def test_Prank_complex_command_line(self): """Round-trip with complex command line.""" cmdline = PrankCommandline(prank_exe) cmdline.set_parameter("d", self.infile1) cmdline.set_parameter("-noxml", True) cmdline.set_parameter("notree", True) cmdline.set_parameter("-gaprate", 0.321) cmdline.set_parameter("gapext", 0.6) cmdline.set_parameter("-dots", 1) # i.e. True # Try using a property: cmdline.kappa = 3 cmdline.skipins = True cmdline.set_parameter("-once", True) cmdline.realbranches = True self.assertEqual( str(cmdline), prank_exe + " -d=Fasta/fa01 -noxml" + " -notree -dots -gaprate=0.321 -gapext=0.6 -kappa=3" + " -once -skipins -realbranches", ) self.assertEqual(str(eval(repr(cmdline))), str(cmdline)) child = subprocess.Popen( str(cmdline), stdout=subprocess.PIPE, stderr=subprocess.PIPE, shell=(sys.platform != "win32") ) return_code = child.wait() self.assertEqual(return_code, 0) self.assert_("Total time" in child.stdout.read()) self.assertEqual(child.stderr.read(), "") del child
def test_Prank_complex_command_line(self): """Round-trip with complex command line.""" cmdline = PrankCommandline(prank_exe) cmdline.set_parameter("d", self.infile1) cmdline.set_parameter("-gaprate", 0.321) cmdline.set_parameter("gapext", 0.6) cmdline.set_parameter("-dots", 1) # i.e. True # Try using a property: cmdline.kappa = 3 cmdline.skipins = True cmdline.set_parameter("-once", True) cmdline.realbranches = True self.assertEqual(str(cmdline), _escape_filename(prank_exe) + " -d=Fasta/fa01" + " -dots -gaprate=0.321 -gapext=0.6 -kappa=3" + " -once -skipins -realbranches") self.assertEqual(str(eval(repr(cmdline))), str(cmdline)) stdout, stderr = cmdline() self.assertTrue("Total time" in stdout, stdout)
def test_Prank_complex_command_line(self): """Round-trip with complex command line.""" cmdline = PrankCommandline(prank_exe) cmdline.set_parameter("d", self.infile1) cmdline.set_parameter("-gaprate", 0.321) cmdline.set_parameter("gapext", 0.6) cmdline.set_parameter("-dots", 1) # i.e. True #Try using a property: cmdline.kappa = 3 cmdline.skipins = True cmdline.set_parameter("-once", True) cmdline.realbranches = True self.assertEqual(str(cmdline), _escape_filename(prank_exe) + " -d=Fasta/fa01" + " -dots -gaprate=0.321 -gapext=0.6 -kappa=3" + " -once -skipins -realbranches") self.assertEqual(str(eval(repr(cmdline))), str(cmdline)) stdout, stderr = cmdline() self.assertTrue("Total time" in stdout, stdout)
def test_Prank_complex_command_line(self): """Round-trip with complex command line.""" cmdline = PrankCommandline(prank_exe) cmdline.set_parameter("d", self.infile1) cmdline.set_parameter("-noxml", True) cmdline.set_parameter("notree", True) cmdline.set_parameter("-gaprate", 0.321) cmdline.set_parameter("gapext", 0.6) cmdline.set_parameter("-dots", 1) #i.e. True #Try using a property: cmdline.kappa = 3 cmdline.skipins = True cmdline.set_parameter("-once", True) cmdline.realbranches = True self.assertEqual(str(cmdline), prank_exe + " -d=Fasta/fa01 -noxml" + \ " -notree -dots -gaprate=0.321 -gapext=0.6 -kappa=3" + \ " -once -skipins -realbranches") self.assertEqual(str(eval(repr(cmdline))), str(cmdline)) result, stdout, stderr = Application.generic_run(cmdline) self.assertEqual(result.return_code, 0) self.assert_("Total time" in stdout.read()) self.assertEqual(stderr.read(), "") self.assertEqual(str(result._cl), str(cmdline))