Hello all. I am a long-term R user who has recently switched platforms from Windows to Linux and I am having a hard time with the syntax difference. I am stuck on something that is likely simple, but I am stuck all the same. I have aligned short reads using Maq 0.7.1 in RedHat and I have the ‘map’ output files as well as the ‘map.txt’ files obtained by mapview. I am trying to input the files into Bioconductor using ShortReads, but I can’t seem to read the files in. I can get ‘readAligned’ to work on Windows, but I need the memory from my Linux computer. I start by creating the dirPath: dir <- “~/Desktop/Maq50bp/Map_files” aln <- readAligned(dir,”s_1_sequence.map”,”MAQMap”) Using this, I get an error that ‘pattern’ must be ‘character(1)’. Alternately, I define pattern by: pattern <- “s_1_sequence.map” aln <- readAligned(dir,pattern,”MAQMap”) And I get the error that my directory is not a readable directory. Though I have the right permissions for this directory. Any insight would be greatly appreciated. Jessica Jessica Ezzell Hunter, MS PhD Postdoctoral Fellow Department of Behavioral Neuroscience Oregon Health & Science University 3181 SW Sam Jackson Park Road L470 Portland, OR 97239 (503) 220-8262 x51988 [[alternative HTML version deleted]]

Hi Jessica -- Jessica Hunter wrote: > Hello all. I am a long-term R user who has recently switched platforms from Windows to Linux and I am having a hard time with the syntax difference. I am stuck on something that is likely simple, but I am stuck all the same. I have aligned short reads using Maq 0.7.1 in RedHat and I have the ???map??? output files as well as the ???map.txt??? files obtained by mapview. I am trying to input the files into Bioconductor using ShortReads, but I can???t seem to read the files in. I can get ???readAligned??? to work on Windows, but I need the memory from my Linux computer. > > > > I start by creating the dirPath: > > dir <- ???~/Desktop/Maq50bp/Map_files??? > > aln <- readAligned(dir,???s_1_sequence.map???,???MAQMap???) what does list.files(dir, "s_1_sequence.map") say? Perhaps you want "^s_1_sequence.map$" I think the error below is really saying that dir/pattern matches more than one file. Also, you might try starting R with the 'locale' set to 'C'; those non-ascii characters in your message make me nervous. Something along the lines of, from a bash command line % LC_ALL=C R Martin > > > > Using this, I get an error that ???pattern??? must be ???character(1)???. Alternately, I define pattern by: > > > > pattern <- ???s_1_sequence.map??? > > aln <- readAligned(dir,pattern,???MAQMap???) > > > > And I get the error that my directory is not a readable directory. Though I have the right permissions for this directory. > > > > Any insight would be greatly appreciated. > > > > Jessica > > > > Jessica Ezzell Hunter, MS PhD > > Postdoctoral Fellow > Department of Behavioral Neuroscience > > Oregon Health & Science University > 3181 SW Sam Jackson Park Road > > L470 > Portland, OR 97239 > > (503) 220-8262 x51988 > > > > > [[alternative HTML version deleted]] > > > > -------------------------------------------------------------------- ---- > > _______________________________________________ > 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 M1 B861 Phone: (206) 667-2793

Hi Jessica, On Aug 27, 2009, at 12:49 PM, Jessica Hunter wrote: > Hello all. I am a long-term R user who has recently switched > platforms from Windows to Linux and I am having a hard time with the > syntax difference. I am stuck on something that is likely simple, > but I am stuck all the same. I have aligned short reads using Maq > 0.7.1 in RedHat and I have the ?map? output files as well as the > ?map.txt? files obtained by mapview. I am trying to input the files > into Bioconductor using ShortReads, but I can?t seem to read the > files in. I can get ?readAligned? to work on Windows, but I need > the memory from my Linux computer. First thing that comes to mind (since it works on windows and not linux) is that you should just double check that the letter casing in your file and dir names. The windows filesystem is not case sensitive (last I knew) and linux is. So: > I start by creating the dirPath: > > dir <- ?~/Desktop/Maq50bp/Map_files? Imagine your directory was actually called "~/Desktop/Maq50bp/map_files? Your command would work in windows, but not in linux. Just something you might want to check real quick before starting to pull any hair out. -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact