# -*- coding: utf-8 -*-
# encoding: utf-8
"""
The class :py:class:`Reader` has been designed to selectively extract data
from a mzML file and to expose the data as a python object.
Necessary information are read in and stored in a fast
accessible format.
The reader itself is an iterator, thus looping over all spectra
follows the classical pythonian syntax.
Additionally one can random access spectra by their nativeID
if the file if not truncated by a conversion Program.
Note:
The class :py:class:`Writer` is still in development.
"""
#
# pymzml
#
# Copyright (C) 2016 M. Kösters, C. Fufezan
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program. If not, see
# <http://www.gnu.org/licenses/>
import re
import os
import xml.etree.ElementTree as ElementTree
from collections import defaultdict as ddict
from . import spec
from . import obo
from . import regex_patterns
from .file_interface import FileInterface
from .file_classes.standardMzml import StandardMzml
[docs]class Reader(object):
"""
Initialize Reader object for a given mzML file.
Arguments:
path (str): path to the mzml file to parse.
Keyword Arguments:
MS_precisions (dict): measured precisions for the different MS levels.
e.g.::
{
1 : 5e-6,
2 : 20e-6
}
obo_version (str, optional): obo version number as string. If not
specified the version will be extracted from the mzML file
Note:
Setting the precision for MS1 and MSn spectra has changed in version 1.2.
However, the old syntax as kwargs is still compatible ( e.g. 'MS1_Precision=5e-6').
"""
def __init__(
self,
path,
MS_precisions = None,
obo_version = None,
build_index_from_scratch=False,
skip_chromatogram = True,
**kwargs
):
"""Initialize and set required attributes."""
self.build_index_from_scratch = build_index_from_scratch
self.skip_chromatogram = skip_chromatogram
if MS_precisions is None:
MS_precisions = {}
if 'MS1_Precision' in kwargs.keys():
MS_precisions[1] = kwargs['MS1_Precision']
if 'MSn_Precision' in kwargs.keys():
MS_precisions[2] = kwargs['MSn_Precision']
# Parameters
self.ms_precisions = {
0 : 0.001, #arbitrary prec for UV spectra
1 : 5e-6,
2 : 20e-6
}
self.ms_precisions.update(MS_precisions)
# File info
self.info = ddict()
self.info['file_name'] = path
self.info['encoding'] = self._determine_file_encoding(path)
self.info['file_object'] = self._open_file(self.info['file_name'])
# if build_index_from_scratch is True:
# print(isinstance(self.info['file_object'], StandardMzml))
# print(type(self.info['file_object']))
# if isinstance(self.info['file_object'], StandardMzml):
# self.info['offset_dict'] = \
# self.info['file_object']._build_index_from_scratch()
# else:
# raise Exception(
# 'Can only build index from scratch '
# 'for standard mzML files.'
# )
# else:
self.info['offset_dict'] = self.info['file_object'].offset_dict
self.info['obo_version'] = obo_version
self.iter = self._init_iter()
self.OT = self._init_obo_translator()
def __next__(self):
"""
Iterator for the class :py:class:`Run`.
Iterates all of the spectra in the file.
Returns:
Spectrum (:py:class:`Spectrum`): a spectrum object with interface
to the original spectrum element.
Example:
>>> for spectrum in Reader:
... print(spectrum.mz, end='\\r')
"""
has_ref_group = self.info.get('referenceable_param_group_list', False)
while True:
event, element = next(self.iter, ('END', 'END'))
if event == 'end':
if element.tag.endswith('}spectrum'):
spectrum = spec.Spectrum(element)
if has_ref_group:
spectrum._set_params_from_reference_group(
self.info['referenceable_param_group_list_element']
)
ms_level = spectrum.ms_level
spectrum.measured_precision = self.ms_precisions[ms_level]
spectrum.calling_instance = self
return spectrum
if element.tag.endswith('}chromatogram'):
if self.skip_chromatogram:
continue
spectrum = spec.Chromatogram(element)
# if has_ref_group:
# spectrum._set_params_from_reference_group(
# self.info['referenceable_param_group_list_element']
# )
spectrum.calling_instance = self
return spectrum
elif event == 'END':
raise StopIteration
[docs] def __getitem__(self, identifier):
"""
Access spectrum with native id 'identifier'.
Arguments:
identifier (str or int): last number in the id tag of the spectrum
element
Returns:
spectrum (Spectrum or Chromatogram): spectrum/chromatogram object
with native id 'identifier'
"""
try:
if int(identifier) > self.get_spectrum_count():
raise Exception('Requested identifier is out of range')
except:
pass
spectrum = self.info['file_object'][identifier]
spectrum.calling_instance = self
if isinstance(spectrum, spec.Spectrum):
spectrum.measured_precision = self.ms_precisions[spectrum.ms_level]
return spectrum
@property
def file_class(self):
"""Return file object in use."""
return type(self.info['file_object'].file_handler)
def _open_file(self, path):
"""
Open the path using the FileInterface class as a wrapper.
Arguments:
path (str): path to the file to parse
Returns:
(FileInterface): Wrapper class for compressed and uncompressed
mzml files
"""
return FileInterface(
path,
self.info['encoding'],
build_index_from_scratch=self.build_index_from_scratch
)
def _determine_file_encoding(self, path):
"""
Determine the encoding used for the file in path.
Arguments:
path (str): path to the mzml files
Returns:
mzml_encoding (str): encoding type of the file
"""
mzml_encoding = 'utf-8'
if os.path.exists(path):
with open(path, 'rb') as sniffer:
header = sniffer.readline()
encoding_pattern = regex_patterns.FILE_ENCODING_PATTERN
match = encoding_pattern.search(header)
if match:
mzml_encoding = bytes.decode(
match.group('encoding')
)
return mzml_encoding
def _init_obo_translator(self):
"""
Initialize the obo translator with the minimum requirement
and extra Accessions.
Returns:
obo_translator (OboTranslator): translator class to translate
accessions to names
"""
# parse obo, check MS tags and if they are ok in minimum.py (minimum
# required) ...
if self.info.get('obo_version', None) is None:
self.info['obo_version'] = '1.1.0'
obo_translator = obo.OboTranslator(version=self.info['obo_version'])
return obo_translator
def _init_iter(self):
"""
Initalize the iterator for the spectra and sets it to the start
of the spectrumList element.
Returns:
mzml_iter (xml.etree.ElementTree._IterParseIterator): Iterator over
all element in the file starting with the first spectrum
"""
mzml_iter = iter(ElementTree.iterparse(
self.info['file_object'],
events=('end', 'start')
)) # NOTE: end might be sufficient
_, self.root = next(mzml_iter)
while True:
event, element = next(mzml_iter, ('END', 'END'))
if element.tag.endswith('}mzML'):
if 'version' in element.attrib \
and len(element.attrib['version']) > 0:
self.info['mzml_version'] = element.attrib['version']
else:
s = element.attrib[
'{http://www.w3.org/2001/XMLSchema-instance}'
'schemaLocation'
]
self.info['mzml_version'] = re.search(
r'[0-9]*\.[0-9]*\.[0-9]*', s).group()
elif element.tag.endswith('}cv'):
if not self.info['obo_version'] \
and element.attrib.get('id', None) == 'MS':
self.info['obo_version'] = element.attrib.get(
'version',
'1.1.0'
)
elif element.tag.endswith('}referenceableParamGroupList'):
self.info['referenceable_param_group_list'] = True
self.info['referenceable_param_group_list_element'] = element
elif element.tag.endswith('}spectrumList'):
spec_cnt = element.attrib.get('count')
self.info['spectrum_count'] = int(spec_cnt) if spec_cnt else None
break
elif element.tag.endswith('}chromatogramList'):
chrom_cnt = element.attrib.get('count', None)
if chrom_cnt is None:
self.info['chromatogram_count'] = None
else:
self.info['chromatogram_count'] = int(chrom_cnt)
break
elif element.tag.endswith('}run'):
run_id = element.attrib.get('id')
start_time = element.attrib.get('startTimeStamp')
self.info['run_id'] = run_id
self.info['start_time'] = start_time
else:
pass
self.root.clear()
return mzml_iter
def __iter__(self):
"""Return self."""
return self
[docs] def next(self):
"""Function to return the next Spectrum element."""
return self.__next__()
[docs] def get_spectrum_count(self):
"""
Number of spectra in file.
Returns:
spectrum count (int): Number of spectra in file.
"""
return self.info['spectrum_count']
[docs] def get_chromatogram_count(self):
"""
Number of chromatograms in file.
Returns:
chromatogram count (int): Number of chromatograms in file.
"""
return self.info['chromatogram_count']
if __name__ == '__main__':
print(__doc__)