[Bioc-devel] converting character vector to DNAStringSetList

[Stephanie M. Gogarten]

Thanks, Herve!

To answer Tim's question (though it has become irrelevant after Herve's 
solution): because I'd rather not add VariantAnnotation to my dependency 
tree for only a couple of lines of code.  It also seemed like the sort 
of thing that should be possible with a DNAStringSetList constructor, so 
I'm glad it will be starting tomorrow.

Stephanie

On 4/19/13 12:35 PM, Hervé Pagès wrote:
> Hi Stephanie,
>
> On 04/19/2013 11:55 AM, Stephanie M. Gogarten wrote:
>> Hi all,
>>
>> There is a non-exported function in VariantAnnotation called
>> .toDNAStringSetList that converts a vector of comma-separated character
>> strings to a DNAStringSetList.  I'd like to use this code in a package
>> I'm working on.  Would it make sense to export this from Biostrings?  If
>> not, what is the proper way to attribute code if I borrow a few lines
>> from .toDNAStringSetList?
>
> This should be a 1-liner but the 1-liner fails at the moment because the
> DNAStringSetList() constructor doesn't work on a list:
>
>    > comma_sep_strings <- c("AA,TT", "ACGT", "", "TT,A,,TAG")
>    > DNAStringSetList(strsplit(comma_sep_strings, ",", fixed=TRUE))
>    Error in strsplit(comma_sep_strings, ",") : non-character argument
>
> Of course this should work (and it will work tomorrow after you run
> biocLite()). In the mean time the workaround is to use do.call():
>
>    > do.call(DNAStringSetList, strsplit(comma_sep_strings, ",",
> fixed=TRUE))
>    DNAStringSetList of length 4
>    [[1]] AA TT
>    [[2]] ACGT
>    [[3]]   A DNAStringSet instance of length 0
>    [[4]] TT A  TAG
>
> Cheers,
> H.
>
> PS: Calling strsplit() with 'fixed=TRUE' makes it about 4x faster :-)
>
>>
>> thanks,
>> Stephanie
>>
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>