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KIT-MBS / pydca

Direct coupling analysis software for protein and RNA sequences
MIT License
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Example for protein DCA analysis #6

Open guochengqian opened 3 years ago

guochengqian commented 3 years ago

Hi Team, Thanks for sharing the code. Could you please kindly provide an runable example for protein analysis? the pydca_demo.py file does not work:

  1. it has typos (in L19, it should be plmdca.PlmDCA(protein_msa_file, 'protein', not plmdca.PlmDCA'protein', msa_file,.
  2. when run at L27, it throws out error: terminate called after throwing an instance of 'std::out_of_range' what(): _Map_base::at
  3. the code does not finish. No DCAVisualizer (needs pdb file). Could you provide instructions how to get pdb file for protein analysis.

Thank you for your help!

HWaymentSteele commented 2 years ago

In case its helpful for anyone else, I was getting the same bug # 2 about std::out_of_range and found that if I removed newline characters from my input alignments (here's an awk script), I no longer got the bug.