1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
|
#!/usr/bin/env python3.2
# -*- coding: utf-8 -*-
# encoding: utf-8
#
# pymzml
#
# Copyright (C) 2010-2013 T. Bald, J. Barth, M. Specht, C. Fufezan, H. Roest
#
# 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 unittest
import os
import pymzml
class TestRun(unittest.TestCase):
def setUp(self):
example_mzml_filename = os.path.join(
os.path.dirname(__file__),
'data',
'example.mzml',
)
self.example_mzml = open(example_mzml_filename)
def tearDown(self):
self.example_mzml.close()
def test_file_object(self):
run = pymzml.run.Reader('', file_object=self.example_mzml)
self.assertEqual(run.info['fileObject'], self.example_mzml)
def test_read_obo_version(self):
run = pymzml.run.Reader('', file_object=self.example_mzml)
self.assertEqual(run.info['obo_version'], '3.25.0')
def test_provided_obo_version(self):
run = pymzml.run.Reader('', file_object=self.example_mzml, obo_version='1.1.0')
self.assertEqual(run.info['obo_version'], '1.1.0')
def test_provided_bad_obo_version(self):
with self.assertRaises(Exception):
run = pymzml.run.Reader('', file_object=self.example_mzml, obo_version='sad')
def test_regex(self):
spectrumIndexPattern = pymzml.run.RegexPatterns.spectrumIndexPattern
simIndexPattern = pymzml.run.RegexPatterns.simIndexPattern
line1 = b'<offset idRef="controllerType=0 controllerNumber=1 scan=1">4363</offset>'
line2 = b'<offset idRef="S16004" nativeID="16004">236442042</offset>'
line3 = b'<offset idRef="SIM SIC 651.5">330223452</offset>\n'
match_spec = spectrumIndexPattern.search(line1)
self.assertTrue(match_spec)
self.assertEqual(match_spec.group('nativeID'), b"1")
self.assertEqual(match_spec.group('type'), b"scan=" )
self.assertEqual(match_spec.group('offset'), b"4363" )
match_spec = spectrumIndexPattern.search(line2)
self.assertTrue(match_spec)
self.assertEqual(match_spec.group('nativeID'), b"16004")
self.assertEqual(match_spec.group('type'), b'nativeID="')
self.assertEqual(match_spec.group('offset'), b"236442042")
match_sim = simIndexPattern.search(line3)
self.assertEqual(match_sim.group('nativeID'), b"SIM SIC 651.5")
self.assertEqual(match_sim.group('offset'), b"330223452")
if __name__ == '__main__':
unittest.main()
|
