-r2h to export the full hierarchy per read as is possible with the GUI. Would be very useful for us. I suppose a -h2c would be useful for many.
(BTW, it would be good if the help message from daa2info reported valid values for the export options, i.e. EGGNOG, INTERPRO2GO etc.)
good idea, I have added a -p (for path) option for the export of taxonomy with an additional option -mro (major ranks only)
Also, the help message now lists all known classifications.
I just noticed that I was probably mistaken in my belief that what you implemented was export of all hierarchies, i.e. including functional ones. (This of course explains why --paths doesn’t work for e.g. SEED export; see my recent reply to a bug report of mine.)
Anyway, it would be very useful for us to be able to use the command line tool to export also the hierarchies of functional assignments.
I have implemented that and it will be available in the next release (later this week)