Import Error - Bio.Alphabet has been removed from Biopython

SBRG / ssbio

A Python framework for structural systems biology

http://ssbio.readthedocs.io/en/latest/

MIT License

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Import Error - Bio.Alphabet has been removed from Biopython #50

Open a-r-j opened 3 years ago

a-r-j commented 3 years ago

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 Biopython version should be specified more tightly in requirements.txt

jetu20 commented 2 years ago

Hi did you solved this issues....I am facing same issues

a-r-j commented 2 years ago

@jetu20 I'm afraid I don't recall. You can probably just install ssbio & then downgrade the Biopython version.

pip install biopython==1.x.x - I'm not sure what the correct version should be, but it will contain the required Bio.Alphabet submodule.

EDIT: I think biopython 1.77 and below should work: https://github.com/biopython/biopython/blob/master/NEWS.rst#4-september-2020-biopython-178