[Bioperl-l] Bio::OntologyIO choking on current GO

[Hilmar Lapp]

Scott, what do you mean by 'choking'? Does the parser bail out with an  
error, does the machine start trashing, does the process come to a  
standstill due to swapping, or does the machine spit up transistors and  
capacitors through the drive slot?

I just happened to parse (and load into biosql) the latest GO download  
this morning and I had zero problems ... If the VERSION definition  
depicts what the version is then that machine has 0.20104 of Graph.pm.  
The bioperl version is from cvs and newer than 1.4 but older than 1.5;  
dagflat.pm has the following Id tag:
$Id: dagflat.pm,v 1.20 2004/08/13 02:20:37 allenday Exp $

Are you sure you're not just running this on a low-memory box?

	-hilmar


On Monday, February 7, 2005, at 08:31  PM, Scott Cain wrote:

> Hello,
>
> It appears that Bio::OntologyIO is choking on the component.ontology
> file in GO cvs.  I ran this simple script:
>
> #!/usr/bin/perl -w
> use strict;
>
> use Bio::OntologyIO;
>
> my $parser = Bio::OntologyIO->new(-format => "go",
>                                   -file=> 'component.ontology');
>
> while(my $ont = $parser->next_ontology()) {
>       print "read ontology ",$ont->name()," with ",
>             scalar($ont->get_root_terms)," root terms, and ",
>             scalar($ont->get_leaf_terms)," leaf terms\n";
> }
>
> when I run this through the debugger, it chokes inside of Graph.pm:
>
> Graph::__edges_to(/usr/lib/perl5/site_perl/5.8.5/Graph.pm:708):
> 708:        my ($v, $i, $vi, $e, $o) = @_;
>
> This is Graph version 0.55.  This script executes as expected with
> sofa.ontology.  I've never looked at the OntologyIO code, so I'm hoping
> someone will have a simple explanation and/or fix.
>
> Thanks,
> Scott
>
> --  
> ----------------------------------------------------------------------- 
> -
> Scott Cain, Ph. D.                                          
> cain at cshl.org
> GMOD Coordinator (http://www.gmod.org/)                      
> 216-392-3087
> Cold Spring Harbor Laboratory
>
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>
>
-- 
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Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
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