[BioC] Error when splitting an AAStringSet

[Hervé Pagès]

Hi Nico, Val,

Sorry Val for introducing some confusion when we discussed this offline
(I should have checked before), but we actually do have the
AAStringSetList class (in addition to BStringSetList, DNAStringSetList,
and RNAStringSetList). Which is good news.

The problem reported by Nico was caused by a typo in the spelling of
the class that split() was trying to stored the result into. Needed
to be AAStringSetList, not AAAStringSetList.

This is fixed in Biostrings release (2.26.3) and devel (2.27.10):

   > aa <- AAStringSet(c("AVVACQIL", "*", "KMFAWY", "NRZXXUBDP", "FFSMAL"))
   > split(aa, c("c", "a", "b", "b", "a"))
   AAStringSetList of length 3
   [["a"]] * FFSMAL
   [["b"]] KMFAWY NRZXXUBDP
   [["c"]] AVVACQIL

Cheers,
H.


On 01/25/2013 01:23 PM, Valerie Obenchain wrote:
> 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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>
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-- 
Hervé Pagès

Program in Computational Biology
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