# 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