ImportError: Bio.Alphabet has been removed from Biopython
UdoGi opened this issue · comments
Several import errors are caused by the removal of this module in Biopython 1.78, e.g in test_dna.py
Bio.Alphabet has been removed from Biopython. In many cases, the alphabet can simply be ignored and removed from scripts. In a few cases, you may need to specify the molecule_type as an annotation on a SeqRecord for your script to work correctly. Please see https://biopython.org/wiki/Alphabet for more information.
I just fixed some of these in #744 but others can't be fixed because the warnings are coming from inside Bio. You can see the locations via env PYTHONWARNINGS=error pytest. Once #744 is merged we'll have no more use of Bio.Alphabet and presumably one day the warning coming out of Bio will disappear.