Source code for pymzml.file_classes.standardGzip

#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Interface for gzipped mzML files.
"""
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__)