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.. code-block:: python
#!/usr/bin/env python3.4
import sys
import os
from pymzml.utils.utils import index_gzip
from pymzml.run import Reader
def main(mzml_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
out_path = '{0}.gz'.format(mzml_path)
index_gzip(
mzml_path,
out_path,
max_idx = max_spec_no,
idx_len = len(str(max_offset_len))
)
print('Wrote file {0}'.format(out_path))
if __name__ == '__main__':
if len(sys.argv) > 1:
main(
sys.argv[1],
)
else:
print(main.__doc__)
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