Usage

The database path defaults to the user's working directory, and there is no way to specify the DB path in the command line options. Therefore, to use the database provided by the developers you need to create a symbolic link to it in your PWD. I've set the database path in the env variable $DB, so the command ln -s $DB DB will set the DB correctly for use.

Install was successfully tested with provided test data with the following commands:

$ ml plasme/1.1

$ ln -s $DB DB

$ PLASMe.py test.fasta test.plasme.fna -c 0.6 -i 0.6 -p 0.5 -t 8