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)
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)
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)
