[BioC] read.DNAStringSet

[Ron Ophir]

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

 

 


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