| import os |
| import argparse |
| import pandas as pd |
| import yaml |
|
|
| from glob import glob |
| from sklearn import metrics |
| from easydict import EasyDict |
|
|
|
|
| def get_args(): |
| parser = argparse.ArgumentParser() |
| parser.add_argument('-c', '--config', help="running configurations", type=str, required=True) |
| return parser.parse_args() |
|
|
|
|
| def main(args): |
| with open(args.config, 'r', encoding='utf-8') as r: |
| config = EasyDict(yaml.safe_load(r)) |
|
|
| output_dir = "output/ClinVar" |
| |
|
|
| label_name = "ClinVar_labels.csv" |
| label_path = os.path.join(output_dir, label_name) |
|
|
| list_variables_to_keep = ["protein_name", "mutations", "evol_indices"] |
| all_evol_indices = pd.concat( |
| [ |
| pd.read_csv(path, low_memory=False)[list_variables_to_keep] |
| for path in glob(f"{config.model.kwargs.log_dir}/*.csv") |
| ], |
| ignore_index=True, |
| ) |
| all_evol_indices = all_evol_indices.drop_duplicates() |
|
|
| labels_dataset = pd.read_csv(label_path, low_memory=False) |
| all_evol_indices_with_labels = pd.merge( |
| all_evol_indices, |
| labels_dataset[["protein_name", "mutations", "ClinVar_labels"]], |
| how="right", |
| on=["protein_name", "mutations"], |
| ) |
|
|
| all_evol_indices_with_labels = all_evol_indices_with_labels[ |
| all_evol_indices_with_labels.ClinVar_labels != 0.5 |
| ] |
|
|
| fpr, tpr, threshold = metrics.roc_curve( |
| all_evol_indices_with_labels["ClinVar_labels"], all_evol_indices_with_labels["evol_indices"] |
| ) |
| roc_auc = metrics.auc(fpr, tpr) |
| print(roc_auc) |
|
|
|
|
| if __name__ == '__main__': |
| main(get_args()) |
