[Bioperl-l] Homologene parser?

neeti somaiya neetisomaiya at gmail.com
Thu Aug 16 05:30:42 EDT 2007


Hi,

For now I am using the homologene parser available here :-
http://bioinformatics.tgen.org/brunit/software/bioparser/docs/pod_bio_parser_homologene_fileparser_pm.shtml
,
for parsing the homologene.data file. But the README at the ftp site says
HOMOLOGENE.XML has much more data, I am still to see how to parse this one.

~Neeti.


On 8/14/07, Andrew Macgregor <amacgregor at ccg.murdoch.edu.au> wrote:
>
> On 14/08/2007, at 11:21 AM, Chris Fields wrote:
>
> > It looks like Heikki responded and thought a good place for it
> > would be Bio::SeqIO, but it didn't go anywhere I suppose.  I see
> > that a few other posts suggest it could be placed in Bio::Cluster
> > as well which I'm not familiar with.  We could add it in if you
> > were still interested, just need to find a good place for it; might
> > be nice to have a Parse::RecDescent-based parser.
> >
> > chris
> >
>
> Hi Chris,
>
> I was also doing some parsing of UniGene at the time but found
> RecDescent was too slow and went back to regexes. That code found
> it's way into Bio::Cluster. Occasionally I see a message with someone
> looking for a Homologene parser but not very often, so I'm not sure
> it is worth the effort of moving the code into bioperl.
>
> Cheers, Andrew.
>



-- 
-Neeti
Even my blood says, B positive


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