def main():
option_parser, opts, args = parse_command_line_parameters(**script_info)
# Create the output dir if it doesn't already exist.
output_dir = opts.output_dir
try:
create_dir(output_dir)
except:
option_parser.error("Could not create or access output directory "
"specified with the -o/--output_dir option.")
otu_table_fp = opts.otu_table_fp
table = load_table(otu_table_fp)
estimator = ObservationRichnessEstimator(table,
Chao1MultinomialPointEstimator)
results = estimator(opts.min, opts.max, opts.num_steps,
opts.confidence_level)
out_fp = join(output_dir, 'estimates_table.txt')
with open(out_fp, 'w') as out_f:
results.toTable(out_f)
def setUp(self):
"""Define some sample data that will be used by the tests."""
# Single sample, 6 observations, one of which isn't observed in sample.
self.biom_table1 = parse_biom_table(biom_table_str1)
self.estimator1 = ObservationRichnessEstimator(
self.biom_table1, Chao1MultinomialPointEstimator)
