# -*- 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.
"""
# 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 re
import os
import xml.etree.ElementTree as ElementTree
from collections import defaultdict as ddict
from io import BytesIO
from pathlib import Path
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_or_file,
MS_precisions=None,
obo_version=None,
build_index_from_scratch=False,
skip_chromatogram=True,
index_regex=None,
**kwargs
):
"""Initialize and set required attributes."""
self.index_regex = index_regex
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"]
MS_precisions[3] = kwargs["MSn_Precision"]
# Parameters
self.ms_precisions = {
None: 0.0001, # if spectra does not contain ms_level information
# e.g. UV-chromatograms (thanks pyeguy) then ms_level is
# returned as None
0: 0.0001,
1: 5e-6,
2: 20e-6,
3: 20e-6,
}
self.ms_precisions.update(MS_precisions)
# File info
self.info = ddict()
self.path_or_file = path_or_file
if isinstance(self.path_or_file, Path):
self.path_or_file = str(self.path_or_file)
if isinstance(self.path_or_file, str):
self.info["file_name"] = self.path_or_file
self.info["encoding"] = self._determine_file_encoding(self.path_or_file)
else:
self.info["encoding"] = self._guess_encoding(self.path_or_file)
self.info["file_object"] = self._open_file(
self.path_or_file, build_index_from_scratch=self.build_index_from_scratch
)
self.info["offset_dict"] = self.info["file_object"].offset_dict
if obo_version:
self.info["obo_version"] = self._obo_version_validator(obo_version)
else:
# obo version not specified -> try to identify from mzML by self._init_iter
self.info["obo_version"] = None
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, obo_version=self.OT.version)
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]
return spectrum
if element.tag.endswith("}chromatogram"):
if self.skip_chromatogram:
continue
spectrum = spec.Chromatogram(element, obo_version=self.OT.version)
# if has_ref_group:
# spectrum._set_params_from_reference_group(
# self.info['referenceable_param_group_list_element']
# )
return spectrum
elif event == "END":
# reinit iter
self.info["file_object"].close()
self.info["file_object"] = self._open_file(
self.path_or_file, build_index_from_scratch=False
)
self.iter = self._init_iter()
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.obo_translator = self.OT
if isinstance(spectrum, spec.Spectrum):
spectrum.measured_precision = self.ms_precisions[spectrum.ms_level]
return spectrum
def __enter__(self):
return self
def __exit__(self, type, value, traceback):
self.close()
@property
def file_class(self):
"""Return file object in use."""
return type(self.info["file_object"].file_handler)
def _open_file(self, path_or_file, build_index_from_scratch=False):
"""
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_or_file,
self.info["encoding"],
build_index_from_scratch=build_index_from_scratch,
index_regex=self.index_regex,
)
def _guess_encoding(self, mzml_file):
"""
Determine the encoding used for the file.
Arguments:
mzml_file (IOBase): an mzml file
Returns:
mzml_encoding (str): encoding type of the file
"""
match = regex_patterns.FILE_ENCODING_PATTERN.search(mzml_file.readline())
if match:
return bytes.decode(match.group("encoding"))
else:
return "utf-8"
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
"""
if os.path.exists(path):
if path.endswith(".gz") or path.endswith(".igz"):
import gzip
_open = gzip.open
else:
_open = open
with _open(path, "rb") as sniffer:
return self._guess_encoding(sniffer)
@staticmethod
def _obo_version_validator(version):
"""
The obo version should fit file names in the obo folder.
However, some software generate mzML with built in obo version string like:
'23:06:2017' or even newer version that not in obo folder yet.
This is to check obo version and try to fit the best obo version
to the obo version in the mzML file.
Arguments:
version (str): The original version to check.
Returns:
version_fixed (str): The checked obo version.
"""
obo_rgx = re.compile(r"(\d\.\d{1,2}\.\d{1,2})(_[rR][cC]\d{0,2})?")
obo_years_rgx = re.compile(r"20\d\d")
obo_year_version_dct = {
2012: "3.40.0",
2013: "3.50.0",
2014: "3.60.0",
2015: "3.75.0",
2016: "4.0.1",
2017: "4.1.0",
2018: "4.1.10",
2019: "4.1.22",
}
version_fixed = None
if obo_rgx.match(version):
version_fixed = version
else:
if obo_years_rgx.search(version):
years_found = obo_years_rgx.search(version)
if years_found:
try:
year = int(years_found.group(0))
except ValueError:
year = 2000
if year in obo_year_version_dct:
version_fixed = obo_year_version_dct[year]
else:
if year > 2019:
version_fixed = "4.1.0"
if version_fixed:
# Check if the corresponding obo file existed in obo folder
obo_root = os.path.dirname(__file__)
obo_file = os.path.join(
obo_root,
"obo",
"psi-ms{0}.obo".format("-" + version_fixed if version_fixed else ""),
)
if os.path.exists(obo_file) or os.path.exists(obo_file + ".gz"):
pass
else:
version_fixed = "1.1.0"
else:
version_fixed = "1.1.0"
return version_fixed
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.from_cache(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)
self.info["chromatogram_count"] = None
self.info["spectrum_count"] = None
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"
):
obo_in_mzml = element.attrib.get("version", "1.1.0")
self.info["obo_version"] = self._obo_version_validator(obo_in_mzml)
elif element.tag.endswith("}fileDescription"):
self.info["file_description"] = True
self.info["file_description_element"] = element
elif element.tag.endswith("}sampleList"):
self.info["sample_list"] = True
self.info["sample_list_element"] = element
elif element.tag.endswith("}referenceableParamGroupList"):
self.info["referenceable_param_group_list"] = True
self.info["referenceable_param_group_list_element"] = element
elif element.tag.endswith("}softwareList"):
self.info["software_list"] = True
self.info["software_list_element"] = element
elif element.tag.endswith("}instrumentConfigurationList"):
self.info["instrument_configuration_list"] = True
self.info["instrument_configuration_list_element"] = element
elif element.tag.endswith("}dataProcessingList"):
self.info["data_processing_list"] = True
self.info["data_processing_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:
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_element"] = element
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"]
def close(self):
self.info["file_object"].close()
if __name__ == "__main__":
print(__doc__)