def test_run_core_diversity_analyses_no_categories(self):
"""run_core_diversity_analyses functions without categories
"""
# this takes a long time, so use a longer sigalrm
run_core_diversity_analyses(
self.test_data['biom'][0],
self.test_data['map'][0],
20,
output_dir=self.test_out,
params=parse_qiime_parameters({}),
qiime_config=self.qiime_config,
categories=None,
tree_fp=self.test_data['tree'][0],
parallel=False,
status_update_callback=no_status_updates)
# Basic sanity test that output directories and files exist
fps = [
'%s/bdiv_even20' % self.test_out,
'%s/arare_max20' % self.test_out,
'%s/taxa_plots' % self.test_out,
'%s/bdiv_even20/unweighted_unifrac_dm.txt' % self.test_out,
'%s/bdiv_even20/weighted_unifrac_pc.txt' % self.test_out,
'%s/index.html' % self.test_out
]
for fp in fps:
self.assertTrue(exists(fp))
# categorical output files don't exist
self.assertFalse(exists(
'%s/arare_max20/days_since_epoch_chao1.txt' % self.test_out))
self.assertFalse(exists(
'%s/arare_max20/SampleType_PD_whole_tree.txt' % self.test_out))
def test_run_core_diversity_analyses_no_tree(self):
"""run_core_diversity_analyses functions without tree
"""
# this takes a long time, so use a longer sigalrm
run_core_diversity_analyses(
self.test_data['biom'][0],
self.test_data['map'][0],
20,
output_dir=self.test_out,
params=parse_qiime_parameters(
['beta_diversity:metrics bray_curtis',
'alpha_diversity:metrics observed_species,chao1']),
qiime_config=self.qiime_config,
categories=['SampleType'],
tree_fp=None,
parallel=False,
status_update_callback=no_status_updates)
# Basic sanity test that output directories and files exist
fps = [
'%s/bdiv_even20' % self.test_out,
'%s/arare_max20' % self.test_out,
'%s/taxa_plots' % self.test_out,
'%s/bdiv_even20/bray_curtis_dm.txt' % self.test_out,
'%s/arare_max20/SampleType_observed_species.txt' % self.test_out,
'%s/index.html' % self.test_out
]
for fp in fps:
self.assertTrue(exists(fp))
# phylogenetic diversity output files do not exist
self.assertFalse(exists(
'%s/bdiv_even20/unweighted_unifrac_dm.txt' % self.test_out))
def main():
option_parser, opts, args = parse_command_line_parameters(**script_info)
verbose = opts.verbose
input_biom_fp = opts.input_biom_fp
output_dir = opts.output_dir
categories = opts.categories
if categories != None:
categories = categories.split(',')
tree_fp = opts.tree_fp
mapping_fp = opts.mapping_fp
verbose = opts.verbose
parallel = opts.parallel
sampling_depth = opts.sampling_depth
nonphylogenetic_diversity = opts.nonphylogenetic_diversity
if opts.parameter_fp != None:
params = parse_qiime_parameters(open(opts.parameter_fp,'U'))
else:
params = parse_qiime_parameters([])
if nonphylogenetic_diversity:
# if the user specified --nonphylogenetic_diversity and they
# didn't define metrics in a parameters file, define them here
if 'metrics' not in params['beta_diversity']:
params['beta_diversity']['metrics'] = 'bray_curtis'
if 'metrics' not in params['alpha_diversity']:
params['alpha_diversity']['metrics'] = 'observed_species,chao1'
jobs_to_start = opts.jobs_to_start
default_jobs_to_start = qiime_config['jobs_to_start']
validate_and_set_jobs_to_start(params,
jobs_to_start,
default_jobs_to_start,
parallel,
option_parser)
create_dir(output_dir,fail_on_exist=True)
command_handler = call_commands_serially
if verbose:
status_update_callback = print_to_stdout
else:
status_update_callback = no_status_updates
run_core_diversity_analyses(
biom_fp=input_biom_fp,
mapping_fp=mapping_fp,
sampling_depth=sampling_depth,
output_dir=output_dir,
qiime_config=load_qiime_config(),
command_handler=command_handler,
tree_fp=tree_fp,
params=params,
categories=categories,
arare_min_rare_depth=10,
arare_num_steps=10,
parallel=parallel,
status_update_callback=status_update_callback)
