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

[Wolfgang Raffelsberger]

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