[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
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor
>
More information about the Bioconductor
mailing list