Closed lgannon248 closed 3 years ago
gamcil
commented
3 years ago I think this might just be a problem with an older version of BioPython - you have version 1.73, but the substition_matrices part was added to that module in version 1.75. I think just doing conda update biopython should fix this issue.
lgannon248
commented
3 years ago Thank you for putting me on the right track!
$ conda update biopython wasn't working for unknown reason, but $ pip install biopython --upgrade did work in the end and now clinker can run. Thankyou!
gamcil
commented
3 years ago Glad you got it working 👍
Hi,
Clinker looks fantastic but I'm having trouble getting it going. I'm using a mac, I used pip to install Clinker:
$ pip install Clinker Requirement already satisfied: Clinker in /anaconda3/lib/python3.7/site-packages (0.0.4) Requirement already satisfied: numpy in /anaconda3/lib/python3.7/site-packages (from Clinker) (1.15.1) Requirement already satisfied: scipy in /anaconda3/lib/python3.7/site-packages (from Clinker) (1.1.0) Requirement already satisfied: biopython in /anaconda3/lib/python3.7/site-packages (from Clinker) (1.73)
but calling Clinker leads to a confusing error message:
$ Clinker Traceback (most recent call last): File "/anaconda3/bin/Clinker", line 6, in
from clinker.main import main
File "/anaconda3/lib/python3.7/site-packages/clinker/main.py", line 14, in
from clinker import align
File "/anaconda3/lib/python3.7/site-packages/clinker/align.py", line 20, in
from Bio.Align import substitution_matrices
ImportError: cannot import name 'substitution_matrices' from 'Bio.Align' (/anaconda3/lib/python3.7/site-packages/Bio/Align/init.py)
Edit: I can now go to /anaconda3/lib/python3.7/site-packages/Bio/Align/init.py and see this file, can't find any "substitution_matrices" string in this text file.
Any help much appreciated.