[Bioperl-l] modules for siRNA design

[Heikki Lehvaslaiho]

San Wang,

The code in SiRNA.pm around line 263 looks like this:

    if ($cds) {
	$left = $cds->start + $self->end_pad;
	$right = $cds->end - $self->start_pad;	
    }
    else {
	$left = $target->start + $self->end_pad;    # line #263
	$right = $target->end - $self->start_pad;
    }

Start and end calls are fine on a SeqFeature object like a CDS, but are not 
defined for a sequence. These lines  should be replaced by something like the 
following:

	$left = 1 + $self->end_pad;
	$right = $target->length - $self->start_pad;

Your example sequence is not too realistic, so you'll get an other error 
caused by the shortness of the sequece. Call 

$sirna_designer->start_pad(0);
$sirna_designer->end_pad(0);

before calling design().

Yours,	
		-Heikki

On Saturday 06 Mar 2004 19:08, ÍõêÉ, San Wang wrote:
> Dear bioperl-l:
>
> 	I have report a bug for it.
> "Can't locate object method "start" via package "Bio::Seq::RichSeq"
> (perhaps you forgot to load "Bio::Seq::RichSeq"?) at
> D:/Tools/perl/site/lib/Bio/Tools/SiRNA.pm line 263."
>
> 	Best Regards!
>
> 			Yours sincerely
> ¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡ÍõêÉ, San Wang
> ¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡bsman at tom.com
> ¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡2004-03-07
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> San Wang
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> Bioinformatics and Gene Network Research Group
> Zhejiang University
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-- 
______ _/      _/_____________________________________________________
      _/      _/                      http://www.ebi.ac.uk/mutations/
     _/  _/  _/  Heikki Lehvaslaiho    heikki_at_ebi ac uk
    _/_/_/_/_/  EMBL Outstation, European Bioinformatics Institute
   _/  _/  _/  Wellcome Trust Genome Campus, Hinxton
  _/  _/  _/  Cambs. CB10 1SD, United Kingdom
     _/      Phone: +44 (0)1223 494 644   FAX: +44 (0)1223 494 468
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