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victoriapascal / gutsmash

gutSMASH
GNU Affero General Public License v3.0
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Bio.Alphabet has been removed from Biopython #2

Open basculethirascule opened 3 years ago

basculethirascule commented 3 years ago

Hi

I've installed all required dependencies and databases for use with gutSMASH, but when I come to run the program I get the following error.

Bio.Alphabet has been removed from Biopython. In many cases, the alphabet can simply be ignored and removed from scripts. In a few cases, you may need to specify the molecule_type as an annotation on a SeqRecord for your script to work correctly. Please see https://biopython.org/wiki/Alphabet for more information." ImportError: Bio.Alphabet has been removed from Biopython. In many cases, the alphabet can simply be ignored and removed from scripts. In a few cases, you may need to specify the molecule_type as an annotation on a SeqRecord for your script to work correctly. Please see https://biopython.org/wiki/Alphabet for more information.

I'm running Python 3.7.6 and installed the Python dependencies using the following code available from your instructions. pip3 install biopython helperlibs bcbio-gff pysvg-py3 scikit-learn matplotlib pyScss Jinja2

Please could you modify the gutSMASH code so it runs with the newer version of Biopython?

Thanks Lesley

victoriapascal commented 3 years ago

Hi Lesley. Thanks for spotting this out. Installing biopython version 1.76 solves the problem (any newer version does not include Bio.Alphabet). I will also clarify it in the README file. You can also try the web server version of it at https://gutsmash.bioinformatics.nl/