On 08/17/2010 02:55 PM, Steve Lianoglou wrote: > Hi Jess, > > On Tue, Aug 17, 2010 at 5:15 PM, JASREET HUNDAL <[email protected]> wrote: >> Hi Martin & Harris >> >> It looks like the bioconductor packages that I am using are updated: > ... >> Also, this is error I get while exporting to fasta file: >>> fa <-sread(trimmed) >> Error in slot(object, "sread") : >> no slot of name "sread" for this object of class "DNAStringSet"
My bad. The script Jess mention says trimmed <- trimLRPatterns(pcrPrimer, subject=sread(seq)) and then trimmed is a DNAStringSet (try class(trimmed)), and writeFastq doesn't make sense. With trimmed <- trimLRPatterns(pcrPrimer, subject=seq) it's a ShortReadQ (i.e., including quality) and writeFastq(trimmed, "/path/to/file") should work. Explanations Steve offers below still apply to th DNAStringSet. Martin > > The "sread" method is used to get the *reads* (which would be a > DNAStringSet object ) out of a ShortRead* object. The ShortRead* class > stores the reads, as well as other information about the reads (phred > scores, etc.) > > It looks like your "trimmed" object is already a DNAStringSet -- so > calling sread() on a DNAStringSet isn't really meaningful ... you > would just get itself. > > In short, the "trimmed" object you have appears to the the > DNAStringSet you are looking to get by using the "sread" function. > >> And while exporting using writeFastq: >> >>> writeFastq(trimmed,"trimmedseqs") >> Error in function (classes, fdef, mtable) : >> unable to find an inherited method for function "writeFastq", for >> signature "DNAStringSet" >> >> It would be great if you could suggest some other method to export the >> trimmed object. > > Here you have the opposite problem. > > You "just" have a DNAStringSet -- no other metadata about your reads > that a ShortRead* class holds, like phred scores, etc. > > The writeFastq file expects to write your object as a FASTQ file. > > If you have a DNAStringSet (which is what your "trimmed" object is), > you can only really hope to write a FASTA file, in which case you can > use the "writeFASTA" function (or the write.XStringSet function that > Martin suggested) from the Biostrings package (which is already > loaded). > > Does that make sense? > > So again (in summary (?)): > the problem you are having is that you think that your "trimmed" > object is something it's not. > > I'm not sure how you got it, or where it came from, but it is "just" a > DNAStringSEt -- which is simply a number of sequences (reads). > > You can't write it as a fastq file (with writeFastq), and there's no > need to get the "reads" out of it (with the sread function) because > that's what they already are. > > Hope that helps, > -- Martin Morgan Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793 _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
