[Bioperl-l] Bio::Restriction::Enzyme exception due to Bio::PrimarySeq

Brian Osborne osborne1 at optonline.net
Fri Apr 7 15:26:43 EDT 2006


Nick,

Minor bug in Bio::DB::Fasta, now fixed. Either install the latest BioPerl or
copy the latest Bio/DB/Fasta.pm from CVS.

Brian O.


On 4/7/06 11:44 AM, "Staffa, Nick (NIH/NIEHS) [C]" <staffa at niehs.nih.gov>
wrote:

> Well!
> What to do when hit with this sort of message?
> I am not working with any circular sequences.
> 
> line 46 is
> my @frags=$ra->fragments($enz);
> 
> 
> ------------- EXCEPTION  -------------
> MSG: Abstract method "Bio::PrimarySeqI::is_circular" is not implemented by
> package Bio::PrimarySeq::Fasta.
> This is not your fault - author of Bio::PrimarySeq::Fasta should be blamed!
> 
> STACK Bio::Root::RootI::throw_not_implemented
> /usr/lib/perl5/site_perl/5.8.5/Bio/Root/RootI.pm:523
> STACK Bio::PrimarySeqI::is_circular
> /usr/lib/perl5/site_perl/5.8.5/Bio/PrimarySeqI.pm:671
> STACK Bio::Restriction::Analysis::_cuts
> /usr/lib/perl5/site_perl/5.8.5/Bio/Restriction/Analysis.pm:807
> STACK Bio::Restriction::Analysis::cut
> /usr/lib/perl5/site_perl/5.8.5/Bio/Restriction/Analysis.pm:370
> STACK Bio::Restriction::Analysis::fragments
> /usr/lib/perl5/site_perl/5.8.5/Bio/Restriction/Analysis.pm:443
> STACK toplevel TestNew.pl:46
> 
> --------------------------------------
>  <<TestNew.pl>> 
> 
> 
> Nick Staffa
> Telephone: 919-316-4569  (NIEHS: 6-4569)
> Scientific Computing Support Group
> NIEHS Information Technology Support Services Contract
> (Science Task Monitor: Jack L. Field( field1 at niehs.nih.gov )
> National Institute of Environmental Health Sciences
> National Institutes of Health
> Research Triangle Park, North Carolina
> 
> 
> 
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