def test_raise_error_on_parallel_unavailable(self): """raise_error_on_parallel_unavailable functions as expected """ self.assertRaises(RuntimeError,raise_error_on_parallel_unavailable,{}) self.assertRaises(RuntimeError,raise_error_on_parallel_unavailable,\ {'jobs_to_start':'1'}) raise_error_on_parallel_unavailable({'jobs_to_start':'2'}) raise_error_on_parallel_unavailable({'jobs_to_start':'24'})
def test_raise_error_on_parallel_unavailable(self): """raise_error_on_parallel_unavailable functions as expected """ self.assertRaises(RuntimeError, raise_error_on_parallel_unavailable, {}) self.assertRaises(RuntimeError,raise_error_on_parallel_unavailable,\ {'jobs_to_start':'1'}) raise_error_on_parallel_unavailable({'jobs_to_start': '2'}) raise_error_on_parallel_unavailable({'jobs_to_start': '24'})
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)
def main(): option_parser, opts, args =\ parse_command_line_parameters(**script_info) fasta_file = opts.split_lib_seqs verbose = opts.verbose print_only = opts.print_only parallel = opts.parallel output_dir=opts.output_dir if output_dir: if exists(output_dir): dir_path=output_dir else: try: mkdir(output_dir) dir_path=output_dir except OSError: pass else: dir_path='./' 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(dir_path) 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 new_output_dir=join(dir_path,'chain_picked_otus') create_dir(new_output_dir) run_chain_pick_otus(fasta_file=fasta_file,\ output_dir=new_output_dir,\ command_handler=command_handler,\ params=parse_qiime_parameters(parameter_f),\ qiime_config=qiime_config,\ parallel=parallel,\ status_update_callback=status_update_callback)