[BioC] load local genbank file

[Hu, Bin]

Thanks Vincent! I came across the ape package but I didn't know the debug() trick to check the source code…

Bin
On Aug 21, 2012, at 12:48 AM, Vincent Carey wrote:

> 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 at 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 Internet
> 
> Description
> 
> 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)
> 
> Arguments
> 
> access.nb	a vector of mode character giving the accession numbers.
> seq.names	the names to give to each sequence; by default the accession numbers are used.
> species.names	a logical indicating whether to attribute the species names to the returned object.
> as.character	a 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 at 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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