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
