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

Chris Fields cjfields at uiuc.edu
Sun Apr 9 12:26:38 EDT 2006


Nick,

I believe Brian fixed this in the last few days (after you posted this this
first time).  

Chris

Christopher Fields
Postdoctoral Researcher - Switzer Lab
Dept. of Biochemistry
University of Illinois Urbana-Champaign 

> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
> bounces at lists.open-bio.org] On Behalf Of Staffa, Nick (NIH/NIEHS) [C]
> Sent: Friday, April 07, 2006 1:39 PM
> To: bioperl-l at bioperl.org
> Subject: [Bioperl-l] Bio::Restriction::Enzyme exception due
> toBio::PrimarySeq
> 
> Maybe this message won't have the suspicious header that got it bounced.
> 
> 
> 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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