def test_run_process_sff_through_pick_otus_parallel(self):
"""run_process_sff_through_pick_otus in parallel runs with out error"""
run_process_sff_through_pick_otus(
sff_input_fp=self.sff_fp,
mapping_fp=self.fasting_mapping_fp,
output_dir=self.wf_out,
denoise=False,
command_handler=call_commands_serially,
params=self.params,
qiime_config=self.qiime_config,
parallel=True,
status_update_callback=no_status_updates)
input_file_basename = splitext(split(self.sff_fp)[1])[0]
otu_fp = join(self.wf_out,'picked_otus','seqs_otus.txt')
split_lib_seqs_fp = join(self.wf_out,'split_libraries',\
'seqs.fna')
# check that the two final output files have non-zero size
self.assertTrue(getsize(split_lib_seqs_fp) > 0)
self.assertTrue(getsize(otu_fp) > 0)
# Check that the log file is created and has size > 0
log_fp = glob(join(self.wf_out,'log*.txt'))[0]
self.assertTrue(getsize(log_fp) > 0)
def main():
option_parser, opts, args =\
parse_command_line_parameters(**script_info)
study_id = opts.study_id
for i in range(1,25):
output_dir='/home/wwwdevuser/user_data/studies/study_%s/processed_data_%s/' % (study_id,i)
if not exists(output_dir):
break
else:
continue
print output_dir
sff_fname=opts.sff_fname
map_fname = opts.map_fname
verbose = opts.verbose
print_only = opts.print_only
parallel = opts.parallel
denoise=opts.denoise
if parallel:
raise_error_on_parallel_unavailable()
try:
parameter_f = open(opts.parameter_fp)
except IOError:
raise IOError,\
"Can't open parameters file (%s). Does it exist? Do you have read access?"\
% opts.parameter_fp
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.
print "Output directory already exists. Please choose "+\
"a different directory, or force overwrite with -f."
exit(1)
if print_only:
command_handler = print_commands
else:
command_handler = web_app_call_commands_serially
if verbose:
status_update_callback = print_to_stdout
else:
status_update_callback = no_status_updates
run_process_sff_through_pick_otus(sff_input_fp=sff_fname,\
mapping_fp=map_fname,\
output_dir=output_dir,\
denoise=denoise,\
command_handler=command_handler,\
params=parse_qiime_parameters(parameter_f),\
qiime_config=qiime_config,\
parallel=parallel,\
status_update_callback=status_update_callback)
