[Bioperl-l] Bio::Restriction::Analysis cut site problem in 1.5.2

Heikki Lehvaslaiho heikki at sanbi.ac.za
Thu Feb 8 04:39:47 EST 2007


The error comes from Bio::PrimarySeq::subseq when it tries to cut beyond an 
existing sequence. Maybe your sequence has a restriction site that is near 
the end of your sequence?

This is a special case which has not been into account in 
Bio::Restriction::Analysis::_cuts method. 

The question is : should the site be be detected if its cut site is not within 
the studied sequence?

Please submit a bugzilla bug, so this gets solved. I probably do not have time 
to tweak the code myself.

	-Heikki


On Thursday 08 February 2007 01:41:13 Steven Brown wrote:
> The module seems to have trouble handling the cut-site specifiers
> that surround the sequence that the enzyme is specific for.  The error:
>
> ------------- EXCEPTION: Bio::Root::Exception -------------
> MSG: Bad end parameter (22). End must be less than the total length
> of sequence (total=6)
> STACK: Error::throw
> STACK: Bio::Root::Root::throw /usr/local/lib/perl5/site_perl/5.8.6/
> Bio/Root/Root.pm:328
> STACK: Bio::PrimarySeq::subseq /usr/local/lib/perl5/site_perl/5.8.6/
> Bio/PrimarySeq.pm:371
> STACK: Bio::Restriction::Analysis::_enzyme_sites /usr/local/lib/perl5/
> site_perl/5.8.6/Bio/Restriction/Analysis.pm:884
> STACK: Bio::Restriction::Analysis::_cuts /usr/local/lib/perl5/
> site_perl/5.8.6/Bio/Restriction/Analysis.pm:785
> STACK: Bio::Restriction::Analysis::cut /usr/local/lib/perl5/site_perl/
> 5.8.6/Bio/Restriction/Analysis.pm:369
> STACK: Bio::Restriction::Analysis::cutters /usr/local/lib/perl5/
> site_perl/5.8.6/Bio/Restriction/Analysis.pm:678
> ---snip (my script line)---
> -----------------------------------------------------------
>
> The offending enzyme:
>
> ---snip---
> <1>AcuI
> <2>Eco57I,Bsp6II,BspD6II,BspKT5I,Eco112I,Eco125I,FsfI
> <3>CTGAAG(16/14)
> ---snip---
>
> If I get rid of the (16/14) the error disappears and the right
> sequence site is matched.  It seems like maybe a decision was made
> not analyze enzymes with remote cut positions, or the code wouldn't
> throw the error...?  Any information on this would be helpful.
>
> Thanks,
> Steve
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> Bioperl-l at lists.open-bio.org
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-- 
______ _/      _/_____________________________________________________
      _/      _/
     _/  _/  _/  Heikki Lehvaslaiho    heikki at_sanbi _ac _za
    _/_/_/_/_/  Associate Professor    skype: heikki_lehvaslaiho
   _/  _/  _/  SANBI, South African National Bioinformatics Institute
  _/  _/  _/  University of Western Cape, South Africa
     _/      Phone: +27 21 959 2096   FAX: +27 21 959 2512
___ _/_/_/_/_/________________________________________________________


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