[Bioperl-l] [Bioperl] LocusLink

[Hilmar Lapp]

This is due to a bug that was fixed on the main trunk in May already but not
migrated to the stable branch. I migrated (and corrected) the fix. Either
wait a few hours and update from anonymous cvs, or pull up
Bio/Annotation/OntologyTerm.pm in your favorite editor change the call to
each_synonym to get_synonyms.

The refseq Ids are not ontology terms though, they are dbxrefs. In order to
get at them you need to extract the correct dbxrefs.

    -hilmar

On 10/13/03 6:17 AM, "Zayed  Albertyn" <zayed at sanbi.ac.za> wrote:

> Hi
> 
> I have been trying to use Bio::SeqIO to parse Locuslink format for
> obtaining all RefSeq mRNAs associated with a Locuslink ID.
> 
> I receive the following error message when I use the hash_tree method from
> Bio:Annotation:
> Can't locate object method "each_synonym" via package
> "Bio::Annotation::OntologyTerm" at OntologyTerm.pm line 187,
> <GEN0> line 1.
> The strange thing is that it does support the as_text() method and I can
> pull values this way yet I would like to store and retrieve the values as
> I like in a hash (as described in the Bio:Annotation documentation).
> 
> Is there some reason why I cannot access this "each_synonym" method and
> how would I obtain the RefSeq entries if I could initialize the hash_tree()
> method?
> 
> Thanks
> Zayed
> -----------------------------------------------
> From: Zayed Albertyn
> Electric Genetics PTY Ltd
> Tel: +27 21 959 3645; Mobile: +2782 480 6097
> www.egenetics.com
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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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