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.. code-block:: python
#!/usr/bin/env python3
import sys
import os
from pymzml.utils.utils import index_gzip
# from pymzml.run import Reader
import pymzml
import glob
def main(folder):
"""
Create an indexed gzip mzML file from a plain mzML of all files in folder
Usage: python3 gzip_mzml.py <folder>
"""
for mzml_path in glob.glob(os.path.join(folder, '*.mzML')):
if os.path.exists('{0}.gz'.format(mzml_path)):
print('Skipping: {0}'.format(mzml_path))
continue
print('Processing file: {0}'.format(mzml_path))
with open(mzml_path) as fin:
fin.seek(0,2)
max_offset_len = fin.tell()
max_spec_no = pymzml.run.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__':
main(sys.argv[1])
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