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Those examples should definitely work. They're from the documentation.

The format has evolved. Test updated accordingly

format_json.py raises an exception if the JSON is not valid.
Using format_json.py needs to slightly rewrite the test
(spaces are deleted, and the order may not be the same).

If the JSON is not valid, raises an exception

format-json.sh is deleted because format_json.py has
similar features while checking syntax additionnally.

    Tests were failed because fuse.py was not packaged with the release.
    This is not the case anymore. So the tests can be un-failed.

And bioinfo.lifl.fr is now bioinfo.lille.inria.fr

Mathieu Giraud authored Feb 20, 2015 and Vidjil Team committed Feb 20, 2015

The previous test (merging 3 files) was not working.

Only one exec per script (otherwise the first overwrites the whole process).
chdir can be performed directly by upstart.

Keycodes are susceptible to keyboard layouts. For instance the < and > are on
the same key in the French layout, hence they share the same keycode, but it
is not necessarily the case on all the layouts.

Using chars make the code more robust to different layouts

The keys are +/-. Not working with the numpad.
By the way this asks the question of the compatibility with the keyboard layout.

Are the key codes dependent on the keyboard layout? Or a + will always be 187, whatever the keyboard?

A top cannot be negative nor larger than the total number of (real) clones.
We add a function telling the number of real clones (for the moment length of the array minus one due to the 'other' clone).

Unit tests added

It loads defs.py so must be launched from its directory.

'sequence.JUNCTION.raw nt seq' is the JUNCTION, including V-Cys and J-Phe/J-Trp,
whereas the CDR3 does not include these amino acids.

The top-level fields are created once when initializing ListWindows(),
whereas sample/ fields are created when loading data into ListWindows()