BioPhi failed with TypeError: predict_scores() got an unexpected keyword argument 'model_version'
Nobody has claimed this yet.
- Dominant language
- Python
- Stars
- 265
- Forks
- 65
- PR merge metrics
- No merged PRs in 30d
Description
I get this, Anybody can give me a hand?
Settings:
-
Predicting using Sapiens model: lasted
-
Numbering scheme: imgt
-
CDR definition: imgt
-
Ignoring mutations in CDR regions
-
Humanizing using 1 iteration
2it [00:00, 12.96it/s]
Writing FASTA to file: humanized_test.fa
0%| | 0/2 [00:00<?, ?it/s]
Traceback (most recent call last):
File "/data/home/sczc830/.conda/envs/IgGM/lib/python3.10/site-packages/biophi/common/cli/main.py", line 11, in call
return self.main(*args, **kwargs)
File "/data/home/sczc830/.conda/envs/IgGM/lib/python3.10/site-packages/click/core.py", line 1383, in main
rv = self.invoke(ctx)
File "/data/home/sczc830/.conda/envs/IgGM/lib/python3.10/site-packages/click/core.py", line 1850, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/data/home/sczc830/.conda/envs/IgGM/lib/python3.10/site-packages/click/core.py", line 1246, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/data/home/sczc830/.conda/envs/IgGM/lib/python3.10/site-packages/click/core.py", line 814, in invoke
return callback(*args, **kwargs)
File "/data/home/sczc830/.conda/envs/IgGM/lib/python3.10/site-packages/biophi/humanization/cli/sapiens.py", line 105, in sapiens
return sapiens_fasta_only(
File "/data/home/sczc830/.conda/envs/IgGM/lib/python3.10/site-packages/biophi/humanization/cli/sapiens.py", line 202, in sapiens_fasta_only
humanization = humanize_chain(chain, params=humanization_params)
File "/data/home/sczc830/.conda/envs/IgGM/lib/python3.10/site-packages/biophi/humanization/methods/humanization.py", line 170, in humanize_chain
return sapiens_humanize_chain(parental_chain, params=params)
File "/data/home/sczc830/.conda/envs/IgGM/lib/python3.10/site-packages/biophi/humanization/methods/humanization.py", line 214, in sapiens_humanize_chain
pred = sapiens_predict_chain(humanized_chain, model_version=params.model_version)
File "/data/home/sczc830/.conda/envs/IgGM/lib/python3.10/site-packages/biophi/humanization/methods/humanization.py", line 250, in sapiens_predict_chain
return sapiens.predict_scores(
TypeError: predict_scores() got an unexpected keyword argument 'model_version'
────────────────────────────────────────────────────────────
BioPhi failed with TypeError: predict_scores() got an unexpected keyword argument 'model_version'
Contributor guide
No contributing guide indexed for this repository
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start with biophi/humanization/methods/humanization.py and trace the Sapiens call into sapiens_predict_chain, then inspect biophi/humanization/cli/sapiens.py for how the command reaches it. Reproduce the reported Sapiens humanization command and verify that prediction completes without the unexpected model_version argument error.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- machine-learning
- Issue type
- Bug
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 35/100