/usr/lib/python2.7/dist-packages/pymzml/obo.py is in python-pymzml 0.7.6-dfsg-4.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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# encoding: utf-8
"""
Class to parse the obo file and set up the accessions library
The OBO parse 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 added, using the extraAccession parameter during
:py:class:`run.Reader` initialization.
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()
>>> len(translator.id.keys()) # Number of parsed entries
737
>>> 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.
::
$ ./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
$
"""
# pymzml
#
# Copyright (C) 2010-2011 T. Bald, J. Barth, 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/>.
from __future__ import print_function
import sys
import os
import pymzml
class oboTranslator(object):
def __init__(self, version=None):
self.version = version
self.allDicts = []
self.id = {}
self.name = {}
self.definition = {}
self.lookups = [self.id, self.name, self.definition]
# replace_by could be another one ...
self._obo_parsed = False
# self.parseOBO()
def __setitem__(self, key, value):
return
def __getitem__(self, key):
if self._obo_parsed is False:
self.parseOBO()
self._obo_parsed = True
for lookup in self.lookups:
if key in lookup:
if key[:2] == 'MS':
try:
return lookup[key]['name']
except:
pass
return lookup[key]
return None
def parseOBO(self):
"""
Parse the obo file in folder obo/
(would be great to have all versions. Must convience PSI to add version
number at the file .. :))
Note:
Is cx_freeze friendly! Place obo folder at the location
of sys.executable.
"""
is_frozen = getattr(sys, 'frozen', False)
if is_frozen:
root_for_obo = os.path.dirname(sys.executable)
else:
root_for_obo = os.path.dirname(__file__)
oboFile = os.path.normpath(
os.path.join(
root_for_obo,
'obo',
"psi-ms{0}.obo".format(
'-' + self.version if self.version else ''
)
)
)
# oboFile = os.path.normpath('{0}/obo/psi-ms{1}.obo'.format(
# os.path.dirname(pymzml.obo.__file__),
# '-' + self.version if self.version else ''
# ))
if os.path.exists(oboFile):
with open(oboFile) 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()
else:
print(
"No obo file version {0} (psi-ms-{0}.obo) found.".format(
self.version
),
file=sys.stderr,
)
raise Exception("Could not find obo file @ {0}".format( oboFile ))
return
def add(self, collection_dict):
self.allDicts.append(collection_dict)
if 'id' in collection_dict.keys():
self.id[collection_dict['id']] = self.allDicts[-1]
if 'name' in collection_dict.keys():
self.name[collection_dict['name']] = self.allDicts[-1]
if 'def' in collection_dict.keys():
self.definition[collection_dict['def']] = self.allDicts[-1]
return
def checkOBO(self, idTag, name):
if self.id[idTag]['name'] == name:
return True
else:
return False
if __name__ == '__main__':
print(__doc__)
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