[Bio] / FigKernelScripts / build_initial_objects_for_start_predictions.pl Repository:
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revision 1.3, Thu May 12 20:38:37 2005 UTC revision 1.4, Sun Jul 24 15:54:40 2005 UTC
# Line 26  Line 26 
26          next;          next;
27      }      }
28    
29        my $lnC = $fig->contig_ln($genome,$contig);
30      ($contig,$begin,$end) = $fig->boundaries_of($loc);      ($contig,$begin,$end) = $fig->boundaries_of($loc);
31      if ($begin < $end)      if ($begin < $end)
32      {      {
33          $l = sprintf("%s_%d_%d",$contig,1,$begin-1);          $l = sprintf("%s_%d_%d",$contig,1,$begin-1);
34            if ($end < ($lnC-3))
35            {
36          $end += 3;          $end += 3;
37      }      }
38        }
39      else      else
40      {      {
41          $l = sprintf("%s_%d_%d",$contig,$begin+1,$fig->contig_ln($genome,$contig));          $l = sprintf("%s_%d_%d",$contig,$begin+1,$fig->contig_ln($genome,$contig));
42            if ($end > 3)
43            {
44          $end -= 3;          $end -= 3;
45      }      }
46        }
47    
48      $loc = join("_",($contig,$begin,$end));      $loc = join("_",($contig,$begin,$end));
49      $seq = uc $fig->dna_seq($genome,$loc);      $seq = uc $fig->dna_seq($genome,$loc);
# Line 53  Line 60 
60      }      }
61      elsif (substr($seq,-3,3) !~ /TAA|TAG|TGA/i)      elsif (substr($seq,-3,3) !~ /TAA|TAG|TGA/i)
62      {      {
63          die "BAD STOP: $peg $genome $loc $seq\n";          warn "BAD STOP: $peg $genome $loc $seq\n";
64      }      }
65    
66      $loc = join("_",($contig,$begin,$end));      $loc = join("_",($contig,$begin,$end));

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