[BioC] read.DNAStringSet

[Thomas Girke]

Dear Ron,

Reading larger sequence sets directly from an ftp/http site into R is not a very 
robust method. In this case you want to first download the sequences onto your computer
and then import them from there:
	read.DNAStringSet("AE004437.ffn", "fasta")

Since you probably have this example from our workshop manual, I have now included a statement
what to do if you encounter this error (http://manuals.bioinformatics.ucr.edu/home/ht-seq). 

Thomas


On Mon, Mar 08, 2010 at 03:54:04PM +0200, Ron Ophir wrote:
> I'm running Biostrings under the following session;
> 
> > sessionInfo()
> 
> R version 2.10.1 (2009-12-14)
> 
> x86_64-unknown-linux-gnu
> 
>  
> 
> locale:
> 
>  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
> 
>  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
> 
>  [5] LC_MONETARY=C              LC_MESSAGES=en_US.UTF-8
> 
>  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
> 
>  [9] LC_ADDRESS=C               LC_TELEPHONE=C
> 
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
> 
>  
> 
> attached base packages:
> 
> [1] stats     graphics  grDevices utils     datasets  methods   base
> 
>  
> 
> other attached packages:
> 
> [1] ShortRead_1.4.0    lattice_0.17-26    BSgenome_1.14.2
> Biostrings_2.14.11
> 
> [5] IRanges_1.4.11
> 
>  
> 
> loaded via a namespace (and not attached):
> 
> [1] Biobase_2.6.1 grid_2.10.1   hwriter_1.1
> 
>  
> 
> And I get
> 
>  
> 
> myseq1 <-
> read.DNAStringSet("ftp://ftp.ncbi.nih.gov/genbank/genomes/Bacteria/Halob
> acterium_sp/AE004437.ffn", "fasta") # Imports
> 
> Error in .read.fasta.in.XStringSet(filepath, set.names, elementType,
> lkup) :
> 
>   cannot open file
> 'ftp://ftp.ncbi.nih.gov/genbank/genomes/Bacteria/Halobacterium_sp/AE0044
> 37.ffn'
> 
>  
> 
> for read.DNAStringSet() whereas for readFASTA() it works well
> 
>  
> 
> myseq1 <-
> readFASTA("ftp://ftp.ncbi.nih.gov/genbank/genomes/Bacteria/Halobacterium
> _sp/AE004437.ffn", strip.descs=T)
> 
>  
> 
> Is it a bug?
> 
> Ron
> 
>  
> 
>  
> 
> 
> This mail was sent via Mail-SeCure System.
> 
> 

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