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']
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_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_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_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_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_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)
parser.add_argument('--version', '-v', help="""A version number. Raises exception if it doesn't
match the MaxQuant version of the template. For usage in the Galaxy tool.""")
# in case numThreads is a environment variable, otherwise it can be specified in the yaml file as well
parser.add_argument('--num_threads', '-t', help="Number of threads to specify in mqpar.")
args = parser.parse_args()
# edit file names, working dir is unknown at the time of galaxy tool configfile creation
if args.yaml:
with open(args.yaml) as f:
conf_dict = yaml.safe_load(f.read())
for n, pg in enumerate(conf_dict['paramGroups']):
for num, fl in enumerate(pg['files']):
if not fl.startswith('/'):
conf_dict['paramGroups'][n]['files'][num] = os.path.join(os.getcwd(), fl)
with open('yaml', 'w') as f:
yaml.safe_dump(conf_dict, stream=f)
args.yaml = 'yaml'
kwargs = dict(yaml=args.yaml)
if args.substitution_rx:
kwargs['substitution_rx'] = args.substitution_rx
mqparam = MQParam(args.template, args.exp_design, **kwargs)
if args.version and mqparam.version != args.version:
raise Exception('mqpar version is ' + mqparam.version + '. Tool uses version {}.'.format(args.version))
mqparam.set_simple_param('numThreads', args.num_threads)
mqparam.write(args.mqpar_out if args.mqpar_out else 'mqpar.xml')
from mqparam import MQParam
parser = argparse.ArgumentParser()
arguments = ('--infiles',
'--version',
'--num_threads',
'--substitution_rx',
'--fasta_files',
'--description_parse_rule',
'--identifier_parse_rule',
'mqpar')
for arg in arguments:
parser.add_argument(arg)
args = parser.parse_args()
mqpar_out = os.path.join(os.getcwd(), 'mqpar.xml')
infiles = [os.path.join(os.getcwd(), f) for f in args.infiles.split(',')]
mqparam = MQParam(args.mqpar, None, substitution_rx=args.substitution_rx)
if mqparam.version != args.version:
raise Exception('mqpar version is ' + mqparam.version + '. Tool uses version {}.'.format(args.version))
mqparam.translate(infiles)
mqparam.add_fasta_files(args.fasta_files.split(','),
{'identifierParseRule': args.identifier_parse_rule,
'descriptionParseRule': args.description_parse_rule})
mqparam.set_simple_param('numThreads', args.num_threads)
mqparam.write('mqpar.xml')
def test_version(self):
t = MQParam(TEMPLATE_PATH)
assert t._root.find('maxQuantVersion').text == '1.6.10.43'