[BioC] Biostrings and A. thaliana genome sequence

[Herve Pages]

Hi René,

Rene Dreos (JIC) wrote:
> Hello list,
> 
>  
> 
> I would like to use Biostrings to work with A. thaliana genome sequence. But, when I tried to extract the sequence from BSgenome.Athaliana.TAIR.01222004 library I've got the following errors. Does anyone know why this happen and how I can solve it?
> 
>  
> 
>> library("Biostrings", lib.loc="/common/users/dreosr/unix/software/lib")
> 
>> library("BSgenome", lib.loc="/common/users/dreosr/unix/software/lib")
> 
>> library("BSgenome.Athaliana.TAIR.01222004", lib.loc="/common/users/dreosr/unix/software/lib")
> 
>> Athaliana$chr1
> 
> Error in readChar(con, 5) : cannot open the connection
> 
> In addition: Warning message:
> 
> In readChar(con, 5) :
> 
>   cannot open compressed file '', probable reason 'No such file or directory'
> 
>> Athaliana[[chr1]]
> 
> Error in readChar(con, 5) : cannot open the connection
> 
> In addition: Warning message:
> 
> In readChar(con, 5) :
> 
>   cannot open compressed file '', probable reason 'No such file or directory'
> 
>  
> 
>> sessionInfo()
> 
> R version 2.6.2 (2008-02-08) 
> 
> x86_64-redhat-linux-gnu 
> 
>  
> 
> locale:
> 
> LC_CTYPE=en_GB.UTF-8;LC_NUMERIC=C;LC_TIME=en_GB.UTF-8;LC_COLLATE=en_GB.UTF-8;LC_MONETARY=en_GB.UTF-8;LC_MESSAGES=en_GB.UTF-8;LC_PAPER=en_GB.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_GB.UTF-8;LC_IDENTIFICATION=C
> 
>  
> 
> attached base packages:
> 
>  [1] grid      splines   tools     stats     graphics  grDevices utils    
> 
>  [8] datasets  methods   base     
> 
>  
> 
> other attached packages:
> 
>  [1] BSgenome.Athaliana.TAIR.01222004_1.3.1
> 
>  [2] BSgenome_1.6.2                        
> 
>  [3] Biostrings_2.6.6                      
> 
>  [4] WiggeNorm_1.0                         
> 
>  [5] quantsmooth_1.4.0                     
> 
>  [6] quantreg_4.17                         
> 
>  [7] SparseM_0.75                          
> 
>  [8] lodplot_1.1                           
> 
>  [9] gcrma_2.10.0                          
> 
> [10] matchprobes_1.10.0                    
> 
> [11] affxparser_1.10.2                     
> 
> [12] affy_1.16.0                           
> 
> [13] preprocessCore_1.0.0                  
> 
> [14] affyio_1.6.1                          
> 
> [15] Biobase_1.16.3
> 
>  

You are using R 2.6.2 + BioC 2.1 (current release) but BSgenome.Athaliana.TAIR.01222004 1.3.1
belongs to BioC 2.2 so unless you know exactly what you are doing, this is not a recommended
situation.
Anyway, because of some recent changes in Biostrings/BSgenome, BSgenome.Athaliana.TAIR.01222004
1.3.1 was broken even for R-2.7.0 + BioC 2.2 users. I've fixed it and the new version of the
package (1.3.3) will be available thru biocLite() in about 30 minutes. Note that you need
R-2.7.0 + the latest versions of Biostrings/BSgenome in order to use any of the latest versions
of the BSgenome.* packages (1.3.3, the 1.3.1 versions are broken and will be fixed ASAP).

Cheers,
H.