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#!/usr/bin/env python3
import sys
import os
from pymzml.utils.utils import index_gzip
import pymzml
import glob
import multiprocessing
def main(folder, num_cpus=1):
"""
Creates indexed gzip mzML files from all mzMLs files in the given folder
using a given number of threads.
Usage:
python multi_threading_file_compression.py <folder> <threads>
Note:
If the number of threads is larger than the number of actual possible
threads, all possible threads will be used.
"""
max_cpus = multiprocessing.cpu_count()
if int(num_cpus) > max_cpus:
num_cpus = max_cpus
else:
num_cpus = int(num_cpus)
mzml_job_list = []
for mzml_path in glob.glob(os.path.join(folder, "*.mzML")):
out_path = "{0}.gz".format(mzml_path)
if os.path.exists(out_path):
print("Skipping: {0}".format(mzml_path))
continue
mzml_job_list.append((mzml_path, out_path))
print(
"Compressing {0} mzML files using {1} threads".format(
len(mzml_job_list), num_cpus
)
)
mp_pool = multiprocessing.Pool(num_cpus)
results = mp_pool.starmap(compress_file, mzml_job_list)
mp_pool.close()
print("Done")
return
def compress_file(file_path, out_path):
print("Working on file {0}".format(file_path))
with open(file_path) as fin:
fin.seek(0, 2)
max_offset_len = fin.tell()
max_spec_no = pymzml.run.Reader(file_path).get_spectrum_count() + 10
index_gzip(
file_path, out_path, max_idx=max_spec_no, idx_len=len(str(max_offset_len))
)
print("Wrote file {0}".format(out_path))
return
if __name__ == "__main__":
if len(sys.argv) < 2:
print(main.__doc__)
exit()
else:
main(*sys.argv[1:])
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