[Biopython-dev] BWA Wrapper

Saket Choudhary saketkc at gmail.com
Mon Mar 4 10:59:26 UTC 2013


I have updated the code here :

I have added unittests for the wrapper. And yes, this did help me in
fixing a lot of minor bugs in my original wrapper.

@Peter :  Is this 'pull request' ready ?



On 19 February 2013 19:55, Peter Cock <p.j.a.cock at googlemail.com> wrote:
> 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

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