Update code for Biopython 1.84 compatibility #391
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GFFSeqFeature is just SeqFeature with an explicit `sub_feature` Bio.SeqFeature should use better types and type hints hints, but we can't rely on them (no direct control). So we might as well use our own, properly typed, subclass
JAlvarezJarreta
requested changes
Jul 3, 2024
Co-authored-by: J. Alvarez-Jarreta <jalvarez@ebi.ac.uk>
JAlvarezJarreta
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Jul 3, 2024
JAlvarezJarreta
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Remade #297 from the latest main.
Various type hints fixes along the way.
One big change: I've added a new
GFFSeqFeatureobject, subclass ofBio.SeqFeature. The only difference is that this one has an additional attribute "sub_features" that the GFF parser adds.By replacing every occurrence, we can make sure that we use the correct typing without ignoring the warnings. Bonus benefit: we no longer need to add
sub_features = []every time we create aSeqFeatureobject.Other change, similar problem: we used to add an attribute
organelleto theSeqRecord. I've changed it to store this information in the existingannotationsinstead.I have set the biopython version to 1.3 for now