[BioC] Error when splitting an AAStringSet

[Valerie Obenchain]

Hi Nico,

We don't currently have an AAStringSetList. The DNAStringSetList is the 
only XStringSetList object we have.

Is this something you would find very useful, i.e., want to request as a 
new feature?

Valerie

On 01/25/2013 03:09 AM, Nicolas Delhomme wrote:
> Hi BioC!
>
> I've got the following error message when I try to split an AAStringSet:
>
> pep<- readAAStringSet("somefile.pep")
>
> labs<- read.delim("someLabel.txt",stringsAsFactors=FALSE,header=FALSE)
>
> peplist<- split(pep,labs[,3])
> Error in relist(x, f) :
>    don't know how to split or relist a AAStringSet object as a AAAStringSetList object
>
> Here are my sessionInfo. I'm not using the latest R version, but one still compatible with Bioc 2.11, so I don't think it's causing the issue.
>
>> sessionInfo()
> R version 2.15.1 (2012-06-22)
> Platform: x86_64-unknown-linux-gnu (64-bit)
>
> locale:
>   [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
>   [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
>   [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
>   [7] LC_PAPER=C                 LC_NAME=C
>   [9] LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] Biostrings_2.26.2  IRanges_1.16.4     BiocGenerics_0.4.0
>
> loaded via a namespace (and not attached):
> [1] parallel_2.15.1 stats4_2.15.1
>
> Cheers,
>
> Nico
>
> ---------------------------------------------------------------
> Nicolas Delhomme
>
> Genome Biology Computational Support
>
> European Molecular Biology Laboratory
>
> Tel: +49 6221 387 8310
> Email: nicolas.delhomme at embl.de
> Meyerhofstrasse 1 - Postfach 10.2209
> 69102 Heidelberg, Germany
>
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