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galaxy-genome-annotation / python-apollo

Python library for talking to Apollo API
MIT License
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biopython dependency error #56

Closed jaspwn closed 1 year ago

jaspwn commented 1 year ago

Hi, I recently installed python-apollo via pip 4.2.13 and I encourntered a dependency error with biopython.

UnknownSeq is a deprecated class in biopython 1.81

File "/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/BCBio/GFF/GFFParser.py", line 34, in <module>
    from Bio.Seq import UnknownSeq
ImportError: cannot import name 'UnknownSeq' from 'Bio.Seq' (/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/Bio/Seq.py)

Not really sure the correct way to fix, but I did it by just getting Bio/Seq.py from biopython '1.79'

abretaud commented 1 year ago

Hi, Yes there's an incompatibilty between bcbio-gff and biopython 1.81, there's an issue descibing that: https://github.com/chapmanb/bcbb/issues/136 The simplest soltion for now is to pin biopython to version 1.80 or lower. I hope there will be a new bcbio-gff release soon to fix this, there are so many projects impacted :(

jaspwn commented 1 year ago

Thanks! Thats probably a better fix than the one i implemented.