I have a process that involves disabling taxa not present in the study country before exporting taxonomy. My issue is that if I close megan, then reopen the file and change LCA parameters (often because I notice an additional taxon that needs disabling), the previously-disabled taxa have been re-enabled. This means I have to be very careful to manually keep and update the list of disabled taxa each time I reopen the file.
Firstly, is it possible to save disabled taxa as part of the rma6 file?
If not, is it possible to input/output a disabled taxa list - ideally by command line? This way, each megan file could have a corresponding “disabled taxa” text file, which could be updated upon command, and read in by running blast2rma again.
I believe this is pertinent also because a number of taxa always need to be disabled to prevent reads being pushed up into cellular organisms or root bins (e.g. “unidentified phage”, “uncultured prokaryote”, “chordata environmental sample” etc.)