def test_set_outfile_directory(self): model_infile_var = "ErrorModelSolexa36bp.mconf" taxon_infile_var = "MetaSim_bint.mprf" outfile_var = "wdir_all_reads_out.fasta" metasim = RunMetaSim(model_file=model_infile_var, no_reads=100, taxon_infile=taxon_infile_var, pdir=self.data_dir, wdir=self.working_dir, filename=outfile_var, check_exist=True) self.assertEqual(metasim.get_all_switches()[3], "-d%s" % self.working_dir) dir_var = self.data_dir metasim = RunMetaSim(model_file=model_infile_var, no_reads=100, taxon_infile=taxon_infile_var, pdir=self.data_dir, wdir=dir_var, filename=outfile_var, check_exist=False) metasim.set_outfile_directory() self.assertEqual(metasim.get_all_switches()[3], "-d%s" % self.data_dir)
def test_no_reads_value(self): model_infile_var = "ErrorModelSolexa36bp.mconf" taxon_infile_var = "MetaSim_bint.mprf" outfile_var = "wdir_all_reads_out.fasta" metasim = RunMetaSim(model_file=model_infile_var, no_reads=100, taxon_infile=taxon_infile_var, pdir=self.data_dir, wdir=self.working_dir, filename=outfile_var, check_exist=True) self.assertRaises(ValueError, metasim.set_number_of_reads, 1.9) self.assertRaises(ValueError, metasim.set_number_of_reads, -1) self.assertRaises(ValueError, metasim.set_number_of_reads, -2.5) self.assertRaises(ValueError, metasim.set_number_of_reads, "string") self.assertRaises(ValueError, metasim.set_number_of_reads, "3.6") # self.assertRaises(TypeError, metasim.set_number_of_reads, "3") metasim.set_number_of_reads("3") self.assertEqual(metasim.get_all_switches()[run_MetaSim.NO_READS_POSITION - 1], "-r3")
def test_init(self): model_infile_var = "ErrorModelSolexa36bp.mconf" taxon_infile_var = "MetaSim_bint.mprf" outfile_var = "wdir_all_reads_out.fasta" no_reads_var = 100 metasim = RunMetaSim(model_file=model_infile_var, no_reads=no_reads_var, taxon_infile=taxon_infile_var, pdir=self.data_dir, wdir=self.working_dir, filename=outfile_var, check_exist=True) expected_model_infile = "-mg%s%s" % (self.working_dir, model_infile_var) expected_taxon_infile = self.working_dir + taxon_infile_var expected_no_reads = "-r%s" % no_reads_var expected_directory = "-d%s" % self.working_dir expected = ["cmd", expected_model_infile, expected_no_reads, expected_directory, expected_taxon_infile] # self.assertEqual(metasim.get_all_switches(), expected)