I am having trouble creating long (~1000+ characters) DNAStrings. Specifically, I seem to get an error when R has to go to a new line in the command window when copy/pasting the sequence from an R script (with no breaks). I recently upgraded R and BioConductor, but previously I did not have this problem. Code and error is below. Any suggestions? Ann ********************************************************** > library(Biostrings) # "Short" example with no error > Temp1<-DNAString( + "AACACACGCATCTCACGCCGAGGACCTGGGATCG.....") > Temp1 969-letter "DNAString" instance # "Long" example, such that R needs a new line to complete the sequence > Temp2<-DNAString( + "AACACACGCATCTCACGCCGAGGACCTGGGATCG..... + TTTTTCGCATAGTGCTCAA") Error in charToXRaw(x, start = start, end = end, width = width, lkup = lkup, : key 10 not in lookup table > sessionInfo() R version 2.7.1 (2008-06-23) i386-pc-mingw32 locale: LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] Biostrings_2.8.17

Hi Ann -- Ann Hess <hess at="" stat.colostate.edu=""> writes: > I am having trouble creating long (~1000+ characters) > DNAStrings. Specifically, I seem to get an error when R has to go to a > new line in the command window when copy/pasting the sequence from an > R script (with no breaks). I recently upgraded R and BioConductor, > but previously I did not have this problem. The problem is the inserted line feed embedded in the string > DNAString("AAA + TTT") Error in charToXRaw(x, start = start, end = end, width = width, lkup = lkup, : key 10 not in lookup table as I guess you've figured out. I *think* (no windows access at the moment) that you can > dna <- readLines(file("clipboard")) to read the clipboard without pasting into the console. You could also > dna <- "AAA + TTT" > dna [1] "AAA\nTTT" > DNAString(gsub("\n", "", dna)) 6-letter "DNAString" instance seq: AAATTT Martin > Code and error is below. Any suggestions? > > Ann > > ********************************************************** > >> library(Biostrings) > > # "Short" example with no error >> Temp1<-DNAString( > + "AACACACGCATCTCACGCCGAGGACCTGGGATCG.....") >> Temp1 > 969-letter "DNAString" instance > > # "Long" example, such that R needs a new line to complete the sequence >> Temp2<-DNAString( > + "AACACACGCATCTCACGCCGAGGACCTGGGATCG..... > + TTTTTCGCATAGTGCTCAA") > Error in charToXRaw(x, start = start, end = end, width = width, lkup = > lkup, : > key 10 not in lookup table > >> sessionInfo() > R version 2.7.1 (2008-06-23) > i386-pc-mingw32 > > locale: > LC_COLLATE=English_United States.1252;LC_CTYPE=English_United > States.1252;LC_MONETARY=English_United > States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] Biostrings_2.8.17 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- Martin Morgan Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M2 B169 Phone: (206) 667-2793