts/iterate-critica $work/orfs $contigs $work/contigs.triplets");      &run("$crit_scripts/iterate-critica -genetic-code=$code $work/orfs $contigs $work/contigs.triplets");
62  }  }
63    
64  #  #
# Line 75  Line 78 
78    
79  my $figv = $job->get_figv();  my $figv = $job->get_figv();
80    
 my $code = $meta->get_metadata("genome.genetic_code");  
 $code = 11 unless $code;  
81  my $code_table = &FIG::genetic_code($code);  my $code_table = &FIG::genetic_code($code);
82    
83  while (<CRIT>)  while (<CRIT>)
# Line 122  Line 123 
123      if ($meta)      if ($meta)
124      {      {
125          $meta->add_log_entry($0, ['fatal error', $msg]);          $meta->add_log_entry($0, ['fatal error', $msg]);
126          $meta->set_metadata("status.bbhs", "error");          $meta->set_metadata("status.critica", "error");
127      }      }
128    
129      croak "$0: $msg";      croak "$0: $msg";

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