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 04000000000 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/
