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error while using docker image (andersenlab/vcf-kit:20200822175018b7b60d: TypeError: a bytes-like object is required, not 'str' about vcf-kit HOT 1 OPEN

andersenlab avatar andersenlab commented on May 29, 2024
error while using docker image (andersenlab/vcf-kit:20200822175018b7b60d: TypeError: a bytes-like object is required, not 'str'

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Comments (1)

tdido avatar tdido commented on May 29, 2024 1

Seems like an encoding problem (also evidenced by the "u" prefix that the developer mentions).

A quick fix would be to decode the string by replacing:
line = line.replace("u'","")
with
line = line.decode().replace("u'","")
in the file /opt/conda/envs/vcf-kit/lib/python3.7/site-packages/vcfkit/vcf2tsv.py.

Bear in mind that this change will likely not survive updates to the docker image or conda environment.

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