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halbritter-lab / Amissense

The Amissense Tool analyzes and visualizes AlphaMissense pathogenicity scores, integrating AlphaFold structures and ClinVar data. It offers automated pipelines, visualizations, and versatile command-line utilities.
MIT License
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bug: error - PDB file not found #49

Closed Claudia518 closed 3 months ago

Claudia518 commented 3 months ago

#49
Description: when running the scrip with an experimental pdb, there's a file related error.

Eg. python -m Amissense.cli pipeline -g SLC7A9 -o out -e 6lid.pdb

Error produced: 

2024-08-27 11:11:33,077 - root - INFO - Retrieving UniProt ID for gene SLC7A9 and organism ID 9606
Retrieving UniProt ID for gene SLC7A9 and organism ID 9606
2024-08-27 11:11:33,352 - root - ERROR - PDB file not found: 6lid.pdb
PDB file not found: 6lid.pdb
2024-08-27 11:11:33,352 - root - ERROR - File-related error: [Errno 2] No such file or directory: '6lid.pdb'
File-related error: [Errno 2] No such file or directory: '6lid.pdb'