Error in conda version of changeo

[Diego Diez]

I am using Change-O from conda but get the following error when running AssignGenes.py:

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 current version of biopython in conda is 1.79 which explains the issue. Are there plans to update Change-O to support biopython >1.77 in the near future? Thanks.

[Diego Diez]

Ah I found that for some reason changeo 1.0 was installed in my environment. Fixing that fixed other problems.

[Diego Diez]

As mentioned in comments the issue was caused by incorrect version of changeo installed.

[Jason Vander Heiden]

Hi Diego, Glad to hear this is sorted out.

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