[Bio] / Sprout / GenomeSproutLoader.pm Repository:
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revision 1.2, Mon Jan 19 21:46:21 2009 UTC revision 1.3, Mon Mar 2 22:24:42 2009 UTC
# Line 161  Line 161 
161              $self->Add(contigIn => 1);              $self->Add(contigIn => 1);
162              # Create the contig ID.              # Create the contig ID.
163              my $sproutContigID = "$genomeID:$contigID";              my $sproutContigID = "$genomeID:$contigID";
164                # Get the contig length.
165                my $contigLen = $fig->contig_ln($genomeID, $contigID);
166              # Create the contig record and relate it to the genome.              # Create the contig record and relate it to the genome.
167              $self->PutE(Contig => $sproutContigID);              $self->PutE(Contig => $sproutContigID, length => $contigLen);
168              $self->PutR(HasContig => $genomeID, $sproutContigID);              $self->PutR(HasContig => $genomeID, $sproutContigID);
169              # Now we need to split the contig into sequences. The maximum sequence size is              # Now we need to split the contig into sequences. The maximum sequence size is
170              # a property of the Sprout object.              # a property of the Sprout object.
171              my $chunkSize = $sprout->MaxSequence();              my $chunkSize = $sprout->MaxSequence();
172              # Now we get the sequence a chunk at a time.              # Now we get the sequence a chunk at a time.
             my $contigLen = $fig->contig_ln($genomeID, $contigID);  
173              for (my $i = 1; $i <= $contigLen; $i += $chunkSize) {              for (my $i = 1; $i <= $contigLen; $i += $chunkSize) {
174                  $self->Add(chunkIn => 1);                  $self->Add(chunkIn => 1);
175                  # Compute the endpoint of this chunk.                  # Compute the endpoint of this chunk.

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