def test_Dialign_simple_with_options(self):
"""Simple round-trip through app with infile and options."""
cmdline = DialignCommandline(dialign_exe)
cmdline.set_parameter("input", self.infile1)
cmdline.set_parameter("-max_link", True)
cmdline.set_parameter("stars", 4)
self.assertEqual(str(cmdline), dialign_exe +
" -max_link -stars 4 Fasta/f002")
stdout, stderr = cmdline()
self.assertEqual(stderr, "")
self.assertEqual(stdout, "")
self.assertTrue(os.path.exists(self.outfile1))
def test_Dialign_simple_with_options(self):
"""Simple round-trip through app with infile and options."""
cmdline = DialignCommandline(dialign_exe)
cmdline.set_parameter("input", self.infile1)
cmdline.set_parameter("-max_link", True)
cmdline.set_parameter("stars", 4)
self.assertEqual(str(cmdline), dialign_exe +
" -max_link -stars 4 Fasta/f002")
stdout, stderr = cmdline()
self.assertEqual(stderr, "")
self.assertEqual(stdout, "")
self.assertTrue(os.path.exists(self.outfile1))
def test_Dialign_simple_with_options(self):
"""Simple round-trip through app with infile and options
"""
cmdline = DialignCommandline(dialign_exe)
cmdline.set_parameter("input", self.infile1)
cmdline.set_parameter("-max_link", True)
cmdline.set_parameter("stars", 4)
self.assertEqual(str(cmdline), dialign_exe + \
" -max_link -stars 4 Fasta/f002")
result, stdout, stderr = Application.generic_run(cmdline)
self.assertEqual(stderr.read(), "")
self.assertEqual(stdout.read(), "")
self.assertEqual(result.return_code, 0)
self.assert_(os.path.exists(self.outfile1))
self.assertEqual(str(result._cl), str(cmdline))
def test_Dialign_simple_with_options(self):
"""Simple round-trip through app with infile and options
"""
cmdline = DialignCommandline(dialign_exe)
cmdline.set_parameter("input", self.infile1)
cmdline.set_parameter("-max_link", True)
cmdline.set_parameter("stars", 4)
self.assertEqual(str(cmdline), dialign_exe + \
" -max_link -stars 4 Fasta/f002")
result, stdout, stderr = Application.generic_run(cmdline)
self.assertEqual(stderr.read(), "")
self.assertEqual(stdout.read(), "")
self.assertEqual(result.return_code, 0)
self.assert_(os.path.exists(self.outfile1))
self.assertEqual(str(result._cl), str(cmdline))
def test_Dialign_simple_with_options(self):
"""Simple round-trip through app with infile and options
"""
cmdline = DialignCommandline(dialign_exe)
cmdline.set_parameter("input", self.infile1)
cmdline.set_parameter("-max_link", True)
cmdline.set_parameter("stars", 4)
self.assertEqual(str(cmdline), dialign_exe + \
" -max_link -stars 4 Fasta/f002")
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.assertEqual(child.stderr.read(), "")
self.assertEqual(child.stdout.read(), "")
self.assert_(os.path.exists(self.outfile1))
del child
def test_Dialign_complex_command_line(self):
"""Round-trip through app with complex command line."""
cmdline = DialignCommandline(dialign_exe)
cmdline.set_parameter("input", self.infile1)
cmdline.set_parameter("-nt", True)
cmdline.set_parameter("-thr", 4)
cmdline.set_parameter("stars", 9)
cmdline.set_parameter("-ow", True)
cmdline.set_parameter("mask", True)
cmdline.set_parameter("-cs", True)
self.assertEqual(str(cmdline), dialign_exe + \
" -cs -mask -nt -ow -stars 9 -thr 4 Fasta/f002")
result, stdout, stderr = Application.generic_run(cmdline)
self.assertEqual(stderr.read(), "")
self.assertEqual(result.return_code, 0)
self.assert_(os.path.exists(self.outfile1))
self.assert_(stdout.read().startswith(" e_len = 633"))
self.assertEqual(str(result._cl), str(cmdline))
def test_Dialign_complex_command_line(self):
"""Round-trip through app with complex command line."""
cmdline = DialignCommandline(dialign_exe)
cmdline.set_parameter("input", self.infile1)
cmdline.set_parameter("-nt", True)
cmdline.set_parameter("-thr", 4)
cmdline.set_parameter("stars", 9)
cmdline.set_parameter("-ow", True)
cmdline.set_parameter("mask", True)
cmdline.set_parameter("-cs", True)
self.assertEqual(str(cmdline), dialign_exe +
" -cs -mask -nt -ow -stars 9 -thr 4 Fasta/f002")
stdout, stderr = cmdline()
self.assertEqual(stderr, "")
self.assertTrue(os.path.exists(self.outfile1))
self.assertTrue(stdout.startswith(" e_len = 633"))
def test_Dialign_complex_command_line(self):
"""Round-trip through app with complex command line."""
cmdline = DialignCommandline(dialign_exe)
cmdline.set_parameter("input", self.infile1)
cmdline.set_parameter("-nt", True)
cmdline.set_parameter("-thr", 4)
cmdline.set_parameter("stars", 9)
cmdline.set_parameter("-ow", True)
cmdline.set_parameter("mask", True)
cmdline.set_parameter("-cs", True)
self.assertEqual(str(cmdline), dialign_exe +
" -cs -mask -nt -ow -stars 9 -thr 4 Fasta/f002")
stdout, stderr = cmdline()
self.assertEqual(stderr, "")
self.assertTrue(os.path.exists(self.outfile1))
self.assertTrue(stdout.startswith(" e_len = 633"))
def test_Dialign_complex_command_line(self):
"""Round-trip through app with complex command line."""
cmdline = DialignCommandline(dialign_exe)
cmdline.set_parameter("input", self.infile1)
cmdline.set_parameter("-nt", True)
cmdline.set_parameter("-thr", 4)
cmdline.set_parameter("stars", 9)
cmdline.set_parameter("-ow", True)
cmdline.set_parameter("mask", True)
cmdline.set_parameter("-cs", True)
self.assertEqual(str(cmdline), dialign_exe + \
" -cs -mask -nt -ow -stars 9 -thr 4 Fasta/f002")
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.assertEqual(child.stderr.read(), "")
self.assert_(os.path.exists(self.outfile1))
self.assert_(child.stdout.read().startswith(" e_len = 633"))
del child
def test_Dialign_complex_command_line(self):
"""Round-trip through app with complex command line."""
cmdline = DialignCommandline(dialign_exe)
cmdline.set_parameter("input", self.infile1)
cmdline.set_parameter("-nt", True)
cmdline.set_parameter("-thr", 4)
cmdline.set_parameter("stars", 9)
cmdline.set_parameter("-ow", True)
cmdline.set_parameter("mask", True)
cmdline.set_parameter("-cs", True)
self.assertEqual(str(cmdline), dialign_exe + \
" -cs -mask -nt -ow -stars 9 -thr 4 Fasta/f002")
result, stdout, stderr = Application.generic_run(cmdline)
self.assertEqual(stderr.read(), "")
self.assertEqual(result.return_code, 0)
self.assert_(os.path.exists(self.outfile1))
self.assert_(stdout.read().startswith(" e_len = 633"))
self.assertEqual(str(result._cl), str(cmdline))