[Bioc-sig-seq] making target from fasta file

[Sean Davis]

On Wed, Jun 4, 2008 at 4:59 PM, Joseph Dhahbi, P.h.D. <jdhahbi at chori.org> wrote:
> Hi Herve
> The read.DNAStringSet works now, I think the problem was my downloaded fasta
> file.
> Here is the result and the session Info:
>
>> Fly_RM
>
> [1]
> "/Users/jdhahbi/JosephDhahbi/SOLEXA/Fly/R/export.files/s-2/*.RData/RepeatMasker.fa"
>>
>> fly_rm=read.DNAStringSet(Fly_RM, format="fasta")
>
> Read 1126586 items
>>
>> fly_rm
>
>  A DNAStringSet instance of length 154993

> A quick question: when I use "" with the file name as you did I get the
> folloiwng error:
>
>>
>> fly_rm=read.DNAStringSet("Fly_RM", format="fasta")
>
> Error in file(file, "r") : cannot open the connection
> In addition: Warning message:
> In file(file, "r") : cannot open file 'Fly_RM': No such file or directory
> Error in XStringSet("DNAString", x, start = start, end = end, width = width,
>  :
>  error in evaluating the argument 'x' in selecting a method for function
> 'XStringSet'
>

Fly_RM is a variable with the value of the path to your file.
"Fly_RM" is a string constant--totally different.  Or is there some
more complication to your question?

Sean

>> sessionInfo()
>
> R version 2.7.0 (2008-04-22)
> i386-apple-darwin8.10.1
>
> locale:
> en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
>
> attached base packages:
> [1] tools     stats     graphics  grDevices utils   datasets  methods   base
>
> other attached packages:
> [1] BiostringsCinterfaceDemo_0.1.2
>  BSgenome.Dmelanogaster.UCSC.dm3_1.3.7 BSgenome_1.8.3
>  Biostrings_2.8.9
> [5] Biobase_2.0.1
>>