gff_to_genbank.py: sub_features is deprecated

chapmanb / bcbb

Incubator for useful bioinformatics code, primarily in Python and R

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gff_to_genbank.py: sub_features is deprecated #82

Closed sjackman closed 9 years ago

sjackman commented 10 years ago

Thanks for gff_to_genbank.py. It's quite useful to me.

gff_to_genbank.py foo.gff foo.fa
/usr/local/lib/python2.7/site-packages/Bio/SeqFeature.py:171: BiopythonDeprecationWarning: Rather using f.sub_features, f.location should be a CompoundFeatureLocation
  BiopythonDeprecationWarning)

chapmanb commented 10 years ago

Shaun; Thanks for the heads up. I haven't yet migrated away from using sub_features but things should still work correctly despite the warning. If not, I'll definitely look at a workaround straight away.

I've been trying to free up some time to do a more general cleanup and migration the Biopython specific export work, which enables the GFF to GenBank conversion, over to Ryan's gffutils (https://github.com/daler/gffutils).

sjackman commented 10 years ago

Hi, Brad. It works just fine, even with the warning. Feel free to close this issue. I just wanted to give you a heads up, and thank you for the tool. Cheers, Shaun