Mussa Prototype Command Line

This refers to the older FLTK version of mussa, for the Qt version type mussa --help to get more information.

Mussa is a command line run python script. The first argument determines the
 run mode the user wants.

prompt> mussa [run mode] [species number] [other args]

The remaining arguments depend on the run mode:

    * 'f' - full analysis, seqcomp, n-way comparisons, and displays
      (does not save nway results, seqcomp analyses kept in datadir)

prompt> mussa f [species number] [config file] [window size] [hard threshold]

    * 's' - seqcomp batch mode only - runs all the seqcomp analyses

prompt> mussa s [species number] [config file] [window size] [hard threshold]

    * 'n' - n-way comparison only, saves results to file and does not display

prompt> mussa n [species number] [datadir]

    * 'v' - loads n-way comparison, displays results graphically
      (must have used option 'n' previously)

prompt> mussa v [species number] [datadir]

    * 'nv' - does n-way comparison and displays
      (does not save n-way comparisons, 'nv' must be used to view again)

prompt> mussa nv [species number] [datadir]

Future version will have GUI to manage what mode user wants (ie selection screen, 
the subselections for specifics in terms of files to analyze, load/save, etc - 
all the things specified by the command line args)