[Bioperl-l] problems with $enzyme->site(); for enzyme NlaIII or TspRI

[felipe wettstein]

> Fixed in CVS now.
thanks for the answer.

> Small bug in the code for cutsites which occur after the specified site
> as in the ChaI, TaiI, TscI, etc.
>
> This patch should take care of your problem:
>
> [jason@sonogno core]$ cvs diff Bio/Tools/RestrictionEnzyme.pm
> Index: Bio/Tools/RestrictionEnzyme.pm
> ===================================================================
> RCS file:
> /home/repository/bioperl/bioperl-live/Bio/Tools/RestrictionEnzyme.pm,v
> retrieving revision 1.24
> diff -r1.24 RestrictionEnzyme.pm
> 898c898,902
I took the 1.25 from webcvs. since 1.24 it did not work for me (cd  
bioperl-1.0.2, perl Makefile.pl, make, make install). definitefely, it  
works with 1.25. thank you.

it looks as if now the MBI Fermentas enzymes are added too. very nice.

felipe wettstein


> <         return $seq->subseq(1,
> $self->cuts_after).'^'.$seq->subseq($self->cuts_after+1, $seq->length);
> ---
>>       if( $cuts_after >= $seq->length) {
>>           return $seq->seq.'^';
>>       } else {
>>           return $seq->subseq(1,
> $self->cuts_after).'^'.$seq->subseq($self->cuts_after+1, $seq->length);
>>       }
>
>
> On Mon, 28 Oct 2002, felipe wettstein wrote:
>
>> doing $enzyme->site(); for the enzymes NlaIII or TspRI stops my  
>> program
>> with the following error:
>>
>> ------------- EXCEPTION  -------------
>> MSG: in subseq, start [5] has to be greater than end [4]
>> STACK Bio::PrimarySeq::subseq /Library/Perl/Bio/PrimarySeq.pm:336
>> STACK Bio::Tools::RestrictionEnzyme::site
>> /Library/Perl/Bio/Tools/RestrictionEnzyme.pm:510
>> STACK toplevel ./restritest.pl:17
>>
>> --------------------------------------
>>
>> i use perl 5.8, mac os x.
>>
>> the following program fails with 'NlaIII' or 'TspRI', but not when i
>> uncomment the line with 'next if...'. does anybody have an idea whats
>> going wrong? i mean, it is not exxxtreeeemly important to know, but
>> maybe it would help. thanks a lot.
>>
>>
>> felipe wettstein
>>
>> ---------------------------------------------------------------------- 
>> --
>> -------
>>
>>
>> #!/usr/bin/perl -w
>> use Bio::Tools::RestrictionEnzyme;
>> use Bio::PrimarySeq;
>>
>> $enzyme = Bio::Tools::RestrictionEnzyme->new(-name=>'EcoRI');
>> @enz_list=$enzyme->available_list();
>>
>> $i=0;
>> foreach $enzyme (@enz_list) {
>> 	$enz_list[$i] = Bio::Tools::RestrictionEnzyme->new(-name=>$enzyme);
>> 	print "\n";
>> 	print $enz_list[$i]->name();
>> 	print "\t";
>> 	print $enz_list[$i]->string();
>> #	next if ($enz_list[$i]->name()eq 'NlaIII')||($enz_list[$i]->name()eq
>> 'TspRI');
>> 	print "\t";
>> 	print $enz_list[$i]->site();
>> 	$i++;
>> }
>>
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>>
>
> -- 
> Jason Stajich
> Duke University
> jason at cgt.mc.duke.edu
>
>
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