[Biopython-dev] [Bug 2475] BioSQL.Loader should reuse existing taxon entries in lineage

[bugzilla-daemon at portal.open-bio.org]

http://bugzilla.open-bio.org/show_bug.cgi?id=2475





------- Comment #12 from mdehoon at ims.u-tokyo.ac.jp  2008-04-02 07:52 EST -------
Peter wrote:
> For the organisation of the code, what I had in mind was a general purpose XML
> parser in Bio.Entrez.Taxonomy (with nothing to do with BioSQL), which would be
> called from an updated BioSQL.Loader to parse a handle to the XML data fetched
> using Bio.Entrez.efetch().

That is what I have in mind also.

Eric wrote:
> Well, I always use DOM as I find it easier whereas SAX seems cumbersome.
> I can try to convert if you want...

I can understand that for your own work, you prefer to use DOM to just pick up
the tags you are interested in. For a Biopython, though, we should have a more
general solution that is useful to other users and in other situations also.
Which is why I was thinking of a parser in Bio.Entrez that parses all of the
XML returned from the Taxonomy database.

If you're interested in writing a full parser for Taxonomy XML, maybe the
parser for EInfo that is currently in CVS may be useful as an example. For
ESearch, I already wrote a SAX parser; I just need to upload it to CVS.


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