Control: tags -1 help
Hi,
I have reported the issue upstream but no response so far. While the
error message contains some hint how to solve the issue I would like
to backup this by some competent advise.
======================================================================
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?
Kind regards
Andreas.
--
http://fam-tille.de
