[Bioperl-l] loading yeast data failing...

[Marc Logghe]

Hi Angshu,
Allow me to make a remark before you run into more (coding and other)
troubles.

> > > I just have no clue about it. After that I think I've to 
> rebuild the 
> > > package. Am I right?
> > >
> > > Here is the accessor.pm:
> > >
> > > use strict;
> > > use vars qw(@ISA);
> > >  use lib '/home/akar/local/perl/';
> > > use Bio::Seq::BaseSeqProcessor;
> > > use Bio::SeqFeature::Generic;
> > >
> > > @ISA = qw(Bio::Seq::BaseSeqProcessor);
> > >
> > >  sub process_seq
> > > {
> > >   my ($self, $seq) = @_;
> > >    $seq->accession_number($seq->display_id);
> > >   return ($seq);
> > >  }
> > >
> > > > > I run:
> > > > >
> > > > > ./load_seqdatabase.pl --dbname=USBA --dbuser=postgres
> > --format=fasta
> > > > > --driver=Pg --pipeline="SeqProcessor::Accession" 
> > > > > yeast_nrpep.fasta

You add SeqProcessor::Accession as the pipeline argument. This means
that your package should be named 'Accession.pm' and not 'accessor.pm'.
Also, the package should reside in the directory
'/home/akar/local/perl/SeqProcessor'.
HTH and good luck,
Marc