ImportError: Bio.Alphabet has been removed from Biopython in Panaroo

[Leytoncito]

Hello,

First, I’d like to thank you for developing this tool. The program is truly interesting, and I’m excited to run it in full. When executing the pipeline in Snakemake, both the Bakta and CheckM stages ran smoothly. However, during the Panaroo stage, I encountered the following error related to the Bio.Alphabet dependency, which seems to have been removed in recent Biopython versions:

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.

The error appears to be in the generate_output.py file, where it tries to import generic_dna from Bio.Alphabet. I’d appreciate any guidance on resolving this issue so I can continue exploring the program’s capabilities.

Best regards,
Benjamin Leyton-Carcaman