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comparison test_mqparam.py @ 4:dcd39bcc7481 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
author galaxyp
date Sat, 11 Apr 2020 11:49:19 -0400
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children 37d669de2828
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3:175e062b6a17 4:dcd39bcc7481
1 """Tests for mqparam class. If testing a new MaxQuant version,
2 create a new parameter file using '<MAXQUANT_CMD> -c ./mqpar.xml'
3 """
4
5 import pytest
6 import xml.etree.ElementTree as ET
7 from mqparam import MQParam, ParamGroup
8
9 TEMPLATE_PATH = './test-data/template.xml'
10
11
12 def mk_pg_root():
13 mqpar = ET.parse(TEMPLATE_PATH).getroot()
14 return mqpar.find('.parameterGroups/parameterGroup')
15
16
17 class TestParamGroup:
18 def test_list_param(self):
19 t = ParamGroup(mk_pg_root())
20 t.set_list_param('enzymes', ('test 1', 'test 2'))
21 assert len(t._root.find('enzymes')) == 2
22
23 t.set_list_param('variableModifications', ('Oxidation (M)', ))
24 assert t._root.find('variableModifications')[0].text == 'Oxidation (M)'
25
26 with pytest.raises(ValueError):
27 t.set_list_param('foo', [])
28
29 def test_simple_params(self):
30 t = ParamGroup(mk_pg_root())
31 t.set_simple_param('fastLfq', False)
32 assert t._root.find('.fastLfq').text == 'False'
33
34 with pytest.raises(ValueError):
35 t.set_simple_param('foo', 2)
36
37 def test_silac(self):
38 t = ParamGroup(mk_pg_root())
39 t.set_silac(None, None, ('Arg10', 'Lys4'))
40 assert t._root.find('.maxLabeledAa').text == '2'
41 assert t._root.find('.multiplicity').text == '2'
42 assert t._root.find('.labelMods')[1].text == 'Arg10;Lys4'
43 assert t._root.find('.labelMods')[0].text == ''
44
45 def test_isobaric_label(self):
46 t = ParamGroup(mk_pg_root())
47 t.set_isobaric_label('iTRAQ4plex-Lys114', 'iTRAQ4plex-Nter114', 0.3, 1, 1.2, 0, True)
48
49 assert len(t._root.find('isobaricLabels')) == 1
50 assert len(t._root.find('isobaricLabels')[0]) == 7
51
52 t.set_isobaric_label('iTRAQ4plex-Lys115', 'iTRAQ4plex-Nter115', 0.3, 1.0, 1.2, 0, True)
53
54 assert len(t._root.find('isobaricLabels')) == 2
55
56 tag_list = [el.tag for el in t._root.find('isobaricLabels')[1]]
57 assert tag_list == ['internalLabel', 'terminalLabel', 'correctionFactorM2',
58 'correctionFactorM1', 'correctionFactorP1', 'correctionFactorP2',
59 'tmtLike']
60
61 text_list = [el.text for el in t._root.find('isobaricLabels')[1]]
62 assert text_list == ['iTRAQ4plex-Lys115', 'iTRAQ4plex-Nter115',
63 '0.3', '1', '1.2', '0', 'True']
64
65
66 class TestMQParam:
67
68 def test_version(self):
69 t = MQParam(TEMPLATE_PATH)
70 assert t._root.find('maxQuantVersion').text == '1.6.10.43'
71
72 def test_validity_check(self):
73 design = {'Name': ['Test1', 'Test2'],
74 'Fraction': ['2', 32767],
75 'PTM': ['False', 'False'],
76 'Experiment': ['e1', 'e1'],
77 'paramGroup': [0, 0]}
78
79 assert MQParam._check_validity(design, 2) is None
80
81 design['Name'][0] = None
82 with pytest.raises(Exception):
83 MQParam._check_validity(design, 2)
84 design['Name'][0] = 'Test1'
85
86 design['Experiment'][0] = ''
87 with pytest.raises(ValueError):
88 MQParam._check_validity(design, 2)
89 design['Experiment'][0] = 'e1'
90
91 design['Fraction'][0] = 'foo'
92 with pytest.raises(ValueError):
93 MQParam._check_validity(design, 2)
94
95 def test_exp_design(self, tmpdir):
96 # default experimental design when None is specified
97 t = MQParam(TEMPLATE_PATH)
98 design = t._make_exp_design((0, 0), ('./Test1.mzXML', './Test2.mzXML'))
99 assert design['Name'] == ('./Test1.mzXML', './Test2.mzXML')
100 assert design['Fraction'] == ('32767', '32767')
101
102 # valid experimental design
103 e1 = tmpdir / "e1.txt"
104 e1.write('Name\tExperiment\tFraction\tPTM\nTest1\te1\nTest2\te1\t\tfalse')
105 t.exp_design = str(e1)
106 design = t._make_exp_design((0, 0), ('./Test1.mzXML', './Test2.mzXML'))
107
108 assert design == {'Name': ['./Test1.mzXML', './Test2.mzXML'],
109 'Experiment': ['e1', 'e1'],
110 'Fraction': ['32767', '32767'],
111 'PTM': ['False', 'false'],
112 'paramGroup': (0, 0)}
113
114 # invalid header
115 e2 = tmpdir / "e2.txt"
116 e2.write('Name\tExperiment\tFraction\tPTM\tparamGroup\n')
117 t.exp_design = str(e2)
118
119 with pytest.raises(Exception):
120 design = t._make_exp_design(('./Test2.mzXML',), (0,))
121
122 def test_add_infiles(self):
123 t = MQParam(TEMPLATE_PATH)
124 t.add_infiles([('/path/Test1.mzXML', '/path/Test2.mzXML'),
125 ('/path/Test3.mzXML', '/path/Test4.mzXML')])
126
127 assert [e.text for e in t._root.find('filePaths')] == ['/path/Test1.mzXML',
128 '/path/Test2.mzXML',
129 '/path/Test3.mzXML',
130 '/path/Test4.mzXML']
131
132 assert [e.text for e in t._root.find('paramGroupIndices')] == ['0', '0', '1', '1']
133 assert t[1]
134
135 def test_translate(self):
136 t = MQParam(TEMPLATE_PATH)
137 t.add_infiles([('/posix/path/to/Test1.mzXML',
138 '/posix/path/to/Test2.mzXML'),
139 ('/path/dummy.mzXML',)]) # mqparam is not designed for windows
140
141 t._root.find('filePaths')[2].text = r'D:\Windows\Path\Test3.mzXML'
142
143 t.translate(('/galaxy/working/Test3.mzXML',
144 '/galaxy/working/Test1.mzXML',
145 '/galaxy/working/Test2.mzXML',
146 '/galaxy/working/Test4.mzXML'))
147
148 assert [e.text for e in t._root.find('filePaths')] == ['/galaxy/working/Test1.mzXML',
149 '/galaxy/working/Test2.mzXML',
150 '/galaxy/working/Test3.mzXML']
151
152 def test_fasta_files(self):
153 t = MQParam(TEMPLATE_PATH)
154 t.add_fasta_files(('test1', 'test2'),
155 parse_rules={'identifierParseRule': r'>([^\s]*)'})
156 assert len(t._root.find('fastaFiles')) == 2
157 assert t._root.find('fastaFiles')[0].find("fastaFilePath").text == 'test1'
158 assert t._root.find('fastaFiles')[0].find("identifierParseRule").text == '>([^\\s]*)'
159
160 def test_simple_param(self):
161 t = MQParam(TEMPLATE_PATH)
162 t.set_simple_param('minUniquePeptides', 4)
163 assert t._root.find('.minUniquePeptides').text == '4'
164
165 with pytest.raises(ValueError):
166 t.set_simple_param('foo', 3)
167
168 def test_from_yaml(self, tmpdir):
169 conf1 = tmpdir / "conf1.yml"
170 conf1.write(r"""
171 numThreads: 4
172 fastaFiles: [test1.fasta,test2.fasta]
173 parseRules:
174 identifierParseRule: ^>.*\|(.*)\|.*$
175 paramGroups:
176 - files: [Test1.mzXML,Test2.mzXML] # paramGroup 0
177 fixedModifications: [mod1,mod2]
178 lfqMode: 1
179 - files: [Test3.mzXML,Test4.mzXML] # paramGroup 1
180 labelMods:
181 - []
182 - []
183 - [label1,label2]
184 """)
185
186 t = MQParam(TEMPLATE_PATH)
187 t._from_yaml(str(conf1))
188 assert t['numThreads'] == '4'
189 assert [child.text for child in t[1]._root.find('labelMods')] == ['', 'label1;label2']
190
191 def test_write(self, tmpdir):
192 yaml_conf = tmpdir / "conf.yml"
193 yaml_conf.write(r"""
194 numThreads: 4
195 fastaFiles: [test1.fasta,test2.fasta]
196 parseRules:
197 identifierParseRule: ^>.*\|(.*)\|.*$
198 paramGroups:
199 - files: [Test1.mzXML,Test2.mzXML] # paramGroup 0
200 fixedModifications: [mod1]
201 variableModifications: [mod2,mod3]
202 maxMissedCleavages: 1
203 """)
204 mqpar_out = tmpdir / "mqpar.xml"
205
206 t = MQParam(TEMPLATE_PATH, yaml=str(yaml_conf))
207 t.write(str(mqpar_out))
208
209 test = ET.parse(str(mqpar_out)).getroot()
210 assert test.find('numThreads').text == '4'
211 assert test.find('fastaFiles')[1].find('identifierParseRule').text == '^>.*\\|(.*)\\|.*$'
212 assert [el.text for el in test.find('parameterGroups')[0].find('variableModifications')] == ['mod2', 'mod3']