[BioC] Help with genbank

Vincent Carey 525-2265 stvjc at channing.harvard.edu
Thu Mar 6 14:51:35 MET 2003

> Hi all,
> I would like to extract the sequence information corresponding to an
> accession number.  I use the function in annotate
> x <- genbank("AK008608")

the short answer is to look at the XML library by Duncan
and in particular to have a look at xmlTreeParse or
xmlEventParse.  if you know what fields you want
to retain and will do this repetitively, we can
consider adding a function that saves those fields
to the annotate package to work in concert with the
genbank function.

writing handlers for the xml*Parse functions is
a little unintuitive at first but ultimately is
not too hard.

> to extract the XML file and hope someone can point me to some functions
> (or directions) to further extract the sequence info from
> x$doc$childern.
> Thanks you.
> Jean
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>  Jean Yee Hwa Yang			 jean at biostat.ucsf.edu
>  Division of Biostatistics,		   Tel: (415) 476-3368
>  University of California,		   Fax: (415) 476-6014
>  500 Parnassus Avenue, MU 420-W,  San Francisco, CA 94143-0560
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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