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