Hi In that case based on my short experience I think you could specify a pattern while reading files from a directory.
pattern-<"regex-pattern-here" reads <- read454(RochePath(experimentPath=experimentPath,readPath=readPath, qualPath=qualPath), pattern) I think should work. Thanks -A -----Original Message----- From: [email protected] on behalf of Wolfgang Raffelsberger Sent: Fri 7/17/2009 1:35 PM Cc: [email protected] Subject: Re: [Bioc-sig-seq] reading 454 data with ShortRead Dear Michael, Thank's a lot, it works now ... If I understand right, I may not have more than one single pair of sequence-reads (.fna) and quality-scores (.qual) in a given directory, since you don't specify the file-names. Wolfgang Michael Mueller a écrit : > Dear Wolfgang, > > readPath and qualPath specify the paths to the directory containing the > .fna and .qual files rather than the paths to the files themselves. > > Try: > > experimentPath <- "/path/to/directory/containing/fna/and/qual/files" > readPath <- experimentPath > qualPath <- experimentPath > > reads <- read454(RochePath(experimentPath=experimentPath, > readPath=readPath, qualPath=qualPath)) > > If only experimentPath is specified all sub-directories of > <experimentPath> matching run are searched for read/quality files. > > Regards, > Michael > > ---------------------------- > Michael Mueller > Bioinformatician > > Imperial College London > MRC Clinical Sciences Centre > Du Cane Road > London, W12 0NN > United Kingdom > > phone +44 (0)20 8383 8537 > fax +44 (0)20 8383 8577 > > > Wolfgang Raffelsberger wrote: >> Dear list, >> I'm trying to read some 454 data into ShortRead, but I'm having some >> difficulties. Basically I have a FASTA concatenated file with all the >> sequence reads and a FASTA-like file with the Phred-quailty scores, >> the identifyiers for each read from both files match. Here I'm >> testing a small sub-set of the reads, so memory etc shouldn't be an >> issue. >> Based on the ShortRead Vignette I thought could do the job and then I >> realized that there are 454-dedicated functions. But so far I didn't >> get either of them of them to work. >> >> > library(ShortRead) >> > Sfile1 <- "01Reads.fna" >> > Qfile1 <- "01Reads.qual" >> > tmp <- read454(".", readPath=Sfile1, qualPath=Qfile1) # I'm >> already in the proper path where both files are located ... >> Error in function (classes, fdef, mtable) : >> unable to find an inherited method for function "read454", for >> signature "character" >> > >> > # the I tried ... >> > tmp <- readXStringColumns(".",pattern=Sfile1, >> colClasses=list("DNAString")) >> Error: Input/Output >> while reading files 'test16seq.fna': >> key 62 not in lookup table >> > >> > # for completeness : >> > sessionInfo() >> R version 2.9.1 (2009-06-26) >> i386-pc-mingw32 >> >> locale: >> LC_COLLATE=French_France.1252;LC_CTYPE=French_France.1252;LC_MONETARY=French_France.1252;LC_NUMERIC=C;LC_TIME=French_France.1252 >> >> >> >> attached base packages: >> [1] stats graphics grDevices utils datasets methods base >> other attached packages: >> [1] ShortRead_1.2.1 lattice_0.17-25 BSgenome_1.12.3 >> Biostrings_2.12.7 IRanges_1.2.3 >> loaded via a namespace (and not attached): >> [1] Biobase_2.4.1 grid_2.9.1 hwriter_1.1 tools_2.9.1 >> >> >> Thanks in advance, >> Wolfgang >> >> >> . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . >> Wolfgang Raffelsberger, PhD >> Laboratoire de BioInformatique et Génomique Intégratives >> CNRS UMR7104, IGBMC, 1 rue Laurent Fries, 67404 Illkirch >> Strasbourg, France >> Tel (+33) 388 65 3300 Fax (+33) 388 65 3276 >> wolfgang.raffelsberger (at) igbmc.fr >> >> _______________________________________________ >> Bioc-sig-sequencing mailing list >> [email protected] >> https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing > > _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing [[alternative HTML version deleted]]
_______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
