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/Hal ob 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/AE00 44 37.ffn' for read.DNAStringSet() whereas for readFASTA() it works well myseq1 <- readFASTA("ftp://ftp.ncbi.nih.gov/genbank/genomes/Bacteria/Halobacteri um _sp/AE004437.ffn", strip.descs=T) Is it a bug? Ron This mail was sent via Mail-SeCure System.

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/H alob > 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/AE 0044 > 37.ffn' > > > > for read.DNAStringSet() whereas for readFASTA() it works well > > > > myseq1 <- > readFASTA("ftp://ftp.ncbi.nih.gov/genbank/genomes/Bacteria/Halobacte rium > _sp/AE004437.ffn", strip.descs=T) > > > > Is it a bug? > > Ron > > > > > > > This mail was sent via Mail-SeCure System. > > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor