# -*- coding: utf-8 -*- # encoding: utf-8 """ Class to parse the obo file and set up the accessions library The OBO parser has been designed to convert MS:xxxxx tags to their appropriate names. A minimal set of MS accession is used in pymzML, but additional accessions can easily be queried. The obo translator is used internally to associate names with MS:xxxxxxx tags. The OboTranslator Class generates a dictionary and several lookup tables. e.g. :: >>> from pymzml.obo import OboTranslator as OT >>> translator = OT() >>> translator['MS:1000127'] 'centroid mass spectrum' >>> translator['positive scan'] {'is_a': 'MS:1000465 ! scan polarity', 'id': 'MS:1000130', 'def': '"Polarity of the scan is positive." [PSI:MS]', 'name': 'positive scan'} >>> translator['scan'] {'relationship': 'part_of MS:0000000 ! Proteomics Standards Initiative Mass Spectrometry Ontology', 'id': 'MS:1000441', 'def': '"Function or process of the mass spectrometer where it records a spectrum." [PSI:MS]', 'name': 'scan'} >>> translator['unit'] {'relationship': 'part_of MS:0000000 ! Proteomics Standards Initiative Mass Spectrometry Ontology', 'id': 'MS:1000460', 'def': '"Terms to describe units." [PSI:MS]', 'name': 'unit'} pymzML comes with the queryOBO.py script that can be used to interrogate the OBO file. Please refer to :ref:`example_scripts` for further usage information. :: $ ./example_scripts/queryOBO.py "scan time" MS:1000016 scan time "The time taken for an acquisition by scanning analyzers." [PSI:MS] Is a: MS:1000503 ! scan attribute $ :: $ ./example_scripts/queryOBO.py 1000016 MS:1000016 scan time "The time taken for an acquisition by scanning analyzers." [PSI:MS] MS:1000503 ! scan attribute $ """ # 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 sys import os import re import gzip import urllib class OboTranslator(object): """ Generates a mapping from MS:xxxxx to names and vice versa for a specific obo version Args: version (str): obo version """ def __init__(self, version=None): self.version = self.__normalize_version(version) self.all_dicts = [] self.id = {} self.name = {} self.definition = {} self.lookups = [self.id, self.name, self.definition] self.MS_tag_regex = re.compile(r"MS:[0-9]*") # Only parse the OBO when necessary, not upon object construction self.__obo_parsed = False def __setitem__(self, key, value): raise TypeError("OBO translator dictionaries only support assignment via .add") def __getitem__(self, key): if not self.__obo_parsed: self.parseOBO() for lookup in self.lookups: if key in lookup: if self.MS_tag_regex.match(key): try: return lookup[key]["name"] except: pass return lookup[key] return None @staticmethod def __normalize_version(version): """ Ensure that a version has 3 components, defaulting to .0 for the missing components. Args: version (str): The original version to modify. Returns: version (str): The version, normalized to ensure that it has 3 parts. """ if version is not None: parts = version.split(".") missing_parts = 3 - len(parts) if missing_parts > 0: version = ".".join(parts + ["0"] * missing_parts) return version def download_obo(self, version, obo_file): uri = f"https://raw.githubusercontent.com/pymzml/psi-ms-CV/v{self.version}/psi-ms.obo" urllib.request.urlretrieve(uri, obo_file) with open(obo_file, "rb") as fin, gzip.open(obo_file + ".gz", "wb") as fout: fout.writelines(fin.readlines()) os.remove(obo_file) return def parseOBO(self): self.__obo_parsed = True """ Locate and parse the OBO file in the OBO root directory. Note: cx_Freeze friendly. If using cx_Freeze, place the OBO folder at the location of sys.executable. """ # TODO: Try to get all the versions, even those without well-defined # version numbers, or get remote hosting of all of the versions # and only download one at will on demand. # Modify the root for cx_freeze if getattr(sys, "frozen", False): obo_root = os.path.dirname(sys.executable) else: obo_root = os.path.dirname(__file__) obo_file = os.path.join( obo_root, "obo", "psi-ms{0}.obo".format("-" + self.version if self.version else ""), ) if os.path.exists(obo_file): pass elif os.path.exists(obo_file + ".gz"): obo_file = obo_file + ".gz" else: self.download_obo(self.version, obo_file) obo_file += ".gz" with open(obo_file, "rb") as fin: # never rely on file extensions! first_two_bytes = fin.read(2) # check if file is gzipped by magic bytes if first_two_bytes == b"\x1f\x8b": open_func = gzip.open else: raise Exception( "Filename has .gz extension but is missing the gzip magic bytes.\n" "The file may be corrupted or not gzipped." ) with open_func(obo_file, "rt", encoding="utf-8") as obo: collections = {} collect = False for line in obo: if line.strip() in ("[Term]", ""): collect = True if not collections: continue self.add(collections) collections = {} else: if line.strip() != "" and collect is True: k = line.find(":") collections[line[:k]] = line[k + 1 :].strip() return def add(self, collection_dict): """ Add a new dict to the translator. Args: collection_dict (dict): python dict containing MS:xxxxxxx name mapping. """ if not self.__obo_parsed: self.parseOBO() self.all_dicts.append(collection_dict) if "id" in collection_dict.keys(): self.id[collection_dict["id"]] = self.all_dicts[-1] if "name" in collection_dict.keys(): self.name[collection_dict["name"]] = self.all_dicts[-1] if "def" in collection_dict.keys(): self.definition[collection_dict["def"]] = self.all_dicts[-1] return def checkOBO(self, idTag, name): """ Check if idTag equals name in currently used obo version. Args: idTag (str): MS accession tag name (str): trivial name of the accession Returns: boolean: True if idTag and name correspond, else False. """ if not self.__obo_parsed: self.parseOBO() if self.id[idTag]["name"] == name: return True else: return False if __name__ == "__main__": print(__doc__)