Re: [R-sig-phylo] problem with write.nexus.data
Hi Liam and Nicholas. write.nexus.data() accepts only lists as specified in the help page, but it's a bit of an anomaly since the same help page says the sequences must be aligned. I have modified this function so that it now accepts both lists and matrices. Best, Emmanuel Le 18/09/2014 07:22, Liam J. Revell a écrit : 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 1 040 etc. I haven't been able to find other posts on this, any help is greatly appreciated. Sincerely, Nick ___ 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/ ___ 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/
Re: [R-sig-phylo] problem with write.nexus.data
This solved the problem exactly, thank you very much. Nick On Thu, Sep 18, 2014 at 12:22 AM, Liam J. Revell 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 >> 1 040 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/
Re: [R-sig-phylo] problem with write.nexus.data
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 1 040 etc. I haven't been able to find other posts on this, any help is greatly appreciated. Sincerely, Nick ___ 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/