Merck / Merck/BioPhi

BioPhi failed with TypeError: predict_scores() got an unexpected keyword argument 'model_version'

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Dominant language
Python
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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'

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First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. 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

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