On 02/28/2012 08:27 AM, Martin Morgan wrote: > On 02/28/2012 08:20 AM, wang peter wrote: >> hi all: i used ShortRead to trim some sequences >> >> max.mismatchs<- 0.25*1:nchar(DNAString(PCR2rc)) > > using 1:nchar(...) can be bad, e.g., when nchar() ==> 0 > > > 1:0 > [1] 1 0 > > use seq_len instead, so > > 0.25 * seq_len(nchar(DNAString(PCR2rc))) > >> trimmedCoords<- trimLRPatterns(Rpattern = PCR2rc, subject = >> sread(highQuaReads), max.Rmismatch= max.mismatchs, >> with.Rindels=T,ranges=T) >> trimmedReads<- narrow(highQuaReads, start=start(trimmedCoords), >> end=end(trimmedCoords)) >> >> but it appear some null lines, but it is the first time to happen in >> my exprience >> >> >> @HWI-ST132:506:D0CNUABXX:3:1101:4456:1871 1:N:0:TTCACA >> >> + >> >> @HWI-ST132:506:D0CNUABXX:3:1101:4331:1931 1:N:0:TTCACA >> GGTGGCTGTAGTTTAGTGGTAAGAATTCTACG >> + >> ? > How can I reproduce this? I took the bug to be that 0-width reads could be written but not read > fl = tempfile() > xx = ShortReadQ(DNAStringSet(""), FastqQuality("")) > writeFastq(xx, fl) > cat(paste(readLines(fl), collapse="\n"), "\n") @ + > readFastq(fl) Error: Input/Output file(s): /tmp/RtmpdORPSm/file2780493c message: unexpected empty line /tmp/RtmpdORPSm/file2780493c:1 This has been fixed in devel, version 1.13.14. If you want to remove zero-width records before writing, then subset as xx[width(xx) != 0] If the problem is with trimLRPatterns then please ask the question again with a simpler illustration. Martin > > >> >> >>> sessionInfo() >> R version 2.14.1 (2011-12-22) >> Platform: x86_64-redhat-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 >>> >> > > -- Computational Biology Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: M1-B861 Telephone: 206 667-2793