[BioC] Error when splitting an AAStringSet

[Nicolas Delhomme]

Thanks!

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
---------------------------------------------------------------





On Jan 26, 2013, at 2:02 AM, Hervé Pagès wrote:

> 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
>>> 
>>> _______________________________________________
>>> Bioconductor mailing list
>>> Bioconductor at r-project.org
>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>>> Search the archives:
>>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>> 
>> _______________________________________________
>> Bioconductor mailing list
>> Bioconductor at r-project.org
>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>> Search the archives:
>> http://news.gmane.org/gmane.science.biology.informatics.conductor
> 
> -- 
> 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 at fhcrc.org
> Phone:  (206) 667-5791
> Fax:    (206) 667-1319