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ERROR [bioconvert:125] #329

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ysuzuki1978 opened this issue Mar 8, 2023 · 1 comment

ysuzuki1978 commented Mar 8, 2023

I tried to install and convert with conda and got the following error I would appreciate if you could tell me possible solutions.

ERROR [bioconvert:125]: cannot import name 'UndefinedSequenceError' from 'Bio.Seq' (/home/yakuri/miniconda3/lib/python3.9/site-packages/Bio/Seq.py)

Contributor

cokelaer commented Mar 9, 2023 •

edited

@ysuzuki1978 thanks for reporting this issue. How did you install bioconvert ? was it with conda ? manda ?
Or just a 'pip install' method ?

Looks like an error with an external package (biopython). Yet, I isntall a fresh version of bioconvert as follows:

conda create --name bioconvert39 python=3.9
conda deactivate
conda activate bioconvert39
conda install mamba
mamba install bioconvert
bioconvert --help
bioconvert fastq2fasta test.fastq test.fasta

seems to work but maybe your error is related to a specific conversion ? If you can provide more information, you may be able to find the error. best

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