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biopython issue! #59

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bhclement opened this issue Dec 30, 2020 · 0 comments
Open

biopython issue! #59

bhclement opened this issue Dec 30, 2020 · 0 comments

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@bhclement
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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.

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