What would be the fastest way to do this with a DNAString?  Just an
alphabetFrequency?


On Fri, May 9, 2014 at 4:07 PM, Hervé Pagès <hpages@fhcrc.org> wrote:

> Hi Michael,
>
>   library(rtracklayer)
>   library(Biostrings)
>   x <- DNAStringSet("AAA-CCC-GGG-TTT-NNN-KKK")
>
> Then:
>
>   > x
>     A DNAStringSet instance of length 1
>       width seq
>   [1]    23 AAA-CCC-GGG-TTT-NNN-KKK
>
>   > export(x, "x.2bit")
>
>   > import("x.2bit")
>     A DNAStringSet instance of length 1
>       width seq                                               names
>   [1]    23 AAATCCCTGGGTTTTTNNNTTTT                           1
>
> What about having the "export" method for TwoBitFile raise an error
> (or at least issue a warning) instead of silently turning everything
> that is not A, C, G, T, or N into a T?
>
> Thanks,
> H.
>
> --
> Hervé Pagès
>
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N, M1-B514
> P.O. Box 19024
> Seattle, WA 98109-1024
>
> E-mail: hpages@fhcrc.org
> Phone:  (206) 667-5791
> Fax:    (206) 667-1319
>
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