diff test_mqparam.py @ 4:dcd39bcc7481 draft

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test_mqparam.py	Sat Apr 11 11:49:19 2020 -0400
@@ -0,0 +1,212 @@
+"""Tests for mqparam class. If testing a new MaxQuant version,
+create a new parameter file using '<MAXQUANT_CMD> -c ./mqpar.xml'
+"""
+
+import pytest
+import xml.etree.ElementTree as ET
+from mqparam import MQParam, ParamGroup
+
+TEMPLATE_PATH = './test-data/template.xml'
+
+
+def mk_pg_root():
+    mqpar = ET.parse(TEMPLATE_PATH).getroot()
+    return mqpar.find('.parameterGroups/parameterGroup')
+
+
+class TestParamGroup:
+    def test_list_param(self):
+        t = ParamGroup(mk_pg_root())
+        t.set_list_param('enzymes', ('test 1', 'test 2'))
+        assert len(t._root.find('enzymes')) == 2
+
+        t.set_list_param('variableModifications', ('Oxidation (M)', ))
+        assert t._root.find('variableModifications')[0].text == 'Oxidation (M)'
+
+        with pytest.raises(ValueError):
+            t.set_list_param('foo', [])
+
+    def test_simple_params(self):
+        t = ParamGroup(mk_pg_root())
+        t.set_simple_param('fastLfq', False)
+        assert t._root.find('.fastLfq').text == 'False'
+
+        with pytest.raises(ValueError):
+            t.set_simple_param('foo', 2)
+
+    def test_silac(self):
+        t = ParamGroup(mk_pg_root())
+        t.set_silac(None, None, ('Arg10', 'Lys4'))
+        assert t._root.find('.maxLabeledAa').text == '2'
+        assert t._root.find('.multiplicity').text == '2'
+        assert t._root.find('.labelMods')[1].text == 'Arg10;Lys4'
+        assert t._root.find('.labelMods')[0].text == ''
+
+    def test_isobaric_label(self):
+        t = ParamGroup(mk_pg_root())
+        t.set_isobaric_label('iTRAQ4plex-Lys114', 'iTRAQ4plex-Nter114', 0.3, 1, 1.2, 0, True)
+
+        assert len(t._root.find('isobaricLabels')) == 1
+        assert len(t._root.find('isobaricLabels')[0]) == 7
+
+        t.set_isobaric_label('iTRAQ4plex-Lys115', 'iTRAQ4plex-Nter115', 0.3, 1.0, 1.2, 0, True)
+
+        assert len(t._root.find('isobaricLabels')) == 2
+
+        tag_list = [el.tag for el in t._root.find('isobaricLabels')[1]]
+        assert tag_list == ['internalLabel', 'terminalLabel', 'correctionFactorM2',
+                            'correctionFactorM1', 'correctionFactorP1', 'correctionFactorP2',
+                            'tmtLike']
+
+        text_list = [el.text for el in t._root.find('isobaricLabels')[1]]
+        assert text_list == ['iTRAQ4plex-Lys115', 'iTRAQ4plex-Nter115',
+                             '0.3', '1', '1.2', '0', 'True']
+
+
+class TestMQParam:
+
+    def test_version(self):
+        t = MQParam(TEMPLATE_PATH)
+        assert t._root.find('maxQuantVersion').text == '1.6.10.43'
+
+    def test_validity_check(self):
+        design = {'Name': ['Test1', 'Test2'],
+                  'Fraction': ['2', 32767],
+                  'PTM': ['False', 'False'],
+                  'Experiment': ['e1', 'e1'],
+                  'paramGroup': [0, 0]}
+
+        assert MQParam._check_validity(design, 2) is None
+
+        design['Name'][0] = None
+        with pytest.raises(Exception):
+            MQParam._check_validity(design, 2)
+        design['Name'][0] = 'Test1'
+
+        design['Experiment'][0] = ''
+        with pytest.raises(ValueError):
+            MQParam._check_validity(design, 2)
+        design['Experiment'][0] = 'e1'
+
+        design['Fraction'][0] = 'foo'
+        with pytest.raises(ValueError):
+            MQParam._check_validity(design, 2)
+
+    def test_exp_design(self, tmpdir):
+        # default experimental design when None is specified
+        t = MQParam(TEMPLATE_PATH)
+        design = t._make_exp_design((0, 0), ('./Test1.mzXML', './Test2.mzXML'))
+        assert design['Name'] == ('./Test1.mzXML', './Test2.mzXML')
+        assert design['Fraction'] == ('32767', '32767')
+
+        # valid experimental design
+        e1 = tmpdir / "e1.txt"
+        e1.write('Name\tExperiment\tFraction\tPTM\nTest1\te1\nTest2\te1\t\tfalse')
+        t.exp_design = str(e1)
+        design = t._make_exp_design((0, 0), ('./Test1.mzXML', './Test2.mzXML'))
+
+        assert design == {'Name': ['./Test1.mzXML', './Test2.mzXML'],
+                          'Experiment': ['e1', 'e1'],
+                          'Fraction': ['32767', '32767'],
+                          'PTM': ['False', 'false'],
+                          'paramGroup': (0, 0)}
+
+        # invalid header
+        e2 = tmpdir / "e2.txt"
+        e2.write('Name\tExperiment\tFraction\tPTM\tparamGroup\n')
+        t.exp_design = str(e2)
+
+        with pytest.raises(Exception):
+            design = t._make_exp_design(('./Test2.mzXML',), (0,))
+
+    def test_add_infiles(self):
+        t = MQParam(TEMPLATE_PATH)
+        t.add_infiles([('/path/Test1.mzXML', '/path/Test2.mzXML'),
+                       ('/path/Test3.mzXML', '/path/Test4.mzXML')])
+
+        assert [e.text for e in t._root.find('filePaths')] == ['/path/Test1.mzXML',
+                                                               '/path/Test2.mzXML',
+                                                               '/path/Test3.mzXML',
+                                                               '/path/Test4.mzXML']
+
+        assert [e.text for e in t._root.find('paramGroupIndices')] == ['0', '0', '1', '1']
+        assert t[1]
+
+    def test_translate(self):
+        t = MQParam(TEMPLATE_PATH)
+        t.add_infiles([('/posix/path/to/Test1.mzXML',
+                        '/posix/path/to/Test2.mzXML'),
+                       ('/path/dummy.mzXML',)])  # mqparam is not designed for windows
+
+        t._root.find('filePaths')[2].text = r'D:\Windows\Path\Test3.mzXML'
+
+        t.translate(('/galaxy/working/Test3.mzXML',
+                     '/galaxy/working/Test1.mzXML',
+                     '/galaxy/working/Test2.mzXML',
+                     '/galaxy/working/Test4.mzXML'))
+
+        assert [e.text for e in t._root.find('filePaths')] == ['/galaxy/working/Test1.mzXML',
+                                                               '/galaxy/working/Test2.mzXML',
+                                                               '/galaxy/working/Test3.mzXML']
+
+    def test_fasta_files(self):
+        t = MQParam(TEMPLATE_PATH)
+        t.add_fasta_files(('test1', 'test2'),
+                          parse_rules={'identifierParseRule': r'>([^\s]*)'})
+        assert len(t._root.find('fastaFiles')) == 2
+        assert t._root.find('fastaFiles')[0].find("fastaFilePath").text == 'test1'
+        assert t._root.find('fastaFiles')[0].find("identifierParseRule").text == '>([^\\s]*)'
+
+    def test_simple_param(self):
+        t = MQParam(TEMPLATE_PATH)
+        t.set_simple_param('minUniquePeptides', 4)
+        assert t._root.find('.minUniquePeptides').text == '4'
+
+        with pytest.raises(ValueError):
+            t.set_simple_param('foo', 3)
+
+    def test_from_yaml(self, tmpdir):
+        conf1 = tmpdir / "conf1.yml"
+        conf1.write(r"""
+        numThreads: 4
+        fastaFiles: [test1.fasta,test2.fasta]
+        parseRules:
+          identifierParseRule: ^>.*\|(.*)\|.*$
+        paramGroups:
+          - files: [Test1.mzXML,Test2.mzXML] # paramGroup 0
+            fixedModifications: [mod1,mod2]
+            lfqMode: 1
+          - files: [Test3.mzXML,Test4.mzXML] # paramGroup 1
+            labelMods:
+              - []
+              - []
+              - [label1,label2]
+        """)
+
+        t = MQParam(TEMPLATE_PATH)
+        t._from_yaml(str(conf1))
+        assert t['numThreads'] == '4'
+        assert [child.text for child in t[1]._root.find('labelMods')] == ['', 'label1;label2']
+
+    def test_write(self, tmpdir):
+        yaml_conf = tmpdir / "conf.yml"
+        yaml_conf.write(r"""
+        numThreads: 4
+        fastaFiles: [test1.fasta,test2.fasta]
+        parseRules:
+          identifierParseRule: ^>.*\|(.*)\|.*$
+        paramGroups:
+          - files: [Test1.mzXML,Test2.mzXML] # paramGroup 0
+            fixedModifications: [mod1]
+            variableModifications: [mod2,mod3]
+            maxMissedCleavages: 1
+        """)
+        mqpar_out = tmpdir / "mqpar.xml"
+
+        t = MQParam(TEMPLATE_PATH, yaml=str(yaml_conf))
+        t.write(str(mqpar_out))
+
+        test = ET.parse(str(mqpar_out)).getroot()
+        assert test.find('numThreads').text == '4'
+        assert test.find('fastaFiles')[1].find('identifierParseRule').text == '^>.*\\|(.*)\\|.*$'
+        assert [el.text for el in test.find('parameterGroups')[0].find('variableModifications')] == ['mod2', 'mod3']