[Biopython-dev] BWA Wrapper

[Peter Cock]

On Tue, Feb 19, 2013 at 1:15 PM, Saket Choudhary <saketkc at gmail.com> wrote:
>
> Thanks Peter.
>
> I will add that. Any pointers to what would be a good reference test_aba.py
> file in Tests/ directory for writing unit tests for this ?
>
> I have worked on BDD before but Unit Tests are new for me, so it may take
> some time.I plan to finish it the coming week once my university
> examinations are done
>
> Thanks
>
> Saket

There's a chapter in the Tutorial about our test framework. In this
case existing command line tool wrappers are the best reference,
e.g. test_Emboss.py or test_Muscle.py

Also if you want to use doctests and have them included in the
test suite, add the module to the list in Tests/run_tests.py - however
this does not handle optional dependencies (other than NumPy).
Therefore all the application wrapper doctests to date have carefully
avoided actually invoking the command line - and instead most
print the string representation instead. This allows us to check
the example use cases should run (and catches silly errors in
the examples like a typo in an argument name).

Thanks,

Peter