This solved the problem exactly, thank you very much. Nick
On Thu, Sep 18, 2014 at 12:22 AM, Liam J. Revell <liam.rev...@umb.edu> wrote: > Hi Nicholas. > > I think this is a bug. Try the following to circumvent: > > write.nexus.data(as.list(data), file="test.nex", interleaved=TRUE, > charsperline=100) > > Since I don't have your dataset, I can't check it; but it fixed the > problem in another dataset with which I was able to reproduce the error. > > All the best, Liam > > Liam J. Revell, Assistant Professor of Biology > University of Massachusetts Boston > web: http://faculty.umb.edu/liam.revell/ > email: liam.rev...@umb.edu > blog: http://blog.phytools.org > > > On 9/17/2014 10:46 PM, Nicholas Crouch wrote: > >> Hi, >> >> I am having a problem with write.nexus.data, such that the file generated >> is nonsense. >> >> I have a very, very large data set, but have been working with a subset >> trying to solve this problem. My data is in .fasta format, and I am >> looking >> to convert it into nexus format. >> >> I load the data: >> >> library(ape) >>> data <- read.dna("concat.fasta", format="fasta", as.matrix=TRUE) >>> >> >> This gives the following: >> >> data >>> 5 DNA sequences in binary format stored in a matrix >>> >> >> All sequences of same length: 5023 >> >> Labels: Species etc. >> >> Base composition: a c g t >> >> Also: >> >> class(data) >>> "DNAbin" >>> >> >> This is exactly the same as the woodmouse example data provided in the >> package ape, which I have been following when trying to solve this issue >> (see ?write.nexus.data). When I export the data: >> >> write.nexus.data(data, file="test.nex", interleaved=TRUE, >>> >> charsperline=100) >> >> a file is produced which begins: >> >> BEGIN DATA; >> DIMENSIONS NTAX=135165 NCHAR=1; >> FORMAT DATATYPE=DNA MISSING=? GAP=- INTERLEAVE=YES; >> MATRIX >> 1 04000000000 etc. >> >> I haven't been able to find other posts on this, any help is greatly >> appreciated. >> >> Sincerely, >> >> Nick >> >> >> -- Nicholas Crouch Graduate Student, Igić Lab Department of Biological Sciences University of Illinois at Chicago [[alternative HTML version deleted]] _______________________________________________ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/
