[Biopython-dev] Bio.Wise checked in

[Brad Chapman]

Hi Michael;

> I have checked in Bio.Wise, which contains modules for running and
> processing the output of some of the models in the Wise package
> available from
> <ftp://ftp.ebi.ac.uk/pub/software/unix/wise2/wise2.2.0.tar.gz>:
> 
> Bio.Wise.psw for protein Smith-Waterman alignments
> Bio.Wise.dnal for Smith-Waterman DNA alignments

Great! Thanks for doing this!

> There are also appropriate unit tests which will not be checked if
> dnal is not in your path.

Right now I don't have wise installed and I am getting the test
failing instead of skipping it:

7:38pm Tests> python run_tests.py test_Wise.py
test_Wise ... dnal: not found
FAIL

======================================================================
FAIL: test_Wise
----------------------------------------------------------------------
Traceback (most recent call last):
  File "run_tests.py", line 148, in runTest
    self.runSafeTest()
  File "run_tests.py", line 185, in runSafeTest
    expected_handle)
  File "run_tests.py", line 285, in compare_output
    assert expected_line == output_line, \
AssertionError: 
Output  : 'test_dnal (test_Wise.TestWiseDryRun) ... FAIL\n'
Expected: 'test_dnal (test_Wise.TestWiseDryRun) ... ok\n'
----------------------------------------------------------------------
Ran 1 tests in 0.075s

It looks like my commands execution returns something different than
on your machine:

>>> import commands
>>> commands.getoutput("dnal")
'dnal: not found'

I changed requires_wise.py a bit so it takes care of this case. So
just a minor thing.

Thanks again for this!
Brad