[Bioperl-l] negative start/end numbers to Bio::SeqFeature::Generic
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.
I'm writing CGI to analyse promoter sequences and output images of locations
regulatory elements (eg transcription binding sites).
after the analysis (all good), i create the graphics panel, and go to add a
## 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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