[Bioperl-l] OBOEngine does not have the function parse()

[Hilmar Lapp]

Ah yes, thanks Siddhartha! -hilmar


On Thu, Feb 13, 2014 at 1:27 PM, Siddhartha Basu <sidd.basu at gmail.com>wrote:

> I think you have to use Bio::OntologyIO for input. Something like this
>
> my $parser = Bio::OntologyIO->new(
>                       -format    => "obo",
>                       -file      => 'gene_ontology.1_2.obo');
> my $ont = $parser->next_ontology;
> say $ont->name;
> my @roots = $ont->get_root_terms;
> say $_->name for $ont->get_child_terms($roots[0]);
>
> Hope this helps,
> -siddhartha
>
> On Fri, 31 Jan 2014, Fenglou Mao wrote:
>
> > Dear all.
> >
> > I am tring to run the code below:
> >   use Bio::Ontology::OBOEngine;
> >
> >   my $parser = Bio::Ontology::OBOEngine->new
> >         ( -file => "gene_ontology.1_2.obo" );
> >
> >   my $engine = $parser->parse();
> >
> >
> > I got an error message:
> > Can't locate object method "parse" via package
> "Bio::Ontology::OBOEngine" at ./GO4.pl line 12.
> >
> > I checked the source code, it seems this function "parse" cannot be
> found anywhere.
> > Any idea? My BioPerl version is 1.6.901
> >
> > Fenglou
> > _______________________________________________
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-- 
Hilmar Lapp -:- lappland.io