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nigyta / dfast_core

DDBJ Fast Annotation and Submission Tool
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Import error #32

Closed blsteven closed 3 years ago

blsteven commented 3 years ago

I am getting the following error when I try to run the program

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.

nigyta commented 3 years ago

Thank you for letting me know. Actually, I’ve just got the same error after updating the Biopython to the latest version. I’m going to fix this as soon as possible, but for now downgrading Biopython may fix this issue.

blsteven commented 3 years ago

Thanks for the quick response and the great tool!

Blaire Steven Associate Scientist Environmental Sciences Connecticut Agricultural Experiment Station 203-974-8461 blaire.steven@ct.gov

Adjunct Assistant Research Professor University of Connecticut Dept. Natural Resources and the Environment

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Thank you for letting me know. Actually, I’ve just got the same error after updating the Biopython to the latest version. I’m going to fix this as soon as possible, but for now downgrading Biopython may fix this issue.

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nigyta commented 3 years ago

@blsteven

As of version 1.2.9, II have fixed this issue following the workaround shown here https://biopython.org/wiki/Alphabet Confirmed that it works on both Biopython 1.71 and 1.78 Thanks again for letting me know.