def test_missed_essential(self):
# When not all essential parameters exist, should fail.
infile = self.unittest_dir + "missedEssentials"
with self.assertRaises(KeyError):
setting = Setting.create_setting_from_file(infile)
assembler = SoftwareAssembler(setting)
def test_min_setting(self):
infile = self.unittest_dir + "testControlFileMin"
setting = Setting.create_setting_from_file(infile)
assembler = SoftwareAssembler(setting)
expected = set(TestSoftwareAssembler.list_all_parameters)
self.assertEqual(expected, set(assembler.get_all_par().viewkeys()))
print assembler.get_all_par().values()
def test_some_optional(self):
infile = self.unittest_dir + "testControlFileOp1"
setting = Setting.create_setting_from_file(infile)
assembler = SoftwareAssembler(setting)
expected = set(TestSoftwareAssembler.list_all_parameters)
self.assertEqual(expected, set(assembler.get_all_par().viewkeys()))
self.assertEqual(run_genovo.DEFAULT_GENOVO_NO_ITER, assembler.get("genovo_num_iter"))
self.assertEqual("1e-10", assembler.get("blast_e_value"))
def test_create_setting_from_file_MINE_only(self):
# When not all essential parameters exist but no optional parameters exist, should pass.
file = self.data_dir + "testControlFileMINE"
setting = Setting.create_setting_from_file(file)
expected = {
"wdir" :"/someDir/subDir/workingDir",
"mine_pdir":"/someDir/subDir/MINE",
"mine_cv":"20",
"mine_infile":"mineInfile",
"csv_files":"out1.csv,out2.csv"
}
# self.assertEqual(setting.all_setting, expected)
self.assertEqual(expected, setting.all_setting)
def test_create_setting_from_file(self):
# When not all essential parameters exist but no optional parameters exist, should pass.
file = self.data_dir + "testControlFileOp1"
setting = Setting.create_setting_from_file(file)
expected = {"wdir" :"/someDir/subDir/workingDir",
"master_tag": "genovoInfile",
"genovo_infile": "genovoInfile",
"genovo_pdir": "/someDir/subDir/genevo",
"genovo_num_iter": "20",
"glimmer_pdir":"/someDir/subDir/glimmer",
"blast_e_value":"1e-10",
}
self.assertEqual(expected, setting.all_setting)
# When not all essential parameters exist, should fail.
file = self.data_dir + "missedEssentials"
with self.assertRaises(KeyError):
Setting.create_setting_from_file(file)
# When all essential parameters exist and all optional parameters exist, should pass.
file = self.data_dir + "allPass"
try:
setting = Setting.create_setting_from_file(file)
except KeyError:
self.fail("raise KeyError unexpectedly")
# When not all essential parameters exist and some optional parameters exist, should pass.
file = self.data_dir + "testControlFileOp1"
try:
setting = Setting.create_setting_from_file(file)
except KeyError:
self.fail("raise KeyError unexpectedly")
def create_from_args(cls, args):
setting = Setting.create_setting_from_file(args)
assembler = cls(setting, args.debug)
return assembler
