laelbarlow/amoebae

Workflow for identifying and classifying homologous gene/protein sequences

amoebae's Issues

"Bio.Alphabet has been removed from Biopython"

Hi,

I'm in the process of running some test installs of amoebae on my laptop (M1 MacBook) using a python virtual environment. When I get to the workflow command "snakemake get_ref_seqs -j 100", I get the following error message multiple times:

"Traceback (most recent call last):
File "/Users/user/amoebae/amoebae", line 36, in
import amoebae_m
File "/Users/user/amoebae/amoebaelib/amoebae_m.py", line 38, in
from Bio.Alphabet import IUPAC, Gapped
File "/Users/useramoebae_python_env/lib/python3.11/site-packages/Bio/Alphabet/init.py", line 20, in
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."

Is this something that needs to be changed in the software or can I resolve it on my end?