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Comments (6)

jorvis avatar jorvis commented on June 22, 2024

Do you mind compressing and attaching your input file? I don't have any augustus ones currently to test with.

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JingXia730 avatar JingXia730 commented on June 22, 2024

This is the input file
Test_augustus.gff.gz

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jorvis avatar jorvis commented on June 22, 2024

Thank you. And did you install biocode via pip or git checkout?

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JingXia730 avatar JingXia730 commented on June 22, 2024

No, I just directly run this script. Should I install biocode first?

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jorvis avatar jorvis commented on June 22, 2024

It's fine to operate from a checkout rather than installing, you just have to modify PYTHONPATH so it knows where to find the modules. From the README:

cd /opt
git clone https://github.com/jorvis/biocode.git

You probably want to add this line to your $HOME/.bashrc file

export PYTHONPATH=/opt/biocode/lib:$PYTHONPATH

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jorvis avatar jorvis commented on June 22, 2024

When I did this the conversion ran fine. Attaching result.
test.gff3.gz

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