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
def gzip_files(mzml_path, out_path):
"""
Create and indexed gzip mzML file from a plain mzML.
"""
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
index_gzip(mzml_path,
out_path,
max_idx=max_spec_no,
idx_len=len(str(max_offset_len)))
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))
)
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
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))
)