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GFF parsing broken with bcbio-gff v0.7.1 and older versions of Biopython #1401

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victorlin opened this issue Jan 29, 2024 · 0 comments · Fixed by #1400
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GFF parsing broken with bcbio-gff v0.7.1 and older versions of Biopython #1401

victorlin opened this issue Jan 29, 2024 · 0 comments · Fixed by #1400
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victorlin commented Jan 29, 2024

Failing scheduled CI:

+    File "/home/runner/micromamba/envs/augur/lib/python3.8/site-packages/BCBio/GFF/GFFParser.py", line 589, in _get_feature
+      new_feature = SeqFeature.SeqFeature(SeqFeature.SimpleLocation(start=rstart, end=rend, strand=feature_dict['strand']), feature_dict['type'],
+  AttributeError: module 'Bio.SeqFeature' has no attribute 'SimpleLocation'

This is similar to #1373. bcbio-gff uses Bio.SeqFeature.SimpleLocation which is not available on older versions of Python supported by Augur. BCBio-GFF should set a minimum version requirement for Biopython (upstream issue).

Potential solutions

  1. (short-term solution) Update Augur's setup.py to the earliest version of Biopython that supports Bio.SeqFeature.SimpleLocation.
  2. (long-term solution) Update bcbio-gff's setup.py to the earliest version of Biopython that supports Bio.SeqFeature.SimpleLocation.
@victorlin victorlin added the bug Something isn't working label Jan 29, 2024
@victorlin victorlin self-assigned this Jan 29, 2024
@victorlin victorlin mentioned this issue Jan 29, 2024
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