[Bio] / FigKernelScripts / build_initial_objects_for_start_predictions.pl Repository:
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revision 1.2, Thu Apr 28 19:07:16 2005 UTC revision 1.3, Thu May 12 20:38:37 2005 UTC
# Line 1  Line 1 
 use FIG_Config;  
1    
2  use FIG;  use FIG;
3  my $fig = new FIG;  my $fig = new FIG;
# Line 41  Line 40 
40    
41      $loc = join("_",($contig,$begin,$end));      $loc = join("_",($contig,$begin,$end));
42      $seq = uc $fig->dna_seq($genome,$loc);      $seq = uc $fig->dna_seq($genome,$loc);
43        if (! $seq)
44        {
45            print STDERR &Dumper($peg,$loc,$seq); die "could not get sequence for $peg";
46        }
47    
48  #   The following hack handles uncertainty about whether SEED gives back the STOP or not  #   The following hack handles uncertainty about whether SEED gives back the STOP or not
49      if (substr($seq,-6,3) =~ /TAA|TAG|TGA/i)      if (substr($seq,-6,3) =~ /TAA|TAG|TGA/i)
50      {      {
# Line 49  Line 53 
53      }      }
54      elsif (substr($seq,-3,3) !~ /TAA|TAG|TGA/i)      elsif (substr($seq,-3,3) !~ /TAA|TAG|TGA/i)
55      {      {
56          die "BAD STOP: $genome $loc $seq\n";          die "BAD STOP: $peg $genome $loc $seq\n";
57      }      }
58    
59      $loc = join("_",($contig,$begin,$end));      $loc = join("_",($contig,$begin,$end));

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