sokrypton / sokrypton/ColabFold
Archana
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- Jupyter Notebook
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Description
Thank you @sokrypton , I could run the msa and get results.
While executing Alphfold step, I got the error below,
NameError Traceback (most recent call last)
in ()
40
41 # prep input features
---> 42 feature_dict = cf_af.prep_feats(mod_I, clean=IN_COLAB)
43 Ls_plot = feature_dict["Ls"]
44
NameError: name 'cf_af' is not defined
Contributor guide
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 by reproducing the AlphaFold step in the relevant notebook and inspect the cell calling cf_af.prep_feats(mod_I, clean=IN_COLAB), then trace where cf_af should be defined. Done means the notebook reaches this step without the reported NameError and continues through the AlphaFold workflow.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- jupyter-notebook, python
- Domain
- bioinformatics, machine-learning
- Issue type
- Bug
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100