I don't see a sig_peptide field.  You should have a look at

http://www.omegahat.org/RSXML/shortIntro.html

and references therein.

It has been a long time since I did anything with XML per se. We did a
certain amount of exposition in Chapter 8
of the 2005 Springer monograph.  Since then more XPath support has come in
and many new ideas help distance users from
details of XML processing.  To illustrate a bit with your example, I trapped
the actual document reference

zz = xmlInternalTreeParse("
http://www.ncbi.nih.gov/entrez/eutils/efetch.fcgi?tool=bioconductor&rettype=xml&retmode=text&db=Nucleotide&id=NM_000610
")

and then performed an XPath query

> getNodeSet(zz, "//Seq-interval_from")
[[1]]
<Seq-interval_from>3244</Seq-interval_from>

[[2]]
<Seq-interval_from>3328</Seq-interval_from>

[[3]]
<Seq-interval_from>5695</Seq-interval_from>

and so on.  I don't recall how to do a relatively simple task like
"enumerate all tags in use in a document" but it can be done with the XML
package tools.  I think it will be more effective to isolate the use case
and see how to use eutils to solve it fairly directly as opposed to wading
through XML, but perhaps wading is inevitable.


On Wed, Sep 21, 2011 at 12:29 PM, Andrew Yee <yee@post.harvard.edu> wrote:

> Hi, I'm looking for some guidance in terms of parsing the XML output
> from a genbank query.
>
> result <- genbank('NM_000610', disp='data', type='uid')
>
> I'm trying to figure out how to use the XML package in order to parse
> out the "sig_peptide" field from the XML output from the genbank
> query.
>
> Any pointers or suggestions would be appreciated, as I'm new to XML.
>
> Thanks,
> Andrew
>
>
>
> > sessionInfo()
> R version 2.13.0 (2011-04-13)
> Platform: x86_64-unknown-linux-gnu (64-bit)
>
> locale:
>  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
>  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
>  [5] LC_MONETARY=C              LC_MESSAGES=en_US.UTF-8
>  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
>  [9] LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] XML_3.2-0             annotate_1.29.4       AnnotationDbi_1.13.21
> [4] Biobase_2.11.10
>
> loaded via a namespace (and not attached):
> [1] DBI_0.2-5     RSQLite_0.9-4 tools_2.13.0  xtable_1.5-6
>
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