[Bio] / FigKernelScripts / build_initial_objects_for_start_predictions.pl Repository:
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revision 1.1, Mon Jan 17 01:27:44 2005 UTC revision 1.2, Thu Apr 28 19:07:16 2005 UTC
# Line 44  Line 44 
44  #   The following hack handles uncertainty about whether SEED gives back the STOP or not  #   The following hack handles uncertainty about whether SEED gives back the STOP or not
45      if (substr($seq,-6,3) =~ /TAA|TAG|TGA/i)      if (substr($seq,-6,3) =~ /TAA|TAG|TGA/i)
46      {      {
47          $end = ($beg < $end) ? $end-3 : $end+3;          $end = ($begin < $end) ? $end-3 : $end+3;
48          $seq = substr($seq,0,length($seq) - 3);          $seq = substr($seq,0,length($seq) - 3);
49      }      }
50      elsif (substr($seq,-3,3) !~ /TAA|TAG|TGA/i)      elsif (substr($seq,-3,3) !~ /TAA|TAG|TGA/i)
# Line 52  Line 52 
52          die "BAD STOP: $genome $loc $seq\n";          die "BAD STOP: $genome $loc $seq\n";
53      }      }
54    
55      $loc = join("_",($contig,$beg,$end));      $loc = join("_",($contig,$begin,$end));
56    
57    
58      # BACK INTO THE STOP FROM START OF PEG      # BACK INTO THE STOP FROM START OF PEG

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