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

[Dan Bolser]

I'm trying to use this function (read454) but it keeps dying..


library(ShortRead)

experimentPath <-
  "Fasta/"

readPath <- experimentPath
qualPath <- experimentPath

pattern <- "FUBJ29X06.sff."

reads <-
  read454(RochePath(experimentPath=experimentPath,
                    readPath=readPath,
                    qualPath=qualPath), pattern)

+   read454(RochePath(experimentPath=experimentPath,
+                     readPath=readPath,
+                     qualPath=qualPath), pattern)
Error in file(file, "r") : cannot open the connection
In addition: Warning message:
In file(file, "r") : cannot open file 'NA': No such file or directory


The contents of the 'Fasta' directory look like this:

ls Fasta/FUBJ29X06.sff.*
Fasta/FUBJ29X06.sff.fna  Fasta/FUBJ29X06.sff.qual



Why can't I just specify a fasta file and a quality file?

Cheers,
Dan.


2009/7/17 Pratap, Abhishek <APratap at som.umaryland.edu>:
> 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: bioc-sig-sequencing-bounces at r-project.org on behalf of Wolfgang Raffelsberger
> Sent: Fri 7/17/2009 1:35 PM
> Cc: bioc-sig-sequencing at r-project.org
> 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
>>> Bioc-sig-sequencing at r-project.org
>>> https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
>>
>>
>
> _______________________________________________
> Bioc-sig-sequencing mailing list
> Bioc-sig-sequencing at r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
>
>
>        [[alternative HTML version deleted]]
>
>
> _______________________________________________
> Bioc-sig-sequencing mailing list
> Bioc-sig-sequencing at r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
>
>