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

[Crabtree, Jonathan]

Mark-

Try setting -offset => -$negSeqLen when you call $panel->new().

Jonathan

> -----Original Message-----
> From: bioperl-l-bounces at portal.open-bio.org 
> [mailto:bioperl-l-bounces at portal.open-bio.org] On Behalf Of mql201
> Sent: Monday, July 26, 2004 3:01 PM
> To: bioperl-l at portal.open-bio.org
> Subject: [Bioperl-l] negative start/end numbers to 
> Bio::SeqFeature::Generic
> 
> 
> Hello
> 
> 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);
>   $panel->add_track($scale,
>                     -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 
> image.
> 
> 
> 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
> Mark
> 
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