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

[Crabtree, Jonathan]

Mark-

Sorry, that should have read "$negSeqLen", not "-$negSeqLen".  You get
the idea, though...

Jonathan

> -----Original Message-----
> From: bioperl-l-bounces at portal.open-bio.org 
> [mailto:bioperl-l-bounces at portal.open-bio.org] On Behalf Of 
> Crabtree, Jonathan
> Sent: Monday, July 26, 2004 3:25 PM
> To: mql201
> Cc: bioperl-l at portal.open-bio.org
> Subject: RE: [Bioperl-l] negative start/end numbers to 
> Bio::SeqFeature::Generic
> 
> 
> 
> 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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> > Bioperl-l at portal.open-bio.org
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> > 
> 
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