Updating current files after system(mv/rename)


I’ve noticed that mothur doesn’t track when current files have been renamed, leading to file not found errors when trying to use the current option (logfile demonstrating this). I imagine this doesn’t often (if ever) come up because generally you rename the file to something shorter so you can type it easily, but it would be neat if mothur tracked the change as well.

I am thinking that if after running system(mv/rename) mothur checked to see if the renamed file was in the current files list, and update the current files list appropriately?


Thanks I’ve added this to the list of future features.


I might request a more “comprehensive” option, if possible.

A function along the lines of

change.prefix(prefix=stuff, deleteOld=T/F)

that would re-name ALL current files to the new prefix, and update current, allowing for a delete (move), or not (copy) of the current files.