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chapmanb / bcbb

Incubator for useful bioinformatics code, primarily in Python and R
http://bcbio.wordpress.com
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Error in GFFParser: AttributeError: module 'Bio.SeqFeature' has no attribute 'SimpleLocation' #142

Open victorlin opened 6 months ago

victorlin commented 6 months ago

The feature in question was added in Biopython 1.80, so it does not work with earlier versions.

This was by a test in one of my repos after the recent release of 0.7.1 (specifically commit https://github.com/chapmanb/bcbb/commit/eec72c3faca1e5e9e4e48dbf46d396a9045baa3b). Error message snippet:

+    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'

Workaround

Install biopython>=1.80

Potential solution

Pin biopython>=1.80 in setup.py so dependency resolvers (e.g. pip) will not be able to install an incompatible version.