[R] Parsing large XML documents in R - how to optimize the speed?

[Martin Morgan]

On 08/10/2012 03:46 PM, Frederic Fournier wrote:
> Hello everyone,
>
> I would like to parse very large xml files from MS/MS experiments and
> create R objects from their content. (By very large, I mean going up to
> 5-10Gb, although I am using a 'small' 40M file to test my code.)

I'm not 100% sure of it's relevance, but

   http://bioconductor.org/packages/2.10/bioc/html/MSnbase.html

There is a vignette here, for instance

 
http://bioconductor.org/packages/2.10/bioc/vignettes/MSnbase/inst/doc/MSnbase-io.pdf

If this is useful, then further questions might be directed to the 
Bioconductor mailing list.

   http://bioconductor.org/help/mailing-list/

Martin

>
> My first attempt at parsing the 40M file, using the XML package, took more
> than 2200 seconds and left me quite disappointed.
> I managed to cut that down to around 40 seconds by:
>      -using the 'useInternalNodes' option of the XML package when parsing
> the xml tree;
>      -vectorizing the parsing (i.e., replacing loops like "for(node in
> group.of.nodes) {...}" by "sapply(group.of.node, function(node){...}")
> I gained another 5 seconds by making small changes to the functions used
> (like replacing 'getNodeset' by 'xmlElementsByTagName' when I don't need to
> navigate to the children nodes).
> Now I am blocked at around 35 seconds and I would still like to cut this
> time by a 5x, but I have no clue what to do to achieve this gain. I'll try
> to expose as briefly as possible the relevant structure of the xml file I
> am parsing, the structure of the R object I want to create, and the type of
> functions I am using to do it. I hope that one of you will be able to point
> me towards a better and quicker way of doing the parsing!
>
>
> Here is the (simplified) structure of the relevant nodes of the xml file:
>
> <model> (many many nodes)
>    <protein> (a couple of proteins per model node)
>      <peptide> (1 per protein node)
>        <domain> (1 or more per peptide node)
>          <aa> (0 or more per domain node)
>          </aa>
>        </domain>
>      </peptide>
>    </protein>
> </model>
>
> Here is the basic structure of the R object that I want to create:
>
> 'result' object that contains:
>    -various attributes
>    -a list of 'protein' objects, each of which containing:
>        -various attributes
>        -a list of 'peptide' objects, each of which containing:
>          -various attributes
>          -a list of 'aa' objects, each of which consisting of a couple of
> attributes.
>
> Here is the basic structure of the code:
>
> xml.doc <- xmlTreeParse("file", getDTD=FALSE, useInternalNodes=TRUE)
> result <- new('S4_result_class')
> result at proteins <- xpathApply(xml.doc, "//model/protein",
> function(protein.node) {
>    protein <- new('S4_protein_class')
>    ## fill in a couple of attributes of the protein object using xmlValue
> and xmlAttrs(protein.node)
>    protein at peptides <- xpathApply(protein.node, "./peptide",
> function(peptide.node) {
>      peptide <- new('S4_peptide_class')
>      ## fill in a couple of attributes of the peptide object using xmlValue
> and xmlAttrs(peptide.node)
>      peptide at aas <- sapply(xmlElementsByTagName(peptide.node, name="aa"),
> function(aa.node) {
>        aa <- new('S4_aa_class')
>        ## fill in a couple of attributes of the 'aa' object using xmlValue
> and xmlAttrs(aa.node)
>      })
>    })
> })
> free(xml.doc)
>
>
> Does anyone know a better and quicker way of doing this?
>
> Sorry for the very long message and thank you very much for your time and
> help!
>
> Frederic
>
> 	[[alternative HTML version deleted]]
>
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