[BiO BB] Parsing GenBank XML?

[Mike Marchywka]

You are probably looking for a SAX parser,

http://en.wikipedia.org/wiki/Simple_API_for_XML

I've got my own hard coded c++ that I use for my string processing rules source
code, FDA AERA SGML parsing, SOAP utilities, etc, that will output all the fields
in a simple format of "label value" per line, but there are SAX libraries in just about
every language. Personally I finally gave up on PERL as speed, at least under cygwin,
was unpredictable and degraded quickly when you ran out of physical memory.



Mike Marchywka
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> Date: Thu, 4 Sep 2008 15:29:20 +0100
> From: dan.bolser at gmail.com
> To: BBB at bioinformatics.org
> Subject: [BiO BB] Parsing GenBank XML?
>
> Hi,
>
> Dumb / noob question I am sure but... I am parsing the results of a
> GenBank query obtained using esearch / efetch:
>
> http://www.ncbi.nlm.nih.gov/entrez/query/static/eutils_help.html
>
>
> The XML looks like this...
>
> http://pastebin.com/f3ef02d85
>
> the only difference being that the real document has (possibly)
> millions of 's.
>
> I decided to try to use XSLT to turn the XML into tabular output. This
> is working fine on a sample of the data. I get one row of data per
> Seq-entry, which is exactly what I want. For reference, my XSLT style
> sheet is here:
>
> http://pastebin.com/f3a512411
>
>
> I am not sure how efficient that XSLT is (I never used XSLT before),
> however, that isn't the real problem. The real problem is that the
> XSLT parsers that I have tried (xsltproc and XML::XSLT) both need to
> slurp up the whole XML document before they output any rows of text.
> This is way too memory intensive, especially as the data my well grow.
>
> I figure that I can't be the first person to parse GenBank, so I was
> wondering what is 'out there' in terms of community consensus on how
> to do it...
>
> I had a quick go with XML::Simple, but I rapidly get lost in the
> resulting data structure, which I find leads to very messy (hard to
> read / write) and generally unmaintainable code.
>
> Are the various 'BioX' modules any good? i.e. do they simplify the
> resulting data to make it easy to get tab delimited dumps of the data?
>
>
> Cheers,
>
> Dan.
>
>
> --
> http://network.nature.com/profile/dan
>
> _______________________________________________
> BBB mailing list
> BBB at bioinformatics.org
> http://www.bioinformatics.org/mailman/listinfo/bbb

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