I hit return too soon.  If you install ape and look at the source for
read.GenBank, you can see how the data are acquired and processed.  For
example, set

debug(read.GenBank)

and then run the example.  You can step through to see where the file is
simply scanned and then chopped up.  It will be simple to make a custom
version of this function that reads from a file instead of the network.

On Tue, Aug 21, 2012 at 2:41 AM, Vincent Carey
<stvjc@channing.harvard.edu>wrote:

> i googled on "read genbank with R".  drilling on one of the responses, i
> found that the "ape" package addresses this issue; this is available on
> CRAN.
>
> read.GenBank {ape}R Documentation Read DNA Sequences from GenBank via
> InternetDescription
>
> This function connects to the GenBank database, and reads nucleotide
> sequences using accession numbers given as arguments.
> Usage
>
> read.GenBank(access.nb, seq.names = access.nb,
>              species.names = TRUE, as.character = FALSE)
>
> Argumentsaccess.nb a vector of mode character giving the accession
> numbers.seq.namesthe names to give to each sequence; by default the
> accession numbers are used. species.namesa logical indicating whether to
> attribute the species names to the returned object.as.charactera logical
> controlling whether to return the sequences as an object of class "DNAbin" (the
> default). Details
>
> The function uses the site http://www.ncbi.nlm.nih.gov/ from where the
> sequences are downloaded.
>
>
> On Tue, Aug 21, 2012 at 12:54 AM, Hu, Bin <binhu@lanl.gov> wrote:
>
>> Hello,
>>
>> Can anyone point me some examples of loading a local genbank file and
>> query its features? Thanks.
>>
>> I just started learning Bioconductor and trying to get myself familiar
>> with its packages. I googled but only found ways to download genbank from
>> Internet.
>>
>> Bin
>> _______________________________________________
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>> Search the archives:
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>>
>
>

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