| import bz2 | |
| import shutil | |
| import tempfile | |
| from pathlib import Path | |
| import gradio as gr | |
| import pypythia.msa | |
| import pypythia.prediction | |
| import pypythia.predictor | |
| import pypythia.raxmlng | |
| def get_default_raxmlng(): | |
| version = "1.1.0" | |
| uncompressed_raxmlng = Path.home() / f"raxml-ng-v{version}-linux-64" | |
| if not uncompressed_raxmlng.exists(): | |
| compressed_raxmlng = Path(__file__).parent / f"raxml-ng-v{version}-linux-64.bz2" | |
| with bz2.BZ2File(compressed_raxmlng) as bz, uncompressed_raxmlng.open( | |
| "wb" | |
| ) as rax: | |
| shutil.copyfileobj(bz, rax) | |
| return uncompressed_raxmlng | |
| def predict_difficulty(uploaded_file): | |
| predictor_file = ( | |
| Path(pypythia.__file__).parent / "predictors" / "predictor_lgb_v1.0.0.pckl" | |
| ) | |
| predictor = pypythia.predictor.DifficultyPredictor(predictor_file.open("rb")) | |
| raxmlng = pypythia.raxmlng.RAxMLNG( | |
| shutil.which("raxml-ng") or get_default_raxmlng() | |
| ) | |
| with tempfile.NamedTemporaryFile() as msa_file: | |
| uploaded_file.seek(0) | |
| shutil.copyfileobj(uploaded_file, msa_file) | |
| msa_file.flush() | |
| msa = pypythia.msa.MSA(msa_file.name) | |
| msa_features = pypythia.prediction.get_all_features(raxmlng, msa) | |
| difficulty = predictor.predict(msa_features) | |
| return difficulty, msa_features | |
| pythia_demo = gr.Interface( | |
| predict_difficulty, | |
| gr.File(label="MSA file (.phy or .msa)"), | |
| [ | |
| gr.Number(label="Difficulty", precision=5), | |
| gr.JSON(label="Features used for prediction"), | |
| ], | |
| ) | |
| pythia_demo.launch() | |