[Bioc-sig-seq] reading 454 data with ShortRead

[Michael Mueller]

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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