If this is an option for you: An xml database can handle (very) huge xml
files and let you query nodes very efficiently.
Then, you could query the xml databse from R (using REST) to do your
statistics.
There are some open source xquery/xml databases available.
2012/8/11 Frederic Fournier <frederic.bioi...@gmail.com>
> 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.)
>
> 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@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@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@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
>
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>
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>
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