[Bioperl-l] Exception thrown with Bio::Restriction::Analysis

[Chris Fields]

What version of Bioperl are you using?  Mark Jensen did some  
refactoring of this code after the 1.6.0 release that should appear in  
1.6.1; I'll be working on the first alpha for that release starting  
Friday.

chris

On Aug 26, 2009, at 9:59 AM, Emmanuel Quevillon wrote:

> Hi,
>
> I am playing with Bio::Restriction::* objects and find it very useful.
> Especially I am filtering output for blunt and cohesive enzymes.
> However, there's an exception thrown when I use 'cutters' method
> from B::R::Analysis :
>
> ------------- EXCEPTION: Bio::Root::Exception -------------
> MSG: Bad end parameter (34). End must be less than the total length
> of sequence (total=7)
> STACK: Error::throw
> STACK: Bio::Root::Root::throw
> /usr/local/share/perl/5.10.0/Bio/Root/Root.pm:357
> STACK: Bio::PrimarySeq::subseq
> /usr/local/share/perl/5.10.0/Bio/PrimarySeq.pm:388
> STACK: Bio::Restriction::Analysis::_enzyme_sites
> /usr/local/share/perl/5.10.0/Bio/Restriction/Analysis.pm:891
> STACK: Bio::Restriction::Analysis::_cuts
> /usr/local/share/perl/5.10.0/Bio/Restriction/Analysis.pm:788
> STACK: Bio::Restriction::Analysis::cut
> /usr/local/share/perl/5.10.0/Bio/Restriction/Analysis.pm:366
> STACK: Bio::Restriction::Analysis::cutters
> /usr/local/share/perl/5.10.0/Bio/Restriction/Analysis.pm:681
> STACK: Bio::Restriction::Analysis::blunt::_load_simple_digestion
> lib/Bio/Restriction/Analysis/blunt.pm:86
> STACK: Bio::Restriction::Analysis::blunt::cut_in_frames
> lib/Bio/Restriction/Analysis/blunt.pm:65
> STACK: ./check_phase.pl:213
> -----------------------------------------------------------
>
> The problem with this enzyme is that the cut site is over the enzyme
> recognition site (from Rebase withrefm.907):
>
> <1>BceSI
> <2>
> <3>SSAAGCG(27/27)
> <4>
> <5>Bacillus cereus
> <6>ATCC 10987
> <7>
> <8>Hegna, I.K., Bratland, H., Kolsto, A., (2001) FEMS Microbiol.
> Lett., vol. 202, pp. 189-193.
> Xu, S.-Y., Unpublished observations.
>
>
> For this enzyme, here are the values stored into B::R::Enzyme object
> ($e):
>
> $e->site => SSAAGCGNNNNNNNNNNNNNNNNNNNNNNNNNNN
> $e->cut  => 34
> $e->string => SSAAGCG
> $e->seq->seq => SSAAGCG
>
>
> So my question is, wouldn't be faire to set B::PrimarySeq::seq with
> value of $e->site when such enzyme are seen in the source file.
>
> NOTE from B::R::Analysis::_enzymes_sites (commented):
>
>    # The following should not be an exception, both Type I and Type  
> III
>    # enzymes cut outside of their recognition sequences
>    #if ($site < 0 || $site > length($enz->string)) {
>    #   $self->throw("This is (probably) not your fault.\nGot a cut
> site of $site and a     # sequence of ".$enz->string);
>    # }
>
> And this is exactly the problem I'm facing!
> In _enzymes_sites the code is trying to subseq our sequence to get
> before and after seq as :
>
>       $beforeseq=$enz->seq->subseq(1, $site);
>       $afterseq=$enz->seq->subseq($site+1, $enz->seq->length);
>
> and this throws an error as the cutting site is far over (pos 34)
> the enzyme know recognition site SSAAGCG (length=7).
>
> Has anybody a clue on how to fix/patch it?
>
> Thanks for any reply
>
> Regards
>
> Emmanuel
>
> -- 
> -------------------------
> Emmanuel Quevillon
> Biological Software and Databases Group
> Institut Pasteur
> +33 1 44 38 95 98
> tuco at_ pasteur dot fr
> -------------------------
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