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

Staffa, Nick (NIH/NIEHS) [C] staffa at niehs.nih.gov
Fri Apr 7 14:38:52 EDT 2006


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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