Incompatibility with biopython v1.78

[Julian Zhou]

presto and changeo appear to be not working with biopython v1.78

(jz_python3.8.5) Julians-MBP:~ jkewz$ pip show biopython
Name: biopython
Version: 1.78
Summary: Freely available tools for computational molecular biology.
Home-page: https://biopython.org/
Author: The Biopython Contributors
Author-email: [e-mail]
License: UNKNOWN
Location: /Users/jkewz/.pyenv/versions/3.8.5/envs/jz_python3.8.5/lib/python3.8/site-packages
Requires: numpy
Required-by: presto, changeo

Error message (same for MakeDb.py --version):

(jz_python3.8.5) Julians-MBP:~ jkewz$ MaskPrimers.py --version
Traceback (most recent call last):
  File "/Users/jkewz/.pyenv/versions/jz_python3.8.5/bin/MaskPrimers.py", line 18, in <module>
    from presto.Commandline import CommonHelpFormatter, checkArgs, getCommonArgParser, parseCommonArgs
  File "/Users/jkewz/.pyenv/versions/3.8.5/envs/jz_python3.8.5/lib/python3.8/site-packages/presto/Commandline.py", line 17, in <module>
    from presto.IO import getFileType, printError, printWarning
  File "/Users/jkewz/.pyenv/versions/3.8.5/envs/jz_python3.8.5/lib/python3.8/site-packages/presto/IO.py", line 15, in <module>
    from Bio.Alphabet import IUPAC
  File "/Users/jkewz/.pyenv/versions/3.8.5/envs/jz_python3.8.5/lib/python3.8/site-packages/Bio/Alphabet/__init__.py", line 20, in <module>
    raise ImportError(
ImportError: 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.

Works fine after downgrading biopython to v1.71.

[Jason Vander Heiden]

Removed `Bio.Alphabet` usage in 0c5e3d7. Needs to be tested still.

[Jason Vander Heiden]

Seems to be working okay. It's a bit hard to test though (no error in unit tests, pipeline tests, or docker tests). I made the same fix in changeo as well.