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_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_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'
]
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)