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innate2adaptive / decombinator

Decombinator v5: fast, error-correcting analysis of TCR repertoires
https://pypi.org/project/decombinator/
MIT License
22 stars 8 forks source link

Import Error: Bio.Alphabet has been removed from Biopython #27

Closed tp-peacock closed 3 years ago

tp-peacock commented 3 years ago

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.

tp-peacock commented 3 years ago

This error may occur for users running the CDR3translator v4.0.1 but the most up-to-date version of Biopython (v1.78).

Users should update to the latest Decombinator version (v4.0.3) where this has now been fixed.

Decombinator v.4.0.3 should still be compatible with older versions of Biopython (>= v.1.75).