def test_run_jackknifed_beta_diversity_parallel(self):
""" run_jackknifed_beta_diversity generates expected results """
run_jackknifed_beta_diversity(
self.test_data['biom'][0],
self.test_data['tree'][0],
20,
self.test_out,
call_commands_serially,
self.params,
self.qiime_config,
self.test_data['map'][0],
parallel=True,
status_update_callback=no_status_updates)
weighted_unifrac_upgma_tree_fp = join(self.test_out,
'weighted_unifrac',
'upgma_cmp', 'jackknife_named_nodes.tre')
unweighted_unifrac_upgma_tree_fp = join(
self.test_out, 'unweighted_unifrac', 'upgma_cmp',
'jackknife_named_nodes.tre')
weighted_unifrac_emperor_index_fp = join(
self.test_out, 'weighted_unifrac', 'emperor_pcoa_plots',
'index.html')
unweighted_unifrac_emperor_index_fp = join(
self.test_out, 'unweighted_unifrac', 'emperor_pcoa_plots',
'index.html')
input_file_basename = splitext(split(self.test_data['biom'][0])[1])[0]
unweighted_unifrac_dm_fp = join(self.test_out,
'unweighted_unifrac_%s.txt' % input_file_basename)
weighted_unifrac_dm_fp = join(self.test_out,
'weighted_unifrac_%s.txt' % input_file_basename)
# check for expected relations between values in the unweighted unifrac
# distance matrix
dm = parse_distmat_to_dict(open(unweighted_unifrac_dm_fp))
self.assertTrue(dm['f1']['f2'] < dm['f1']['p1'],
"Distance between pair of fecal samples is larger than distance"
" between fecal and palm sample (unweighted unifrac).")
self.assertEqual(dm['f1']['f1'], 0)
# check for expected relations between values in the weighted unifrac
# distance matrix
dm = parse_distmat_to_dict(open(weighted_unifrac_dm_fp))
self.assertTrue(dm['f1']['f2'] < dm['f1']['p1'],
"Distance between pair of fecal samples is larger than distance"
" between fecal and palm sample (unweighted unifrac).")
self.assertEqual(dm['f1']['f1'], 0)
# check that final output files have non-zero size
self.assertTrue(getsize(weighted_unifrac_upgma_tree_fp) > 0)
self.assertTrue(getsize(unweighted_unifrac_upgma_tree_fp) > 0)
self.assertTrue(getsize(weighted_unifrac_emperor_index_fp) > 0)
self.assertTrue(getsize(unweighted_unifrac_emperor_index_fp) > 0)
# Check that the log file is created and has size > 0
log_fp = glob(join(self.test_out, 'log*.txt'))[0]
self.assertTrue(getsize(log_fp) > 0)
def main():
option_parser, opts, args = \
parse_command_line_parameters(**script_info)
verbose = opts.verbose
otu_table_fp = opts.otu_table_fp
output_dir = opts.output_dir
tree_fp = opts.tree_fp
seqs_per_sample = opts.seqs_per_sample
verbose = opts.verbose
print_only = opts.print_only
master_tree = opts.master_tree
parallel = opts.parallel
# No longer checking that jobs_to_start > 2, but
# commenting as we may change our minds about this.
#if parallel: raise_error_on_parallel_unavailable()
if opts.parameter_fp:
try:
parameter_f = open(opts.parameter_fp, 'U')
except IOError:
raise IOError("Can't open parameters file (%s). Does it exist? Do you have read access?"
% opts.parameter_fp)
params = parse_qiime_parameters(parameter_f)
parameter_f.close()
else:
params = parse_qiime_parameters([])
# empty list returns empty defaultdict for now
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)
try:
makedirs(output_dir)
except OSError:
if opts.force:
pass
else:
# Since the analysis can take quite a while, I put this check
# in to help users avoid overwriting previous output.
option_parser.error("Output directory already exists. Please choose"
" a different directory, or force overwrite with -f.")
if print_only:
command_handler = print_commands
else:
command_handler = call_commands_serially
if verbose:
status_update_callback = print_to_stdout
else:
status_update_callback = no_status_updates
run_jackknifed_beta_diversity(otu_table_fp=otu_table_fp,
tree_fp=tree_fp,
seqs_per_sample=seqs_per_sample,
output_dir=output_dir,
command_handler=command_handler,
params=params,
qiime_config=qiime_config,
mapping_fp=opts.mapping_fp,
parallel=parallel,
status_update_callback=status_update_callback,
master_tree=master_tree)
def main():
option_parser, opts, args = \
parse_command_line_parameters(**script_info)
verbose = opts.verbose
otu_table_fp = opts.otu_table_fp
output_dir = opts.output_dir
tree_fp = opts.tree_fp
seqs_per_sample = opts.seqs_per_sample
verbose = opts.verbose
print_only = opts.print_only
master_tree = opts.master_tree
parallel = opts.parallel
# No longer checking that jobs_to_start > 2, but
# commenting as we may change our minds about this.
#if parallel: raise_error_on_parallel_unavailable()
if opts.parameter_fp:
try:
parameter_f = open(opts.parameter_fp, 'U')
except IOError:
raise IOError(
"Can't open parameters file (%s). Does it exist? Do you have read access?"
% opts.parameter_fp)
params = parse_qiime_parameters(parameter_f)
parameter_f.close()
else:
params = parse_qiime_parameters([])
# empty list returns empty defaultdict for now
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)
try:
makedirs(output_dir)
except OSError:
if opts.force:
pass
else:
# Since the analysis can take quite a while, I put this check
# in to help users avoid overwriting previous output.
option_parser.error(
"Output directory already exists. Please choose"
" a different directory, or force overwrite with -f.")
if print_only:
command_handler = print_commands
else:
command_handler = call_commands_serially
if verbose:
status_update_callback = print_to_stdout
else:
status_update_callback = no_status_updates
run_jackknifed_beta_diversity(
otu_table_fp=otu_table_fp,
tree_fp=tree_fp,
seqs_per_sample=seqs_per_sample,
output_dir=output_dir,
command_handler=command_handler,
params=params,
qiime_config=qiime_config,
mapping_fp=opts.mapping_fp,
parallel=parallel,
status_update_callback=status_update_callback,
master_tree=master_tree)
