[Bioperl-l] Possible parsing bug for Bio::Restriction::IO::withrefm?

[Mark A. Jensen]

Hi Emanuel- I would not be surprised if there were a problem here;
I would say if your patch passes tests and also solves the issue you
raise, make the patch and add a test for this particular situation, if you
have time. 
thanks! MAJ
----- Original Message ----- 
From: "Emmanuel Quevillon" <tuco at pasteur.fr>
To: "BioPerl List" <bioperl-l at lists.open-bio.org>
Sent: Monday, February 22, 2010 10:39 AM
Subject: [Bioperl-l] Possible parsing bug for Bio::Restriction::IO::withrefm?


> Hi,
> 
> I am just playing with Bio::Restriction::* modules and found a
> possible bug in parsing the site part of the enzyme definition in
> Rebase file.
> 
> It looks like it does not take into account enzyme cutting such site :
> <3>CCTCAGC(-5/-2)
> <3>CCGCTC(-3/-3)
> <3>CCGC(-3/-1)
> <3>CACGTC(-3/-3)
> <3>GAATGC(1/-1)
> <3>GAATGC(1/-1)
> <3>GAATGC(1/-1)
> 
> Is it a normal behaviour where as parsing is supposed to support
> kind of stuff (B::R::IO::withrefm line 143):
> 
> 
> my ($precut, $recog, $postcut) = ( $site =~
> m/^(?:\((\w+\/\w+)\))?([\w^]+)(?:\((\w+\/\w+)\))?/ );
> 
> For example, this regex is incapable of determining the overhang of
> BmgBI which is defined as :
> 
> <1>BmgBI
> <2>BtrI,AjiI
> <3>CACGTC(-3/-3)
> <4>?(5)
> <5>Bacillus thermoglucosidasius
> <6>NEB 1353
> <7>N
> 
> Shouldn't it be a blunt enzyme?
> 
> The overhang for this enzyme is returned as 'unknown' and cut and
> complementary cut are undef.
> 
> I propose to change the regex to :
> 
> m/^(?:\((-?\w+\/-?\w+)\))?([\w^]+)(?:\((-?\w+\/-?\w+)\))?/ )
> 
> unless I making a terrible mistake?
> 
> Thanks in advance
> 
> Regards
> 
> -- 
> -------------------------
> Emmanuel Quevillon
> Biological Software and Databases Group
> Institut Pasteur
> +33 1 44 38 95 98
> tuco at_ pasteur dot fr
> -------------------------
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