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Looks like you may need to pin BioPython or update the imports. On a new environment I installed fanc with lead to Biopython being installed with version 1.83 where GC has changed to gc_fraction (since 1.80). Running fanc with this installed leads to
File "/usr/local/lib/python3.8/dist-packages/fanc/architecture/compartments.py", line 11, in <module>
from Bio.SeqUtils import GC as calculate_gc_content
ImportError: cannot import name 'GC' from 'Bio.SeqUtils' (/usr/local/lib/python3.8/dist-packages/Bio/SeqUtils/__init__.py)
For now installing via the following solves the issue.
pip install biopython==1.80 fanc
The text was updated successfully, but these errors were encountered:
Could not get myself to completely abandon Biopython < 1.8.0, so I put a catch block around the import. Tested this myself on Python 3.12.2, fresh venv.
Looks like you may need to pin BioPython or update the imports. On a new environment I installed fanc with lead to Biopython being installed with version 1.83 where GC has changed to gc_fraction (since 1.80). Running fanc with this installed leads to
For now installing via the following solves the issue.
The text was updated successfully, but these errors were encountered: