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

[Jason Stajich]

I believe I fixed the problems interacting with Graph 0.5x before the  
1.5.0 release but someone else is going to have to deal with the fact  
that we're using a legacy API for Graph now.

Scott - do the tests pass for you?

-jason
--
Jason Stajich
jason.stajich at duke.edu
http://www.duke.edu/~jes12/

On Feb 8, 2005, at 2:23 AM, Hilmar Lapp wrote:

> 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
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at portal.open-bio.org
>> http://portal.open-bio.org/mailman/listinfo/bioperl-l
>>
>>
> -- 
> -------------------------------------------------------------
> Hilmar Lapp                            email: lapp at gnf.org
> GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
> -------------------------------------------------------------
>
>
> _______________________________________________
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>
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