def test_parse_and_submit_params(self): """parse_and_submit_params: separates the split-library sequences \ into separate fasta files and posts the sequence data to mg-rast""" obs = parse_and_submit_params(self.key, self.project_id, self.seq_file, self.output_dir, submit_to_server=False) self.assertEqual(obs, mg_rast_exp_log) for i in glob("%s/*" % (self.output_dir)): self._paths_to_clean_up.append(path.join(self.output_dir, i))
def test_parse_and_submit_params(self): """parse_and_submit_params: separates the split-library sequences \ into separate fasta files and posts the sequence data to mg-rast""" obs=parse_and_submit_params(self.key,self.project_id,self.seq_file,\ self.output_dir,submit_to_server=False) self.assertEqual(obs, mg_rast_exp_log) for i in glob('%s/*' % (self.output_dir)): self._paths_to_clean_up.append(path.join(self.output_dir, i))
def main(): option_parser, opts, args =\ parse_command_line_parameters(**script_info) # define the variables project_id = opts.project_id files = opts.input_fasta_fp key = opts.web_key_auth # create directory path if opts.output_dir: if exists(opts.output_dir): output_dir = opts.output_dir else: try: mkdir(opts.output_dir) output_dir = opts.output_dir except OSError: pass else: dir_path = './' # call the main function log_info = parse_and_submit_params(key, project_id, files, output_dir)
def main(): option_parser, opts, args =\ parse_command_line_parameters(**script_info) #define the variables project_id=opts.project_id files=opts.input_fasta_fp key = opts.web_key_auth #create directory path if opts.output_dir: if exists(opts.output_dir): output_dir=opts.output_dir else: try: mkdir(opts.output_dir) output_dir=opts.output_dir except OSError: pass else: dir_path='./' #call the main function log_info=parse_and_submit_params(key,project_id,files,output_dir)