[Biopython-dev] Re: Ensembl<->Biocorba bridge - sequence gets working.

[Thomas Sicheritz-Ponten]

Ewan Birney <birney at ebi.ac.uk> writes:

> > Ewan Birney <birney at ebi.ac.uk> writes:
> > 
> > > > I think I have everything, but I still get following error: 
> > > > Can't locate object method "new" via package "Bio::EnsEMBL::CORBA::Base" at
> > > > /home/thomas/cbs/python/biopython/biopython-corba/ensembl-corba-server/modules/Bio/EnsEMBL/CORBA/Base.pm
> > > > line 54.
> > > 
> > > Aha. This is because I wrote the ensembl-corba-server too quickly without
> > > a Makefile.PL
> > > 
> > > You need to point the PERL5LIB environment variable to
> > > ensembl-corba-server/modules and/or use the -I argument to perl to put the
> > > corba-server objects in your path. 
> > 
> > I had tried that before, but it won't work. 
> > 
> > The problem occurs in:
> > @ISA = qw(Bio::Root::RootI);
> > 
> > sub new {
> >     my ($class, @args) = @_;
> >         my $self = $class->SUPER::new(@args);   <=== 
> > 
> > Whats SUPER is that a general perl OO qualifier or something bioperl
> > special ?
> 
> It is not a bioperl special but (hmmmm... Ewan thinks). I think I know why
> this is happening. Do the following: Either
> 
> (a) check out the main trunk of bioperl (bioperl-live) from the cvs
> server. This should work.
> 
> (b) replace the above SUPER::new lines with
> 
> $self = {};
> bless $self,$class;
> 
> 
> 
> This was an expected 0.6.2<->Main trunk bioperl difference.

Nope - bioperl-live didn't solve the problem, and I don't feel like
solution b) is the right way to go ...  
I wait until the admnistrators installed perls ORBit at CBS so I can test
the script on our IRIX'es.

In the meantime, I use the logs of mysql to see what SQL queries perl
executes for a virtualcontig. I am going to implement these in python.


waiting-for-root-to-install-things'ly y'rs
-thomas
-- 
Sicheritz-Ponten Thomas, Ph.D  CBS, Department of Biotechnology
thomas at biopython.org           The Technical University of Denmark
CBS:  +45 45 252489            Building 208, DK-2800 Lyngby
Fax   +45 45 931585            http://www.cbs.dtu.dk/thomas

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