[Bioperl-l] Restriction::Analysis strange error - please help

[Garrett Sorensen]

Thanks so much Remo, the modification to Analysis.pm worked
beautifully.  I will submit the bug report as you suggested.

Many thanks,
Garrett


On Wed, 26 Jan 2005 19:05:52 +0100, Remo Sanges <sanges at biogem.it> wrote:
> 
> On Jan 26, 2005, at 3:57 PM, Garrett Sorensen wrote:
> 
> > Thanks Remo..   To test this module that is the only code I'm using
> > right now...  I'm no longer grabbing a subsequence so it can't be
> > calculation error.  To test all I'm trying to do is read in sequences
> > from a fasta file and digest them.  It runs fine for a few hundred
> > sequences generating fragments as it should, then out of nowhere it
> > will run into the same error, but with different coordinates.
> >
> > Possibly this module isn't working properly for me?
> >
> >  ------------- EXCEPTION  -------------
> >  MSG: Bad start,end parameters. Start [2002] has to be less than end
> >  [2001]
> > STACK Bio::PrimarySeq::subseq
> > /home/garrett/Perl/lib/perl5/site_perl/5.8.5/Bio/PrimarySeq.pm:362
> > STACK Bio::Seq::subseq
> >  /home/garrett/Perl/lib/perl5/site_perl/5.8.5/Bio/Seq.pm:636
> > STACK Bio::Restriction::Analysis::fragment_maps
> >  /home/garrett/Perl/lib/perl5/site_perl/5.8.5/Bio/Restriction/
> >  Analysis.pm:552
> >  STACK toplevel Restriction_analyser_multi_CpG_a.pl:182
> 
> OK,
> 
> it seems to be a bug, you should submit it to
> http://bugzilla.bioperl.org/enter_bug.cgi?product=Bioperl
> 
> Basically it happens when you have a site for a blunt-end cutter
> at the end of your sequence.
> 
> I think you are not interested in that site because
> is a cut at the end of a non-circular sequence that
> don' t produce fragments....
> 
> If so you can simply change line 552 in your Analysis.pm
> module from this:
> 
> $seq{$start}=$self->{'_seq'}->subseq($start, $stop);
> 
> to this:
> 
> $seq{$start}=$self->{'_seq'}->subseq($start, $stop) unless $start >
> $stop;
> 
> HTH
> 
> Remo
> 
>