Command line interfaceΒΆ
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