Source code for gzip_mzml

#!/usr/bin/env python3

import sys
import os
from pymzml.utils.utils import index_gzip
from pymzml.run import Reader




def main(mzml_path, out_path):
    """
    Create and indexed gzip mzML file from a plain mzML.

    Usage: python3 gzip_mzml.py <path/to/mzml> <path/to/output>
    """
    with open(mzml_path) as fin:
        fin.seek(0, 2)
        max_offset_len = fin.tell()
        max_spec_no = Reader(mzml_path).get_spectrum_count() + 10

    index_gzip(
        mzml_path, out_path, max_idx=max_spec_no, idx_len=len(str(max_offset_len))
    )



if __name__ == "__main__":
    if len(sys.argv) > 2:
        main(sys.argv[1], sys.argv[2])
    else:
        print(main.__doc__)