Command Line ScriptsΒΆ

We would like to add a command line tool that allows users to run PlotMAPQ from the command line. As mentioned in Project Setup, we have included a bin directory that contains scripts that can be run from the command line. This allows users to call our modules from a script, as well as python. To do so, all we have to do is add a script that calls PlotMAPQ, and then declare the script in our setup script.

  1. First, make a file called bin/plot-mapq. This file will call PlotMAPQ.
  2. Next, modify the file to include your new script in the package:
        scripts = ['/bin/plot-mapq']

For more information on command line tools, see the python packaging documentation.

Now, we can run PlotMAPQ from the command line:

>> plot-mapq
usage: plot-mapq [options] alignment_bam sample_name out_directory
plot-mapq: error: the following arguments are required: bamIn, sampleName, dirOut

We can also just print the version:

>> plot-mapq -v