def test_RunGlimmer_check_outfiles_exist(self): """ check if ./g3iterated.csh finished running, should produce 10 output files only pass if all 10 exist """ infile_var = "tIn.fasta" outfile_var = "tOut" glimmer = RunGlimmer(infile=infile_var, outfile=outfile_var, pdir=self.data_dir, check_exist=False) is_exist, _ = glimmer.check_outfiles_with_filetag_exist(self.data_dir + outfile_var) self.assertFalse(is_exist) glimmer.run(True) is_exist, _ = glimmer.check_outfiles_with_filetag_exist(self.data_dir + outfile_var) self.assertTrue(is_exist) # negative test, outfiles are not suppose to exist outfile_var = "fileNotExist" glimmer = RunGlimmer(infile=infile_var, outfile=outfile_var, pdir=self.data_dir, check_exist=False) is_exist, _ = glimmer.check_outfiles_with_filetag_exist(self.data_dir + outfile_var) self.assertFalse(is_exist)
def test_RunGlimmer_run(self): """ with debug=True should be able to see all 8 steps debug - output message: Step 1 of 8: Finding long orfs for training Step 2 of 8: Extracting training sequences Step 3 of 8: Building ICM Step 4 of 8: Running first Glimmer3 Step 5 of 8: Getting training coordinates Step 6 of 8: Making PWM from upstream regions Step 7 of 8: Getting start-codon usage Step 8 of 8: Running second Glimmer3 """ infile_var = "tIn.fasta" outfile_var = "tOut" glimmer = RunGlimmer(infile=infile_var, outfile=outfile_var, pdir=self.data_dir, check_exist=False) is_exist, _ = glimmer.check_outfiles_with_filetag_exist(self.data_dir + outfile_var) self.assertFalse(is_exist) glimmer.run(debug=1) is_exist, _ = glimmer.check_outfiles_with_filetag_exist(self.data_dir + outfile_var) self.assertTrue(is_exist)