[Bioperl-l] modules for siRNA design

[Donald Jackson]

Thanks Heikki,
I thought I'd fixed all my code to handle that change from 1.0 to 1.2,
but clearly I messed one.
I'll get a patch into CVS later today and will also try to get some
better error checking on sequence lengths and start/end pad.

Don

Heikki Lehvaslaiho wrote:

>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
>> ,-,-.     ,-,-.     ,-,-.     ,-,-.     ,-
>>/ / \ \   / / \ \   / / \ \   / / \ \   / /
>>     \ \ / /   \ \ / /   \ \ / /   \ \ / /
>>      `-'-'     `-'-'     `-'-'     `-'-'
>>
>>
>>San Wang
>>Dr. Student
>>Bioinformatics and Gene Network Research Group
>>Zhejiang University
>>P.R.China
>>
>>Address:
>>Room 415# ,Bio-technology Institute,
>>Zhejiang University,
>>Kaixuan Road 268#  Hangzhou
>>Zhejiang, P.R.China
>>310027
>>
>>Tel:
>>0086-571-86892051
>>Fax:
>>0086-571-86961525
>>E-mail:
>>bsman at 163.com
>>Website:
>>http://www.estarray.org
>>
>>£­£­£­£­£­£­£­£­£­£­
>>  Innovation is everything. When you are on the forefront, you can see what
>>the next innovation needs to be? --- from Robert Noyce, Founder of Intel
>>  The more things change, the more they stay the same!
>>  The more things seem to be complicated ,the more they are simple in fact!
>>
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>
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>