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sanger-pathogens / seroba

k-mer based Pipeline to identify the Serotype from Illumina NGS reads
https://sanger-pathogens.github.io/seroba/
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biopython issue! #59

Open bhclement opened 3 years ago

bhclement commented 3 years ago

i install seroba by conda and encounter this message.

$ seroba Traceback (most recent call last): File "/home/ctsui/.conda/envs/seroBA/bin/seroba", line 3, in import seroba File "/home/ctsui/.conda/envs/seroBA/lib/python3.6/site-packages/seroba/init.py", line 16, in from seroba import File "/home/ctsui/.conda/envs/seroBA/lib/python3.6/site-packages/seroba/tasks/init.py", line 10, in from seroba.tasks import File "/home/ctsui/.conda/envs/seroBA/lib/python3.6/site-packages/seroba/tasks/getPneumocat.py", line 2, in from seroba import get_pneumocat_data File "/home/ctsui/.conda/envs/seroBA/lib/python3.6/site-packages/seroba/get_pneumocat_data.py", line 6, in from Bio.Alphabet import generic_dna File "/home/ctsui/.conda/envs/seroBA/lib/python3.6/site-packages/Bio/Alphabet/init.py", line 21, in "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.