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guogenglin / SsuisChara

An integrated analysis pipeline for Streptococcus suis
GNU General Public License v3.0
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no module Bio #1

Open matiajan opened 1 year ago

matiajan commented 1 year ago

When I try to run SuisChara on Debian 11, blast+ and prodigal installed, I got this message: (base) honza@T-30:~/Downloads/SsuisChara-main$ python SsuisChara.py -i *.fasta Traceback (most recent call last): File "/home/honza/Downloads/SsuisChara-main/SsuisChara.py", line 15, in from Bio import SeqIO ModuleNotFoundError: No module named 'Bio'

Should I install some Bio module?

guogenglin commented 1 year ago

Yes, biopython module is required for SsuisChara, try to install this module by pip: pip install biopython

matiajan commented 1 year ago

I installed biopython as you recommended, add /usr/local/lib/python3.9/dist-packages/Bio into PATH but still got the same message: (base) honza@T-30:~/Downloads/SsuisChara-main$ echo $PATH /usr/local/lib/python3.9/dist-packages/Bio:/home/honza/anaconda3/bin:/home/honza/anaconda3/condabin:/usr/local/bin:/usr/bin:/bin:/usr/local/games:/usr/games (base) honza@T-30:~/Downloads/SsuisChara-main$ python SsuisChara.py -i *.fasta Traceback (most recent call last): File "/home/honza/Downloads/SsuisChara-main/SsuisChara.py", line 15, in from Bio import SeqIO ModuleNotFoundError: No module named 'Bio'

guogenglin commented 1 year ago

This may because of the setting of your system or python, you can get help from the official website of biopython: https://biopython.org/