[BioC] read.DNAStringSet
Ron Ophir
ron at volcani.agri.gov.il
Mon Mar 8 14:54:04 CET 2010
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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