Command line interface

Some of the functionality in Wiggelen is provided through a simple command line interface.

Since the average scientist is too lazy to write complete documentation, you’ll just find a quick dump of the command line help output below.

martijn@hue:~$ wiggelen -h
usage: wiggelen [-h]
                {index,sort,scale,fill,derivative,plot,coverage,merge,distance} ...

Wiggelen command line interface.

optional arguments:
  -h, --help            show this help message and exit

subcommands:
  {index,sort,scale,derivative,plot,merge,distance}
                        subcommand help
    index               build index for wiggle track
    sort                sort wiggle track regions alphabetically
    scale               scale values in a wiggle track
    fill                fill undefined positions in a wiggle track
    derivative          create derivative of a wiggle track
    plot                visualize wiggle tracks in a plot (requires
                        matplotlib)
    coverage            create coverage BED track of a wiggle track
    merge               merge any number of wiggle tracks in various ways
    distance            calculate the distance between wiggle tracks

Well, I guess nobody ever got fired for showing a quick example, so here you go:

martijn@hue:~$ wiggelen distance tests/data/*.wig
A: tests/data/a.wig
B: tests/data/b.wig
C: tests/data/complex.wig
D: tests/data/c.wig
E: tests/data/empty.wig

      A     B     C     D     E
A     x
B   0.687   x
C   0.000 0.687   x
D   0.901 0.958 0.901   x
E   0.974 0.952 0.974 0.748   x