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Bio.Alphabet has been removed from Biopython error in Binsanity-refine #56

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jolespin opened this issue Mar 27, 2021 · 0 comments
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jolespin commented Mar 27, 2021

(binsanity_env) -bash-4.1$ Binsanity-refine
Traceback (most recent call last):
  File "/usr/local/devel/ANNOTATION/jespinoz/anaconda3/envs/binsanity_env/bin/Binsanity-refine", line 14, in <module>
    from Bio.Alphabet import IUPAC
  File "/usr/local/devel/ANNOTATION/jespinoz/anaconda3/envs/binsanity_env/lib/python3.6/site-packages/Bio/Alphabet/__init__.py", line 21, in <module>
    "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."
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.
(binsanity_env) -bash-4.1$ conda list | grep "biopython"
biopython                 1.78             py36h8f6f2f9_2    conda-forge
(binsanity_env) -bash-4.1$ Binsanity --version
Binsanity v0.4.4
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