split_bioscan_1m.py

import os

def split_file(input_file, output_dir, chunk_size):
    if not os.path.exists(output_dir):
        os.makedirs(output_dir)

    file_size = os.path.getsize(input_file)
    base_name = os.path.basename(input_file)
    num_chunks = (file_size + chunk_size - 1) // chunk_size
    print(f"Total size: {file_size} bytes, split to {num_chunks} files")

    with open(input_file, 'rb') as f:
        for i in range(num_chunks):
            part_filename = os.path.join(output_dir, f"{base_name}.part{i + 1:03d}")
            with open(part_filename, 'wb') as part_file:
                bytes_written = 0
                while bytes_written < chunk_size:
                    buffer = f.read(min(1024 * 1024, chunk_size - bytes_written))
                    if not buffer:
                        break
                    part_file.write(buffer)
                    bytes_written += len(buffer)
            print(f"Write to: {part_filename} Size: {bytes_written} bytes")


if __name__ == '__main__':
    input_file = "data/BIOSCAN_1M/split_data/BioScan_data_in_splits.hdf5"
    output_dir = "data/BIOSCAN_1M/split_data/splitted_files"
    chunk_size = 45 * (1024 ** 3)
    split_file(input_file, output_dir, chunk_size)