[Bioperl-l] Reading a XML sequence (UniParc) into a BioSeq object

Samuel GRANJEAUD - IR/IFR137 granjeau at tagc.univ-mrs.fr
Wed Mar 14 11:39:32 EDT 2007


Chris Fields wrote:
> That's probably the best short-term fix though I'm sure it's quite a 
> bit slower than a direct UniParc XML-to-Bio::Seq via SeqIO.  I am 
> looking into adding a few more XML::SAX-based parsers (INSDSeqXML, 
> GBSeqXML, EMBLXML, etc), so we could add UniProt XML to the list 
> (which I think Uniparc uses, correct?).
I think so, but I am not sure of that since I am a dummy of XML and 
UniParc is using a very small subset of uniprot features. Best thing is 
to have an expert look at

http://www.pir.uniprot.org/support/docs/uniprot.xsd

http://www.pir.uniprot.org/support/docs/xml_news.htm

Adding the listed XML parsers to BioPerl would be nice.

Regards,
--Samuel


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