Setup
I am reporting a problem with Biopython version, Python version, and operating
system as follows:
3.9.6 (default, Jun 29 2021, 06:20:32)
[Clang 12.0.0 (clang-1200.0.32.29)]
CPython
macOS-10.15.7-x86_64-i386-64bit
1.79
Expected vs. Actual behaviour
Loading the attached GenBank file (renamed for upload to GitHub): pME_B_0_08_0005_Akan(Vn)_(sfgfp).gb.txt
discards the origin-spanning feature as being from an undefined sequence topology, despite the fact that sequence topology is recognized as circular.
Steps to reproduce
> records = [r for r in SeqIO.parse('pME_B_0_08_0005_Akan(Vn)_(sfgfp).gb','gb')]
/usr/local/lib/python3.9/site-packages/Bio/GenBank/__init__.py:352: BiopythonParserWarning: It appears that '3093..570' is a feature that spans the origin, but the sequence topology is undefined. Skipping feature.
warnings.warn(
> records[0].annotations
{'topology': 'circular', 'data_file_division': 'UNK', 'date': '22-SEP-2021', 'accessions': ['urn.local...ef-c2dp9c9'], 'keywords': [''], 'source': '', 'organism': '.', 'taxonomy': [], 'molecule_type': 'DNA'}
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