[Bioperl-l] negative start/end numbers to Bio::SeqFeature::Generic

mql201 M.Q.Lewis at exeter.ac.uk
Mon Jul 26 15:01:14 EDT 2004


quick q: i want to supply Bio::SeqFeature::Generic with NEGATIVE start and end 
values, or get 
round it somehow, cos i'm looking at gene promoters, and not genes.

less quick:
I'm writing CGI to analyse promoter sequences and output images of locations 
of upstream 
regulatory elements (eg transcription binding sites).

after the analysis (all good), i create the graphics panel, and go to add a 
scale track:

  ## create and add scale as an anchored arrow
  $scale = Bio::SeqFeature::Generic->new(-start=>1,-end=>$seqLen);
  #$scale = Bio::SeqFeature::Generic->new(-start=>$negSeqLen,-end=>-1);
                    -glyph   => 'anchored_arrow',
                    -tick    => 2,
                    -fontcolor => '#3d5315',
                    -fgcolor => '#3d5315',
                    -bgcolor => '#e3ffb7');

as you can see from the commented $scale instantiation, i can supply positive 
integers to start and 
end as long as end > start, but if i give negative numbers, i get an empty 

i've looked at the Bio::SeqFeature::Gene::Promoter module, but there is no 
help information about 
how to extract and use the return values.

Anyone know of a way of using bioperl using negative numbers?

Many thanks IA

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