def main(): option_parser, opts, args = parse_command_line_parameters(**script_info) adiv_fs = [open(adiv_fp, 'U') for adiv_fp in opts.alpha_div_fps] plotting_data, plot_fig = alpha_diversity_by_sample_type( adiv_fs, open(opts.mapping_fp, 'U'), opts.mapping_category, opts.min_num_samples, opts.category_values_to_exclude.split(',')) plot_fig.savefig(opts.output_fp)
def test_alpha_diversity_by_sample_type_min_num_samples(self): exp = [(4.0, 'Env1 (n=5)', [7.0, 4.0, 0.0, 1.0, 9.0])] obs = alpha_diversity_by_sample_type(self.adiv_fs, self.mapping_f, self.mapping_category, 4) self.assertFloatEqual(obs[0], exp) ax = obs[1].get_axes()[0] self.assertEqual(ax.get_title(), "Alpha Diversity by Environment") self.assertEqual(ax.get_xlabel(), "Environment") self.assertEqual(ax.get_ylabel(), "Alpha Diversity") self.assertEqual(len(ax.get_xticklabels()), 1)
def test_alpha_diversity_by_sample_type_excluded_category_value(self): exp = [(2.0, 'Env2 (n=3)', [5.0, 2.0, 2.0])] obs = alpha_diversity_by_sample_type(self.adiv_fs, self.mapping_f, self.mapping_category, 2, ['Env1']) self.assertFloatEqual(obs[0], exp) ax = obs[1].get_axes()[0] self.assertEqual(ax.get_title(), "Alpha Diversity by Environment") self.assertEqual(ax.get_xlabel(), "Environment") self.assertEqual(ax.get_ylabel(), "Alpha Diversity") self.assertEqual(len(ax.get_xticklabels()), 1)
def main(): option_parser, opts, args = parse_command_line_parameters(**script_info) adiv_fs = [open(adiv_fp, "U") for adiv_fp in opts.alpha_div_fps] plotting_data, plot_fig = alpha_diversity_by_sample_type( adiv_fs, open(opts.mapping_fp, "U"), opts.mapping_category, opts.min_num_samples, opts.category_values_to_exclude.split(","), ) plot_fig.savefig(opts.output_fp)
def test_alpha_diversity_by_sample_type(self): """Functions correctly using standard valid input data.""" exp = [(2.0, 'Env2 (n=3)', [5.0, 2.0, 2.0]), (4.0, 'Env1 (n=5)', [7.0, 4.0, 0.0, 1.0, 9.0])] obs = alpha_diversity_by_sample_type(self.adiv_fs, self.mapping_f, self.mapping_category, 2) self.assertFloatEqual(obs[0], exp) ax = obs[1].get_axes()[0] self.assertEqual(ax.get_title(), "Alpha Diversity by Environment") self.assertEqual(ax.get_xlabel(), "Environment") self.assertEqual(ax.get_ylabel(), "Alpha Diversity") self.assertEqual(len(ax.get_xticklabels()), 2)