def main():
option_parser, opts, args = parse_command_line_parameters(**script_info)
params = eval(str(opts))
params["metrics"] = ",".join(opts.metrics)
# create local copies of command-line options
input_path = opts.input_path
output_dir = opts.output_path
metrics_list = opts.metrics
tree_fp = opts.tree_path
# Check the tree exists if phylogenetically-aware measure is used
for metric in metrics_list:
try:
metric_f = get_phylogenetic_metric(metric)
if tree_fp is None:
option_parser.error("metric %s requires a tree, but " "none found" % metric)
except AttributeError:
pass
if isfile(input_path):
# single otu table mode
parallel_runner = ParallelBetaDiversitySingle(
cluster_jobs_fp=opts.cluster_jobs_fp,
jobs_to_start=opts.jobs_to_start,
retain_temp_files=opts.retain_temp_files,
suppress_polling=opts.suppress_polling,
seconds_to_sleep=opts.seconds_to_sleep,
)
parallel_runner(
input_path,
output_dir,
params,
job_prefix=opts.job_prefix,
poll_directly=opts.poll_directly,
suppress_submit_jobs=opts.suppress_submit_jobs,
)
else:
input_fps = glob("%s/*" % input_path)
parallel_runner = ParallelBetaDiversityMultiple(
cluster_jobs_fp=opts.cluster_jobs_fp,
jobs_to_start=opts.jobs_to_start,
retain_temp_files=opts.retain_temp_files,
suppress_polling=opts.suppress_polling,
seconds_to_sleep=opts.seconds_to_sleep,
)
parallel_runner(
input_fps,
output_dir,
params,
job_prefix=opts.job_prefix,
poll_directly=opts.poll_directly,
suppress_submit_jobs=opts.suppress_submit_jobs,
)
def main():
option_parser, opts, args = parse_command_line_parameters(**script_info)
params = eval(str(opts))
params['metrics'] = ','.join(opts.metrics)
# create local copies of command-line options
input_path = opts.input_path
output_dir = opts.output_path
metrics_list = opts.metrics
tree_fp = opts.tree_path
# Check the tree exists if phylogenetically-aware measure is used
for metric in metrics_list:
try:
metric_f = get_phylogenetic_metric(metric)
if tree_fp == None:
stderr.write("metric %s requires a tree, but none found\n"\
% (metric,))
exit(1)
except AttributeError:
pass
if isfile(input_path):
# single otu table mode
parallel_runner = ParallelBetaDiversitySingle(
cluster_jobs_fp=opts.cluster_jobs_fp,
jobs_to_start=opts.jobs_to_start,
retain_temp_files=opts.retain_temp_files,
suppress_polling=opts.suppress_polling,
seconds_to_sleep=opts.seconds_to_sleep)
parallel_runner(input_path,
output_dir,
params,
job_prefix=opts.job_prefix,
poll_directly=opts.poll_directly,
suppress_submit_jobs=False)
else:
input_fps = glob('%s/*' % input_path)
parallel_runner = ParallelBetaDiversityMultiple(
cluster_jobs_fp=opts.cluster_jobs_fp,
jobs_to_start=opts.jobs_to_start,
retain_temp_files=opts.retain_temp_files,
suppress_polling=opts.suppress_polling,
seconds_to_sleep=opts.seconds_to_sleep)
parallel_runner(input_fps,
output_dir,
params,
job_prefix=opts.job_prefix,
poll_directly=opts.poll_directly,
suppress_submit_jobs=False)