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