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

[Wolfgang Raffelsberger]

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
>>
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>
>