def test_compute_sample_novelty(self):
"""Test computing the novelty of a sample using various metrics."""
exp = [('B', 4, 57.692307692307686), ('C', 3, 57.142857142857139),
('A', 0, 0.0)]
obs = compute_sample_novelty([self.table1_f, self.table2_f],
self.ref_seqs_f)
self.assertFloatEqual(obs, exp)
# Test that table order doesn't matter.
obs = compute_sample_novelty([self.table2_f, self.table1_f],
self.ref_seqs_f)
self.assertFloatEqual(obs, exp)
# Test duplicate table (should still work).
exp = [('B', 2, 44.444444444444443), ('A', 0, 0.0)]
obs = compute_sample_novelty([self.table1_f, self.table1_f],
self.ref_seqs_f)
self.assertFloatEqual(obs, exp)
def test_compute_sample_novelty(self):
"""Test computing the novelty of a sample using various metrics."""
exp = [('B', 4, 57.692307692307686), ('C', 3, 57.142857142857139),
('A', 0, 0.0)]
obs = compute_sample_novelty([self.table1_f, self.table2_f],
self.ref_seqs_f)
self.assertFloatEqual(obs, exp)
# Test that table order doesn't matter.
obs = compute_sample_novelty([self.table2_f, self.table1_f],
self.ref_seqs_f)
self.assertFloatEqual(obs, exp)
# Test duplicate table (should still work).
exp = [('B', 2, 44.444444444444443), ('A', 0, 0.0)]
obs = compute_sample_novelty([self.table1_f, self.table1_f],
self.ref_seqs_f)
self.assertFloatEqual(obs, exp)
def main():
option_parser, opts, args = parse_command_line_parameters(**script_info)
sample_novelty_data = compute_sample_novelty(
[qiime_open(otu_table_fp) for otu_table_fp in opts.otu_table_fps],
qiime_open(opts.rep_set_fp), opts.verbose)
with open(opts.output_fp, 'w') as out_f:
header = ['SampleID', 'Number of novel OTUs',
'Percent novel sequences']
table_writer = writer(out_f, delimiter='\t', lineterminator='\n')
table_writer.writerow(header)
table_writer.writerows(sample_novelty_data)
def main():
option_parser, opts, args = parse_command_line_parameters(**script_info)
sample_novelty_data = compute_sample_novelty(
[qiime_open(otu_table_fp) for otu_table_fp in opts.otu_table_fps],
qiime_open(opts.rep_set_fp), opts.verbose)
with open(opts.output_fp, 'w') as out_f:
header = [
'SampleID', 'Number of novel OTUs', 'Percent novel sequences'
]
table_writer = writer(out_f, delimiter='\t', lineterminator='\n')
table_writer.writerow(header)
table_writer.writerows(sample_novelty_data)