[Bioperl-l] Bio::Ontology help solicited

Hilmar Lapp hlapp at gmx.net
Thu Jun 19 10:07:39 EDT 2008


I think you want to use -identifier rather than -name if you are  
querying by an identifier.

Let us know if that doesn't work either.

	-hilmar

On Jun 19, 2008, at 9:42 AM, Govind Chandra wrote:

> Hi,
>
> In the code snippet below it seems I get the Bio::Ontology::Ontology
> object $ontology but $ontology->find_terms is failing. It will help
> greatly if someone points out what is wrong with this code and  
> suggest a
> correction. That the obo file is being read is obvious from the time  
> it
> takes from invocation to output.
>
> I wrote another version of this script which read the "go" format  
> and it
> works fine. I cannot use the go format because it is deprecated and  
> not
> frequently updated. Even if I am willing to use the go format, the
> process.ontology file (from geneontology.org) has an error in it which
> causes Bio::OntologyIO->next_ontology() to fail. It will be best if I
> could make the obo format work for me.
>
> Cheers
>
> Govind
>
> ### code begins ###
>
> use strict;
> use Bio::OntologyIO;
>
> my $file='gene_ontology.1_2.obo';
> my $parser = Bio::OntologyIO->new(
>  -format => "obo",
>  -file => $file
>  );
> my $ontology = $parser->next_ontology();
> print(ref($ontology), "\n");
> my ($term)=$ontology->find_terms(-name => "GO:0000072");
> print($term->definition(), "\n");
> print("$term\n");
> print(ref($term),"\n");
>
> ### code ends ###
>
> ### output begins ###
> Bio::Ontology::Ontology
>
>
> Can't call method "definition" on an undefined value at
> ontology_check.pl line 26, <GEN0> line 288014.
> ### output ends ###
>
>
> Other Possibly relevant information:
> ------------------------------------
>
> Perl is: v5.8.8 built for x86_64-linux-thread-multi
>
> BioPerl is: bioperl-1.5.2_102
>
> Output of uname -a: Linux n61347 2.6.18-92.1.1.el5 #1 SMP Thu May 22
> 09:01:47 EDT 2008 x86_64 x86_64 x86_64 GNU/Linux
>
> Contents of /etc/redhat-release: Red Hat Enterprise Linux Server  
> release
> 5.2 (Tikanga)
>
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

-- 
===========================================================
: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
===========================================================





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