def test_parameter_values(self): infile_var = "Spellman.csv" jobID_var = "tOut" mine = RunMINE(infile=infile_var, pdir=self.data_dir, wdir=self.working_dir, jobID=jobID_var, comparison='-allPairs', cv=0.0, clumps=15, check_exist=False) self.assertRaises(ValueError, mine.set_cv_threshold, 1.1) self.assertRaises(ValueError, mine.set_cv_threshold, 0) self.assertRaises(ValueError, mine.set_cv_threshold, -1) self.assertRaises(ValueError, mine.set_cv_threshold, -2.5) self.assertRaises(ValueError, mine.set_cv_threshold, "string") try: mine.set_cv_threshold("0.3") except ValueError as e: self.fail(e) self.assertRaises(ValueError, mine.set_clumping_factor, 1.1) self.assertRaises(ValueError, mine.set_clumping_factor, 0) self.assertRaises(ValueError, mine.set_clumping_factor, -1) self.assertRaises(ValueError, mine.set_clumping_factor, -2.5) self.assertRaises(ValueError, mine.set_clumping_factor, "string") try: mine.set_clumping_factor("3") except ValueError as e: self.fail(e)
def test_RunMINE_run(self): infile_var = "Spellman2.csv" jobID_var = "tOut" mine = RunMINE(infile=infile_var, pdir=self.data_dir, wdir=self.working_dir, jobID=jobID_var, comparison="-allPairs", check_exist=False) mine.run(True) self.assertTrue(mine.check_outfiles_with_filetag_exist(self.working_dir + infile_var + "," + jobID_var))
def test_outfile_already_exist(self): """ check if out file already exists, maybe should not raise error, should TODO: maybe it should be handle it at different way, auto rename? """ infile_var = "Spellman2.csv" jobID_var = "exist" mine = RunMINE(infile=infile_var, pdir=self.data_dir, wdir=self.working_dir, jobID=jobID_var, comparison="0", check_exist=False) mine.run(debug=0) with self.assertRaises(IOError): RunMINE(infile=infile_var, pdir=self.data_dir, wdir=self.working_dir, jobID=jobID_var, comparison="0", check_exist=True)
def test_RunMINE_init(self): infile_var = "Spellman.csv" jobID_var = "tOut" mine = RunMINE(infile=infile_var, pdir=self.data_dir, wdir=self.working_dir, jobID=jobID_var, comparison='-allPairs', cv=0.0, exp=0.6, clumps=15, check_exist=False) expected_infile = "%s%s" % (self.working_dir, infile_var) expected_outfile = "id=%s" % jobID_var expected = ["-jar", "MINE.jar", expected_infile, '-allPairs', "cv=0.0", "exp=0.6", "c=15", expected_outfile] # print expected self.assertEqual(mine.get_all_switches(), expected) mine = RunMINE(infile=infile_var, pdir=self.data_dir, wdir=self.working_dir, jobID=jobID_var, comparison='-allPairs', cv=0.0, exp=0.6, clumps=15, check_exist=False, csv_files=["f1", "f2", "f3"]) self.assertEqual([self.working_dir + "f1", self.working_dir + "f2", self.working_dir + "f3"], mine.csv_files)
def init_program(self): # self.metasim = RunMetaSim.create_metasim_from_setting(self.setting) if self.setting.run_mine: self.mine = RunMINE.create_class_from_setting(self.setting) else: if self.setting.get("assembler_prog") is "genovo": self.assembler = RunGenovo.create_genovo_from_setting(self.setting) elif self.setting.get("assembler_prog") is "xgenovo": self.assembler = RunXGenovo.create_xgenovo_from_setting(self.setting) self.glimmer = RunGlimmer.create_glimmer_from_setting(self.setting) # self.blast = run_BLAST.RunBlast.create_blast_from_setting(self.setting) self.blast = RunBlast.create_blast_from_setting(self.setting)