From c130fda4300b9420a3a0c2a34ffdd12b8e9d708b Mon Sep 17 00:00:00 2001 From: Brandon Invergo Date: Wed, 22 Feb 2012 12:51:33 +0100 Subject: [PATCH] update test_PAML_tools to accomodate new test resource directory structure --- Tests/test_PAML_tools.py | 56 +++++++++++++++++----------------------- 1 file changed, 24 insertions(+), 32 deletions(-) diff --git a/Tests/test_PAML_tools.py b/Tests/test_PAML_tools.py index 0c155d80dff..336156f9279 100644 --- a/Tests/test_PAML_tools.py +++ b/Tests/test_PAML_tools.py @@ -28,9 +28,10 @@ def which(program): #do that, we can check for it in Program Files. likely_dirs = ["", #Current dir prog_files, - os.path.join(prog_files,"paml41"), - os.path.join(prog_files,"paml43"), - os.path.join(prog_files,"paml44")] + sys.path + os.path.join(prog_files, "paml41"), + os.path.join(prog_files, "paml43"), + os.path.join(prog_files, "paml44"), + os.path.join(prog_files, "paml45")] + sys.path os_path.extend(likely_dirs) for path in os.environ["PATH"].split(os.pathsep): exe_file = os.path.join(path, program) @@ -70,22 +71,19 @@ def __del__(self): class CodemlTest(Common): "Tests for PAML tool codeml.""" - align_file = os.path.join("PAML", "alignment.phylip") - tree_file = os.path.join("PAML", "species.tree") - out_file = os.path.join("PAML", "temp.out") - working_dir = os.path.join("PAML", "codeml_test") - ctl_file = os.path.join("PAML", "codeml.ctl") - del_files = [out_file, "2NG.dN", "2NG.dS", "2NG.t", "codeml.ctl", - "lnf", "rst", "rst1", "rub"] - def setUp(self): - self.cml = codeml.Codeml(working_dir=self.working_dir) + self.cml = codeml.Codeml() def testCodemlBinary(self): """Test that the codeml binary runs and generates correct output and is the correct version. """ - self.cml.read_ctl_file(self.ctl_file) + ctl_file = os.path.join("PAML", "Control_files", "codeml", "codeml.ctl") + self.cml.read_ctl_file(ctl_file) + self.cml.alignment = os.path.join("PAML", "Alignments", "alignment.phylip") + self.cml.tree = os.path.join("PAML", "Trees", "species.tree") + self.cml.out_file = os.path.join("PAML", "temp.out") + self.cml.working_dir = os.path.join("PAML", "codeml_test") results = self.cml.run() self.assertTrue(results["version"] > "4.0") self.assertTrue("NSsites" in results) @@ -96,22 +94,19 @@ def testCodemlBinary(self): class BasemlTest(Common): """Tests for PAML tool baseml.""" - align_file = os.path.join("PAML", "alignment.phylip") - tree_file = os.path.join("PAML", "species.tree") - out_file = os.path.join("PAML", "temp.out") - working_dir = os.path.join("PAML", "baseml_test") - ctl_file = os.path.join("PAML", "baseml.ctl") - del_files = [out_file, "2base.t", "in.basemlg", "baseml.ctl", - "lnf", "rates", "rst", "rst1", "rub", "temp.out"] - def setUp(self): - self.bml = baseml.Baseml(working_dir=self.working_dir) + self.bml = baseml.Baseml() def testBasemlBinary(self): """Test that the baseml binary runs and generates correct output and is the correct version. """ - self.bml.read_ctl_file(self.ctl_file) + ctl_file = os.path.join("PAML", "Control_files", "baseml", "baseml.ctl") + self.bml.read_ctl_file(ctl_file) + self.bml.alignment = os.path.join("PAML", "Alignments", "alignment.phylip") + self.bml.tree = os.path.join("PAML", "Trees", "species.tree") + self.bml.out_file = os.path.join("PAML", "temp.out") + self.bml.working_dir = os.path.join("PAML", "baseml_test") results = self.bml.run() self.assertTrue(results["version"] > "4.0") self.assertTrue("parameters" in results) @@ -121,21 +116,18 @@ def testBasemlBinary(self): class Yn00Test(Common): """Tests for PAML tool yn00.""" - align_file = os.path.join("PAML", "alignment.phylip") - out_file = os.path.join("PAML", "temp.out") - working_dir = os.path.join("PAML", "yn00_test") - ctl_file = os.path.join("PAML", "yn00.ctl") - del_files = [out_file, "2YN.dN", "2YN.dS", "2YN.t", "yn00.ctl", - "rst", "rst1", "rub"] - def setUp(self): - self.yn = yn00.Yn00(working_dir=self.working_dir) + self.yn = yn00.Yn00() def testYn00Binary(self): """Test that the yn00 binary runs and generates correct output. yn00 output does not specify the version number. """ - self.yn.read_ctl_file(self.ctl_file) + ctl_file = os.path.join("PAML", "Control_files", "yn00", "yn00.ctl") + self.yn.read_ctl_file(ctl_file) + self.yn.alignment = os.path.join("PAML", "Alignments", "alignment.phylip") + self.yn.out_file = os.path.join("PAML", "temp.out") + self.yn.working_dir = os.path.join("PAML", "yn00_test") results = self.yn.run() self.assertEqual(len(results), 5)