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

[Remo Sanges]

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