| import argparse |
| import yaml |
| import scanpy as sc |
| from atac_preprocess import quality_control |
| from atac_preprocess import deepen_atac_data |
| from atac_preprocess import tfidf |
|
|
|
|
| if __name__ == '__main__': |
| parser = argparse.ArgumentParser() |
| parser.add_argument("--config_path", type=str, help="path to config file") |
| args = parser.parse_args() |
| with open(args.config_path, 'r') as file: |
| config = yaml.safe_load(file) |
| data_args = config["data_args"] |
| adata = sc.read_h5ad(data_args.get('atac_file_path')) |
| |
| if data_args.get("quality_control", False): |
| print(f"Before quality control: {adata.shape}") |
| adata = quality_control( |
| adata, |
| min_features=data_args.get("min_features"), |
| max_features=data_args.get("max_features"), |
| min_percent=data_args.get("min_percent"), |
| cell_type_col=data_args.get("cell_type_col", "cell type") |
| ) |
| print(f"After quality control: {adata.shape}") |
|
|
| if data_args.get("tfidf", False): |
| print(f"Before tfidf: {adata.shape}") |
| adata.X = tfidf(adata.X) * 1e4 |
|
|
| if data_args.get("deepen_atac", False): |
| adata = deepen_atac_data(adata, num_cell_merge=10) |
| print(f"After deepen: {adata.shape}") |
| if data_args.get("normalize", False): |
| sc.pp.normalize_total(adata) |
| if data_args.get("log_transform", False): |
| sc.pp.log1p(adata) |
|
|
| output_file_name = f"{data_args.get('atac_file_path')}".replace(".h5ad", "") |
| if data_args.get("quality_control", False): |
| output_file_name = f"{output_file_name}_quality_control" |
| if data_args.get("deepen_atac", False): |
| output_file_name = f"{output_file_name}_deepen" |
| if data_args.get("normalize", False): |
| output_file_name = f"{output_file_name}_normalized" |
| if data_args.get("log_transform", False): |
| output_file_name = f"{output_file_name}_log" |
|
|
| output_file_name = f"{output_file_name}.h5ad" |
| adata.write_h5ad(output_file_name) |
|
|
