6 Oct 2012 00:31
issue with Views on PairwiseAlignmentsSingleSubject?
Janet Young <jayoung@...>
2012-10-05 22:31:52 GMT
2012-10-05 22:31:52 GMT
Hi there, I've been using Biostrings' pairwiseAlignment for various things. I just saw the Views feature described in help("PairwiseAlignments-class") and thought I'd give it a try, but it's not behaving as I'd expect in cases where my subject sequence is one sequence selected from a DNAStringSet (rather than starting with a DNAString). I think I found a bug (?) although I could also be misunderstanding what Views is supposed to do. I updated to the new Bioc devel and new R today, but had the same issue before updating. I think the code chunk below will explain - does it make sense? thanks very much, Janet library(Biostrings) ## example seqs (taken from ?pairwiseAlignment) s1 <- DNAString("ACTTCACCAGCTCCCTGGCGGTAAGTTGATCAAAGGAAACGCAAAGTTTTCAAG") s2 <- DNAString("GTTTCACTACTTCCTTTCGGGTAAGTAAATATATAAATATATAAAAATATAATTTTCATC") ### make some sequence sets s1a <- DNAStringSet(c(as.character(s1),as.character(s1))) s2a <- DNAStringSet(c(as.character(s2),as.character(s2))) ### align myAln <- pairwiseAlignment ( s1a, s2a) ### I think the next line of code should give me a Views on s1a, but instead it gives me Views on all the seqs of s1a concatenated together Views(myAln) ##### and, an aside, it would seem intuitive to me that the code below should work to make a stringset of two sequences, but instead it concetenates them to one sequence s1b <- DNAStringSet(c(s1,s1)) ######### sessionInfo() R Under development (unstable) (2012-10-03 r60868) Platform: x86_64-unknown-linux-gnu (64-bit) locale:  LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C  LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8  LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8  LC_PAPER=C LC_NAME=C  LC_ADDRESS=C LC_TELEPHONE=C  LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages:  stats graphics grDevices utils datasets methods base other attached packages:  Biostrings_2.27.1 IRanges_1.17.0 BiocGenerics_0.5.0 loaded via a namespace (and not attached):  parallel_2.16.0 stats4_2.16.0 _______________________________________________ Bioconductor mailing list Bioconductor@... https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor