Closed patena closed 10 years ago
Weronika; Sorry for the delay in getting back with you. The most recent release of bcbio-gff (0.4) supports newer location models in Biopython so if you upgrade:
pip install --upgrade bcbio-gff
This should work cleanly. Sorry about the issue and hope this fixes it for you.
I had already installed the new release, but I looked around some more now and realized that I also had an old one hanging around for some reason, and python was loading that. Thanks!
I upgraded my system from Xubuntu 12.10 to 14.04, and GFF parsing stopped working.
I get this error:
The file I'm using is this extremely simple one (and I get the same error on real files from Phytozome that used to parse fine):
I tried reinstalling BCBio (now on version 0.1) and Biopython (1.64), it didn't help. Is this something I should submit to biopython rather than here?