Python DialignCommandline.set_parameter 예제들

예제 #1

파일: test_Dialign_tool.py 프로젝트: zyha/biopython

 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))

예제 #2

파일: test_Dialign_tool.py 프로젝트: HuttonICS/biopython

 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))

예제 #3

파일: test_Dialign_tool.py 프로젝트: andyoberlin/biopython

 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))

예제 #4

 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))

예제 #5

파일: test_Dialign_tool.py 프로젝트: Mat-D/biopython

 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

예제 #6

파일: test_Dialign_tool.py 프로젝트: andyoberlin/biopython

 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))

예제 #7

파일: test_Dialign_tool.py 프로젝트: HuttonICS/biopython

 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"))

예제 #8

파일: test_Dialign_tool.py 프로젝트: zyha/biopython

 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"))

예제 #9

파일: test_Dialign_tool.py 프로젝트: Mat-D/biopython

 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

예제 #10

 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))