#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Interface for gzipped mzML files.
"""
# Python mzML module - pymzml
# Copyright (C) 2010-2019 M. Kösters, C. Fufezan
# The MIT License (MIT)
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
# copies of the Software, and to permit persons to whom the Software is
# furnished to do so, subject to the following conditions:
# The above copyright notice and this permission notice shall be included in all
# copies or substantial portions of the Software.
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
# SOFTWARE.
import codecs
import gzip
from xml.etree.ElementTree import iterparse
from .. import regex_patterns
from .. import spec
[docs]
class StandardGzip(object):
[docs]
def __init__(self, path, encoding):
"""
Initalize Wrapper object for gzipped mzML files.
Arguments:
path (str) : path to the file
encoding (str) : encoding of the file
"""
self.path = path
self.file_handler = codecs.getreader(encoding)(gzip.open(path))
self.offset_dict = self._build_index()
return
def close(self):
self.file_handler.close()
[docs]
def _build_index(self):
"""
Cant build index for standard gzip files
"""
# raise Exception('Cant build index for gzip files')
pass
[docs]
def read(self, size=-1):
"""
Read binary data from file handler.
Keyword Arguments:
size (int): Number of bytes to read from file, -1 to read to end of file
Returns:
data (str): byte string of len size of input data
"""
return self.file_handler.read(size)
[docs]
def __getitem__(self, identifier):
"""
Access the item with id 'identifier' in the file by iterating the xml-tree.
Arguments:
identifier (str): native id of the item to access
Returns:
data (str): text associated with the given identifier
"""
old_pos = self.file_handler.tell()
self.file_handler.seek(0, 0)
mzml_iter = iter(iterparse(self.file_handler, events=["end"]))
while True:
event, element = next(mzml_iter)
if event == "end":
if element.tag.endswith("}spectrum"):
if (
int(
regex_patterns.SPECTRUM_ID_PATTERN.search(
element.get("id")
).group(1)
)
== identifier
):
self.file_handler.seek(old_pos, 0)
return spec.Spectrum(element, measured_precision=5e-6)
elif element.tag.endswith("}chromatogram"):
if element.get("id") == identifier:
self.file_handler.seek(old_pos, 0)
return spec.Chromatogram(element, measured_precision=5e-6)
if __name__ == "__main__":
print(__doc__)