On 05/06/2018 01:00, Andreas Tille wrote:
> ======================================================================
> ERROR: test_consistent_gap_degen_handling
> (test_core.test_sequence.ModelSequenceTests)
> gap degen character should be treated consistently
> ----------------------------------------------------------------------
> Traceback (most recent call last):
> File
> "/tmp/autopkgtest-lxc.5a99fnj6/downtmp/autopkgtest_tmp/tests/test_core/test_sequence.py",
> line 660, in test_consistent_gap_degen_handling
> self.assertEqual(dna.stripBadAndGaps(), raw_ungapped)
> File "/usr/lib/python2.7/dist-packages/cogent/core/sequence.py", line 1251,
> in stripBadAndGaps
> valid_indices -= self._data == i
> TypeError: numpy boolean subtract, the `-` operator, is deprecated, use the
> bitwise_xor, the `^` operator, or the logical_xor function instead.
>
> ======================================================================
>
>
> I would be happy for some suggested patch how to solve this. The line
> in question is
>
>
> https://salsa.debian.org/med-team/python-cogent/blob/master/cogent/core/sequence.py
>
> Line 1251
>
> If my feeling is not totally wrong the correct patch would be
>
> valid_indices -= (self._data == i)
>
> since the left value is rather an integer than boolean.
>
> What do you think?
Without analyzing the code in the fine details, and assuming self._data
is a numpy array or a subclass, I think the name of the variable is
misleading. Looking at the whole function it seems to be a bool array.
It should be easy to confirm this with pdb or simply inserting a print()
statement in the right place.
def stripBadAndGaps(self):
"""Returns copy of self with bad chars and gaps excised."""
gap_indices = map(self.Alphabet.index, self.MolType.Gaps)
valid_indices = self._data < len(self.Alphabet)
for i in gap_indices:
valid_indices -= self._data == i
result = compress(valid_indices, self._data)
return self.__class__(result, Info=self.Info)
The fix should be to replace the subtraction with:
valid_indices ^= self._data == i
Cheers,
Dan
