Re: [Gusdev-gusdev] LoadGoOntology

[Jonathan C. <cra...@pc...>]

Hi Chetna-

Chetna D. Warade wrote:
> I am trying to:
> ga GUS::GOPredict::Plugin::LoadGoOntology --usage and I am getting @INC 
> error whereas when I run:
> ga GUS::GOPredict::Plugin::LoadGoAssoc --usage <--- runs fine!
> 
> Following is the error:
> 
> [chetna@mango Plugin]$ ga GUS::GOPredict::Plugin::LoadGoOntology 
> --usage
> Reading properties from /home/gus_home/config/GUS-PluginMgr.prop
> 
> ERROR: Can't locate CBIL/Bio/GeneOntologyParser/Parser.pm in @INC (@INC 

I don't know the answer to this, but Dave Barkan has been working actively
on the GO-related plugins, and should be able to shed some light on the
problem.

> Both LoadGoAssoc and LoadGoOntology need 
> CBIL/Bio/GeneOntologyParser/Parser.pm but I am wondering why would it 
> fail for one and run for other.

Are you sure about that?  I just checked what's currently in CVS and
while LoadGoOntology.pm does "use" CBIL::Bio::GeneOntologyParser::Parser,
it looks like LoadGoAssoc uses CBIL::Bio::GeneAssocParser::Parser instead,
which would account for the difference in behavior you're seeing.  Perhaps
you have to download a new version of the CBIL tar file (and perhaps we
first need to generate one!)

Jonathan

-- 
Jonathan Crabtree
Senior Programmer Analyst
CBIL, Center for Bioinformatics
University of Pennsylvania, Philadelphia, PA