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revision 1.13, Fri Jul 22 19:20:11 2011 UTC revision 1.14, Wed Aug 24 21:11:36 2011 UTC
# Line 259  Line 259 
259      $loaderObject->LoadContigs();      $loaderObject->LoadContigs();
260    
261  Load the contig information into the database. This includes the contigs themselves and  Load the contig information into the database. This includes the contigs themselves and
262  the DNA. The number of contigs will be recorded as the C<contigs> statistic and the  the DNA. The number of contigs will be recorded as the C<contigs> statistic, the
263  number of base pairs as the C<dna> statistic.  number of base pairs as the C<dna> statistic, and the number of GC instances as the
264    C<gc_content> statistic.
265    
266  =cut  =cut
267    
# Line 368  Line 369 
369      $sap->InsertObject('DNASequence', id => $chunkID, sequence => $chunk);      $sap->InsertObject('DNASequence', id => $chunkID, sequence => $chunk);
370      # Record the chunk.      # Record the chunk.
371      $self->{stats}->Add(chunks => 1);      $self->{stats}->Add(chunks => 1);
372        # Update the GC count.
373        $self->{stats}->Add(gc_content => ($chunk =~ tr/GCgc//));
374  }  }
375    
376  =head3 OutputContig  =head3 OutputContig
# Line 958  Line 961 
961      $fields{'dna-size'} = $stats->Ask('dna');      $fields{'dna-size'} = $stats->Ask('dna');
962      $fields{pegs} = $stats->Ask('peg');      $fields{pegs} = $stats->Ask('peg');
963      $fields{rnas} = $stats->Ask('rna');      $fields{rnas} = $stats->Ask('rna');
964        $fields{gc_content} = $stats->Ask('gc_content') * 100 / $stats->Ask('dna');
965      # Get the genetic code. The default is 11.      # Get the genetic code. The default is 11.
966      $fields{'genetic-code'} = 11;      $fields{'genetic-code'} = 11;
967      my $geneticCodeFile = "$dir/GENETIC_CODE";      my $geneticCodeFile = "$dir/GENETIC_CODE";

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