Check weblogo is available in PBstat.py

[HubLot]

This PR aims to solve the issue #60.

The availability of the weblogo program is now tested during the parsing step when the --logo option is set.

Since it's not possible to add a callback with a store_trueaction, I created a custom action class (CommandAction). The docstring of this class is pretty straightforward to understand how it works. Basically, it behaves the same way as the store_true but add 2 new keywords:

• command: the name (and it's possible arguments) of the external program to test (here weblogo --help)
• cmd_help: to print a useful message (here, a link to the documentation) when the external program is not found (here weblogo).

The test of the availability is done through the subprocess library with the cmd_exists function which is called by CommandAction. This class can be used for any external program, then it can be useful for R for example.

From #60, I choose to prevent PBstat.py to run if the --logo option is set and weblogo is not found by raising a exception which will be handle automatically by argparse. I think it's better to stop the script than silent the error.

[jbarnoud]

This is great! I tested it and it works. The use of a custom argparse action is a bit scary but very clever.

The pull request causes the demo2 to stop prematurely in the absence of weblogo, though. I submitted a pull request to @HubLot branch to fix the issue; see https://github.com/HubLot/PBxplore/pull/1. (Yes, I submitted a pull request to a pull request. It's too bad it does not appear in the initial pull request.)

[HubLot]

Thanks. Indeed, I forgot to adapt demo2. I just merged your pull request.