Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Account for X aminoacid letter #5

Open
francosimonetti opened this issue Jul 28, 2021 · 0 comments
Open

Account for X aminoacid letter #5

francosimonetti opened this issue Jul 28, 2021 · 0 comments

Comments

@francosimonetti
Copy link

I found this issue, maybe it's a good idea to account for unknown aminoacid letters in case the sequences are not sanitized before.

worker_1_7b57679bcd66 | File "/usr/local/lib/python3.7/site-packages/amphipathic/init.py", line 139, in index
worker_1_7b57679bcd66 | index_secondary(seq)
worker_1_7b57679bcd66 | File "/usr/local/lib/python3.7/site-packages/amphipathic/init.py", line 132, in index_secondary
worker_1_7b57679bcd66 | for protein in seq.resume_secondary()
worker_1_7b57679bcd66 | File "/usr/local/lib/python3.7/site-packages/amphipathic/init.py", line 132, in
worker_1_7b57679bcd66 | for protein in seq.resume_secondary()
worker_1_7b57679bcd66 | File "/usr/local/lib/python3.7/site-packages/amphipathic/init.py", line 130, in
worker_1_7b57679bcd66 | for aa in protein
worker_1_7b57679bcd66 | File "/usr/local/lib/python3.7/site-packages/amphipathic/init.py", line 116, in add_indexes_to_secuence
worker_1_7b57679bcd66 | index, mean = calculate_amphipathic_index(struct)
worker_1_7b57679bcd66 | File "/usr/local/lib/python3.7/site-packages/amphipathic/init.py", line 105, in calculate_amphipathic_index
worker_1_7b57679bcd66 | mean = sum([hydrophobic.table[aa] for aa in seq]) / amount
worker_1_7b57679bcd66 | File "/usr/local/lib/python3.7/site-packages/amphipathic/init.py", line 105, in
worker_1_7b57679bcd66 | mean = sum([hydrophobic.table[aa] for aa in seq]) / amount
worker_1_7b57679bcd66 | KeyError: 'x'

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

1 participant