2008/9/4 Mike Marchywka <[EMAIL PROTECTED]> > > > You are probably looking for a SAX parser, > > http://en.wikipedia.org/wiki/Simple_API_for_XML
Hi Mike, Thanks for the link. The relevant lines seems to be: "Additionally, some kinds of XML processing simply require having access to the entire document. XSLT and XPath, for example, need to be able to access any node at any time in the parsed XML tree. While a SAX parser could be used to construct such a tree, the DOM already does so by design." So it looks like I can't combine SAX with XSLT unless I somehow trigger an XSLT parse of one 'chunk' of XML per SAX 'new-record' event... I'll try! > 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 > 586 Saint James Walk > Marietta GA 30067-7165 > 415-264-8477 (w)<- use this > 404-788-1216 (C)<- leave message > 989-348-4796 (P)<- emergency only > [EMAIL PROTECTED] > Note: If I am asking for free stuff, I normally use for hobby/non-profit > information but may use in investment forums, public and private. > Please indicate any concerns if applicable. > Note: hotmail is getting cumbersom, try also [EMAIL PROTECTED] > > > > > Date: Thu, 4 Sep 2008 15:29:20 +0100 > > From: [EMAIL PROTECTED] > > To: [email protected] > > 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 > > [email protected] > > http://www.bioinformatics.org/mailman/listinfo/bbb > > _________________________________________________________________ > Stay up to date on your PC, the Web, and your mobile phone with Windows Live. > http://clk.atdmt.com/MRT/go/msnnkwxp1020093185mrt/direct/01/ > _______________________________________________ > BBB mailing list > [email protected] > http://www.bioinformatics.org/mailman/listinfo/bbb -- http://network.nature.com/profile/dan _______________________________________________ BBB mailing list [email protected] http://www.bioinformatics.org/mailman/listinfo/bbb
