mothur seems to send output to whatever directory held parameter files, such as the distance matrix or the names files. I’d like to keep those kinds of files in one directory and have different directories for different kinds of analysis. This would be facilitated if mothur always wrote to the directory from which it was invoked, or had a “setwd” command to explicitly set the current working directory.
For example, If have directories Analysis1 and Analysis2, and generate the distance matrixes and cluster files in Analysis1, and then switch to Analysis2 for a new kind of analysis I can read the relevant files with:
read.dist(column=…/AllLumpedAnalysis/all_lumped.unique.filter.dist,name=…/AllLumpedAnalysis/all_lumped.names)
But if I then execute cluster(), the output is written to Analysis1, rather than to Analysis2
I wasn’t sure if this was a bug, or a feature request, so I put it here.
Thanks!
This is the mothur of all programs for the work I do…