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']
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')