Disabling taxa by command line, or saving in file


#1

Hi Again,

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.)

Thanks!


#2

Sorry, this is a bug. MEGAN is supposed to remember the list of disabled taxa. I have fixed this feature and will upload a new release today.

Then, which ever taxa you disable will stay disabled across different runs of MEGAN until you enable the taxa again.

In particular, the list of disabled taxa is a program property, rather than the property of any individual files.