def testArgs(self):
"""
It must be possible to parse command line arguments to create a new
instance of FindParameters.
"""
parser = argparse.ArgumentParser()
FindParameters.addArgsToParser(parser)
args = parser.parse_args([
'--significanceMethod',
'Always',
'--significanceFraction',
'0.4',
'--binScoreMethod',
'MinHashesScore',
'--featureMatchScore',
'5',
'--featureMismatchScore',
'6',
'--weights',
'AlphaHelix 2',
'--deltaScale',
'0.2',
])
# Parsing must do the expected thing.
self.assertEqual('Always', args.significanceMethod)
self.assertEqual(0.4, args.significanceFraction)
self.assertEqual('MinHashesScore', args.binScoreMethod)
self.assertEqual(5, args.featureMatchScore)
self.assertEqual(6, args.featureMismatchScore)
self.assertEqual(0.2, args.deltaScale)
# We must be able to make an instance from the parsed args.
findParams = FindParameters.fromArgs(args)
self.assertEqual('Always', findParams.significanceMethod)
self.assertEqual(0.4, findParams.significanceFraction)
self.assertEqual('MinHashesScore', findParams.binScoreMethod)
self.assertEqual(5, findParams.featureMatchScore)
self.assertEqual(6, findParams.featureMismatchScore)
self.assertEqual(0.2, findParams.deltaScale)
help=('A test id prefix. Tests whose ids do not contain this pattern '
'will not be run. The pattern is case-sensitive.'))
FindParameters.addArgsToParser(parser)
DatabaseParameters.addArgsToParser(parser)
args = parser.parse_args()
# If no parameter sets were specified, use the ones on the command line.
if not args.parameterSets:
args.parameterSets = ['command-line']
if 'command-line' in args.parameterSets:
PARAMETER_SETS['command-line'] = {
'dbParams': DatabaseParameters.fromArgs(args),
'findParams': FindParameters.fromArgs(args),
}
if args.printParams:
for parameterSet in args.parameterSets:
print('Parameter set %r' % parameterSet, file=sys.stderr)
params = PARAMETER_SETS[parameterSet]
print(params['dbParams'].print_(margin=' '), file=sys.stderr)
print(params['findParams'].print_(margin=' '), file=sys.stderr)
# Make the command-line args available to the tests. There doesn't seem
# to be another way to pass information like this when using a unittest
# test suite.
light.performance.testArgs = args
suite = unittest.defaultTestLoader.discover(args.startDir,
for i, feature in enumerate(ALL_FEATURES):
print(ALL_FEATURES[i][0], '\t', ALL_FEATURES[i][1], '\t',
COLORS[i])
if args.params:
givenParams = []
for paramsStr in args.params:
paramsParser = argparse.ArgumentParser()
# Change '+' to ' ' to make it easy to specify finders that
# have a space in their names.
subArgs = [arg.replace('+', ' ') for arg in paramsStr.split()]
FindParameters.addArgsToParser(paramsParser)
DatabaseParameters.addArgsToParser(paramsParser)
paramArgs = paramsParser.parse_args(subArgs)
dbParams = DatabaseParameters.fromArgs(paramArgs)
findParams = FindParameters.fromArgs(paramArgs)
givenParams.append((dbParams, findParams))
if len(givenParams) < len(args.structureNames):
# We were given fewer parameter sets than structures. Re-use
# the final given parameters for structures that don't have a
# correspondign set of given parameters.
params = ichain(givenParams, repeat(givenParams[-1]))
else:
params = givenParams
else:
# The parameter settings for all structures will be the defaults.
params = zip(repeat(DatabaseParameters()), repeat(FindParameters()))
first = True