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#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Interface for indexed gzipped files
@author: Manuel Koesters
"""
# 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 XML
from .. import spec
from ..utils.GSGR import GSGR
class IndexedGzip:
def __init__(self, path, encoding):
"""
Initialize Wrapper object for indexed gzipped 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 = dict()
self._build_index()
def __del__(self):
"""Close handlers when deleting object."""
self.Reader.close()
self.file_handler.close()
def _build_index(self):
"""Use the GSGR class to retrieve the index from the file and save it."""
self.Reader = GSGR(self.path)
self.offset_dict = self.Reader.index
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)
def __getitem__(self, identifier):
"""
Access the item with id 'identifier' in the file.
Arguments:
identifier (str): native id of the item to access
Returns:
data (str): text associated with the given identifier
"""
# TODO more elegant way to add NameSpace (.register_namespace maybe??)
ns_prefix = '<mzML xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://psi.hupo.org/ms/mzml http://psidev.info/files/ms/mzML/xsd/mzML1.1.0.xsd" id="test_Creinhardtii_QE_pH8" version="1.1.0" xmlns="http://psi.hupo.org/ms/mzml">'
ns_suffix = "</mzML>"
data = self.Reader.read_block(identifier)
element = XML(ns_prefix + data.decode("utf-8") + ns_suffix)
if "chromatogram" in element[0].tag:
return spec.Chromatogram(list(element)[0], measured_precision=5e-6)
else:
return spec.Spectrum(list(element)[0], measured_precision=5e-6)
def close(self):
"""Close the handlers."""
self.Reader.close()
self.file_handler.close()
if __name__ == "__main__":
print(__doc__)
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