def main():
option_parser, opts, args = parse_command_line_parameters(**script_info)
output_dir = opts.output_dir
mapping_category = opts.mapping_category
try:
makedirs(output_dir)
except OSError:
pass
percent_failures_data, percent_failures_plot, num_new_otus_data, \
num_new_otus_plot = generate_new_diversity_plots(
[open(otu_table_fp, 'U') for otu_table_fp in opts.otu_table_fps],
open(opts.gg_fasta_fp, 'U'), open(opts.mapping_fp, 'U'),
mapping_category, opts.min_num_samples,
opts.category_values_to_exclude.split(','), opts.verbose)
# Save plots as PDFs.
percent_failures_plot.savefig(join(output_dir,
'percent_novel_seqs_by_%s.pdf' %
mapping_category))
num_new_otus_plot.savefig(join(output_dir,
'num_novel_otus_by_%s.pdf' %
mapping_category))
# Pickle plot raw data in case we need to load up the data again into new
# plots and interactively tweak them (it'll take too long to rerun the
# whole script for these tweaks).
dump(percent_failures_data, open(join(output_dir,
'percent_novel_seqs_by_%s.p' % mapping_category), 'wb'))
dump(num_new_otus_data, open(join(output_dir,
'num_novel_otus_by_%s.p' % mapping_category), 'wb'))
def test_generate_new_diversity_plots(self):
exp = ([(28.846153846153843, 'Env1 (n=2)', [0.0, 57.692307692307686]),
(57.142857142857139, 'Env2 (n=1)', [57.142857142857139])],
[(2.0, 'Env1 (n=2)', [0, 4]), (3.0, 'Env2 (n=1)', [3])])
obs = generate_new_diversity_plots(
[self.otu_table1_f, self.otu_table2_f], self.ref_seqs_f,
self.mapping_f, self.mapping_category, 1)
self.assertEqual(len(obs[0]), len(exp[0]))
self.assertFloatEqual(obs[0][0][:2], exp[0][0][:2])
self.assertFloatEqual(sorted(obs[0][0][2]), sorted(exp[0][0][2]))
self.assertFloatEqual(obs[0][1][:2], exp[0][1][:2])
self.assertFloatEqual(sorted(obs[0][1][2]), sorted(exp[0][1][2]))
self.assertEqual(len(obs[2]), len(exp[1]))
self.assertFloatEqual(obs[2][0][:2], exp[1][0][:2])
self.assertFloatEqual(sorted(obs[2][0][2]), sorted(exp[1][0][2]))
self.assertFloatEqual(obs[2][1][:2], exp[1][1][:2])
self.assertFloatEqual(sorted(obs[2][1][2]), sorted(exp[1][1][2]))
ax = obs[1].get_axes()[0]
self.assertEqual(ax.get_title(), "% Novel Seqs by Environment")
self.assertEqual(ax.get_xlabel(), "Environment")
self.assertEqual(ax.get_ylabel(), "% Novel Seqs")
self.assertEqual(len(ax.get_xticklabels()), 2)
ax = obs[3].get_axes()[0]
self.assertEqual(ax.get_title(), "Number of Novel OTUs by Environment")
self.assertEqual(ax.get_xlabel(), "Environment")
self.assertEqual(ax.get_ylabel(), "Number of Novel OTUs")
self.assertEqual(len(ax.get_xticklabels()), 2)
def test_generate_new_diversity_plots(self):
exp = ([(28.846153846153843, 'Env1 (n=2)', [0.0, 57.692307692307686]),
(57.142857142857139, 'Env2 (n=1)', [57.142857142857139])],
[(2.0, 'Env1 (n=2)', [0, 4]), (3.0, 'Env2 (n=1)', [3])])
obs = generate_new_diversity_plots(
[self.otu_table1_f, self.otu_table2_f], self.ref_seqs_f,
self.mapping_f, self.mapping_category, 1)
self.assertEqual(len(obs[0]), len(exp[0]))
self.assertFloatEqual(obs[0][0][:2], exp[0][0][:2])
self.assertFloatEqual(sorted(obs[0][0][2]), sorted(exp[0][0][2]))
self.assertFloatEqual(obs[0][1][:2], exp[0][1][:2])
self.assertFloatEqual(sorted(obs[0][1][2]), sorted(exp[0][1][2]))
self.assertEqual(len(obs[2]), len(exp[1]))
self.assertFloatEqual(obs[2][0][:2], exp[1][0][:2])
self.assertFloatEqual(sorted(obs[2][0][2]), sorted(exp[1][0][2]))
self.assertFloatEqual(obs[2][1][:2], exp[1][1][:2])
self.assertFloatEqual(sorted(obs[2][1][2]), sorted(exp[1][1][2]))
ax = obs[1].get_axes()[0]
self.assertEqual(ax.get_title(), "% Novel Seqs by Environment")
self.assertEqual(ax.get_xlabel(), "Environment")
self.assertEqual(ax.get_ylabel(), "% Novel Seqs")
self.assertEqual(len(ax.get_xticklabels()), 2)
ax = obs[3].get_axes()[0]
self.assertEqual(ax.get_title(), "Number of Novel OTUs by Environment")
self.assertEqual(ax.get_xlabel(), "Environment")
self.assertEqual(ax.get_ylabel(), "Number of Novel OTUs")
self.assertEqual(len(ax.get_xticklabels()), 2)
def test_generate_new_diversity_plots_excluded_category_value(self):
exp = ([(57.142857142857139, 'Env2 (n=1)', [57.142857142857139])],
[(3.0, 'Env2 (n=1)', [3])])
obs = generate_new_diversity_plots(
[self.otu_table1_f, self.otu_table2_f], self.ref_seqs_f,
self.mapping_f, self.mapping_category, 1, ['Env1'])
self.assertFloatEqual(obs[0], exp[0])
self.assertFloatEqual(obs[2], exp[1])
ax = obs[1].get_axes()[0]
self.assertEqual(ax.get_title(), "% Novel Seqs by Environment")
self.assertEqual(ax.get_xlabel(), "Environment")
self.assertEqual(ax.get_ylabel(), "% Novel Seqs")
self.assertEqual(len(ax.get_xticklabels()), 1)
ax = obs[3].get_axes()[0]
self.assertEqual(ax.get_title(), "Number of Novel OTUs by Environment")
self.assertEqual(ax.get_xlabel(), "Environment")
self.assertEqual(ax.get_ylabel(), "Number of Novel OTUs")
self.assertEqual(len(ax.get_xticklabels()), 1)
def test_generate_new_diversity_plots_excluded_category_value(self):
exp = ([(57.142857142857139, 'Env2 (n=1)', [57.142857142857139])],
[(3.0, 'Env2 (n=1)', [3])])
obs = generate_new_diversity_plots(
[self.otu_table1_f, self.otu_table2_f], self.ref_seqs_f,
self.mapping_f, self.mapping_category, 1, ['Env1'])
self.assertFloatEqual(obs[0], exp[0])
self.assertFloatEqual(obs[2], exp[1])
ax = obs[1].get_axes()[0]
self.assertEqual(ax.get_title(), "% Novel Seqs by Environment")
self.assertEqual(ax.get_xlabel(), "Environment")
self.assertEqual(ax.get_ylabel(), "% Novel Seqs")
self.assertEqual(len(ax.get_xticklabels()), 1)
ax = obs[3].get_axes()[0]
self.assertEqual(ax.get_title(), "Number of Novel OTUs by Environment")
self.assertEqual(ax.get_xlabel(), "Environment")
self.assertEqual(ax.get_ylabel(), "Number of Novel OTUs")
self.assertEqual(len(ax.get_xticklabels()), 1)
