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    • Removed SC2 and SC2 calculations. · a53a653e
      Since we are not using SC2 and SC3 calculations anymore in SGEMME, I decided to remove them. They were making the computations quite slow due to multiple external calls to JET. In addition, I updated the bash script in the examples directory. We have an example to calculate all possible single point mutations. Besides, we have an example to calculate only mutations of interest given in a blah-blah.mut file.
      Mustafa Tekpinar authored
  19. 06 Jan, 2023 2 commits
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  25. 03 Aug, 2022 1 commit
    • Several interface and computational changes. · 7db0ac49
      1-Moved the normweighmode to the beginning of the program.
      In this way, the weight will be applied at the beginning
      instead of just the final normalization step. Our tests
      show that it improves the results when Max(JET, (PC+CV)2)
      is used at the beginning. Most of the changes in this part
      are in computePred.R file.
      2-When the user provides a mutation list
      as a file, it was giving an error. The error in apply(...)
      part of normalizePredWithNbSeqsPCSelMult function. The bug
      is corrected now and it produces results consistent with
      the web server.
      
      3-A small bug in gemme.py was also corrected.
      If a mutation list file is given, the model is not 'simple'
      and therefore, it will not produce a map of single point
      mutations.
      Mustafa Tekpinar authored
  26. 22 Jul, 2022 1 commit