Score variants with public Encodon

Run general masked-codon mutation_prediction only. This produces a research signal, not a clinical diagnosis or an expression-direction prediction.

Instructions

First confirm CodonFM or Encodon context in the user's request or established conversation. If that context is missing, ask for any missing variant details and the intended analysis before choosing a model or inspecting model-specific files. The presence of this skill or source files alone does not establish the user's intent.

For source reviews and command preparation, inspect the supplied source and metadata without installing the ML runtime. Use an available Python 3 interpreter with standard-library zipfile, json, and csv; do not assume the python alias or unzip exists. Read archive members directly with ZipFile.namelist() and ZipFile.read() where possible. If extraction is needed, use a fresh directory from tempfile.mkdtemp() or mktemp -d and preserve existing checkouts and scratch directories. Check whether rg is available; use grep or Python if it is absent. Read the source sections needed for the requested command or compatibility question.

Check whether the request is executable in public v1 before installing or downloading anything. For synonymous-codon aggregation or Decodon, inspect the parser and model configuration, explain the missing feature, and finish. Do not implement the missing workflow, search private code, or keep retrying unsupported commands.