def test_Probcons_complex_commandline(self): """Round-trip through app with complex command line and output file.""" cmdline = ProbconsCommandline(probcons_exe, pre=1) cmdline.set_parameter("input", "Fasta/fa01") cmdline.consistency = 4 cmdline.set_parameter("--iterative-refinement", 222) cmdline.set_parameter("a", True) cmdline.annot = self.annotation_outfile self.assertEqual(str(cmdline), probcons_exe + " -c 4 -ir 222 -pre 1 -annot Fasta/probcons_annot.out" " -a Fasta/fa01") stdout, stderr = cmdline() self.assertTrue(stderr.startswith("\nPROBCONS")) self.assertTrue(stdout.startswith(">AK1H_ECOLI/1-378"))
def test_Probcons_complex_commandline(self): """Round-trip through app with complex command line and output file.""" cmdline = ProbconsCommandline(probcons_exe, pre=1) cmdline.set_parameter("input", "Fasta/fa01") cmdline.consistency = 4 cmdline.set_parameter("--iterative-refinement", 222) cmdline.set_parameter("a", True) cmdline.annot = self.annotation_outfile self.assertEqual( str(cmdline), probcons_exe + " -c 4 -ir 222 -pre 1 -annot Fasta/probcons_annot.out" " -a Fasta/fa01") stdout, stderr = cmdline() self.assertTrue(stderr.startswith("\nPROBCONS")) self.assertTrue(stdout.startswith(">AK1H_ECOLI/1-378"))
def test_Probcons_complex_commandline(self): """Round-trip through app with complex command line and output file """ cmdline = ProbconsCommandline(probcons_exe, pre=1) cmdline.set_parameter("input", "Fasta/fa01") cmdline.consistency = 4 cmdline.set_parameter("--iterative-refinement", 222) cmdline.set_parameter("a", True) cmdline.annot = self.annotation_outfile self.assertEqual(str(cmdline), probcons_exe + " -c 4 -ir 222 -pre 1 -annot Fasta/probcons_annot.out " "-a Fasta/fa01") result, stdout, stderr = Application.generic_run(cmdline) self.assertEqual(str(cmdline), str(result._cl)) self.assertEquals(result.return_code, 0) self.assert_(stderr.read().startswith("\nPROBCONS")) self.assert_(stdout.read().startswith(">AK1H_ECOLI/1-378"))
def test_Probcons_complex_commandline(self): """Round-trip through app with complex command line and output file """ cmdline = ProbconsCommandline(probcons_exe, pre=1) cmdline.set_parameter("input", "Fasta/fa01") cmdline.consistency = 4 cmdline.set_parameter("--iterative-refinement", 222) cmdline.set_parameter("a", True) cmdline.annot = self.annotation_outfile self.assertEqual( str(cmdline), probcons_exe + " -c 4 -ir 222 -pre 1 -annot Fasta/probcons_annot.out " "-a Fasta/fa01") result, stdout, stderr = Application.generic_run(cmdline) self.assertEqual(str(cmdline), str(result._cl)) self.assertEquals(result.return_code, 0) self.assert_(stderr.read().startswith("\nPROBCONS")) self.assert_(stdout.read().startswith(">AK1H_ECOLI/1-378"))
def test_Probcons_complex_commandline(self): """Round-trip through app with complex command line and output file """ cmdline = ProbconsCommandline(probcons_exe, pre=1) cmdline.set_parameter("input", "Fasta/fa01") cmdline.consistency = 4 cmdline.set_parameter("--iterative-refinement", 222) cmdline.set_parameter("a", True) cmdline.annot = self.annotation_outfile self.assertEqual(str(cmdline), probcons_exe + " -c 4 -ir 222 -pre 1 -annot Fasta/probcons_annot.out " "-a Fasta/fa01") 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_(child.stderr.read().startswith("\nPROBCONS")) self.assert_(child.stdout.read().startswith(">AK1H_ECOLI/1-378")) del child