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
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