[Bioperl-guts-l] [Bug 2646] New: MSG: Abstract method "Bio::Assembly::Contig::length" is not implemented by package Bio::Assembly::Contig.

bugzilla-daemon at portal.open-bio.org bugzilla-daemon at portal.open-bio.org
Mon Nov 10 07:37:53 EST 2008


http://bugzilla.open-bio.org/show_bug.cgi?id=2646

           Summary: MSG: Abstract method "Bio::Assembly::Contig::length" is
                    not implemented by package Bio::Assembly::Contig.
           Product: BioPerl
           Version: main-trunk
          Platform: PC
        OS/Version: Linux
            Status: NEW
          Severity: normal
          Priority: P2
         Component: Core Components
        AssignedTo: bioperl-guts-l at bioperl.org
        ReportedBy: dan.bolser at gmail.com


My code looks (more or less) like this:

my $parser =
  new Bio::Assembly::IO( -file   => 'my.phrap.ace',
                         -format =>          'ace');

my $ass = $parser->next_assembly();

foreach my $contig ($ass->all_contigs()){
  print $contig->get_consensus_length(), "\n";
}



And the error is ...

------------- EXCEPTION: Bio::Root::NotImplemented -------------
MSG: Abstract method "Bio::Assembly::Contig::length" is not implemented by
package Bio::Assembly::Contig.
This is not your fault - author of Bio::Assembly::Contig should be blamed!

STACK: Error::throw
STACK: Bio::Root::Root::throw /homes/me/perl5/lib/perl5/Bio/Root/Root.pm:357
STACK: Bio::Root::RootI::throw_not_implemented
/homes/me/perl5/lib/perl5/Bio/Root/RootI.pm:680
STACK: Bio::Assembly::Contig::length
/homes/me/perl5/lib/perl5/Bio/Assembly/Contig.pm:1713
STACK: ./test.01.plx:77
----------------------------------------------------------------


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