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mbhall88 / drprg

Drug Resistance Prediction with Reference Graphs
https://mbh.sh/drprg/
MIT License
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Consequence of unknown mutations #8

Closed mbhall88 closed 2 years ago

mbhall88 commented 2 years ago

At the moment, for an unknown mutation, we just output the nucleotide sequence and coordinates. It might be more useful to know the amino acid consequence. This will also be useful for being able to ignore synonymous mutations, which account for a lot of the unknown mutations.

mbhall88 commented 2 years ago

An example of the output of unknown mutations

    "Capreomycin": {
      "evidence": [
        {
          "gene": "tlyA",
          "residue": "DNA",
          "variant": "A133G",
          "vcfid": "9976be1b"
        }
      ],
      "predict": "U"
    },
    "Levofloxacin": {
      "evidence": [
        {
          "gene": "gyrB",
          "residue": "DNA",
          "variant": "GAGCAG2223CAGCAG",
          "vcfid": "3f53e611"
        }
      ],
      "predict": "U"
    },