def load_qiime_config():
 qiime_config_filepaths = []
 qiime_project_dir = get_qiime_project_dir()
 qiime_config_filepaths.append((qiime_project_dir + '/qiime/support_files/qiime_config'))
 qiime_config_env_filepath = getenv('QIIME_CONFIG_FP')
 if qiime_config_env_filepath:
  qiime_config_filepaths.append(qiime_config_env_filepath)
 home_dir = getenv('HOME')
 if home_dir:
  qiime_config_home_filepath = (home_dir + '/.qiime_config')
  qiime_config_filepaths.append(qiime_config_home_filepath)
 qiime_config_files = []
 for qiime_config_filepath in qiime_config_filepaths:
  if exists(qiime_config_filepath):
   qiime_config_files.append(open(qiime_config_filepath))
 qiime_config = parse_qiime_config_files(qiime_config_files)
 qiime_config['pick_otus_reference_seqs_fp'] = (qiime_config['pick_otus_reference_seqs_fp'] or get_reference_sequences())
 qiime_config['pynast_template_alignment_fp'] = (qiime_config['pynast_template_alignment_fp'] or get_template_alignment())
 qiime_config['assign_taxonomy_reference_seqs_fp'] = (qiime_config['assign_taxonomy_reference_seqs_fp'] or get_reference_sequences())
 qiime_config['assign_taxonomy_id_to_taxonomy_fp'] = (qiime_config['assign_taxonomy_id_to_taxonomy_fp'] or get_reference_taxonomy())
 temp_dir = (qiime_config['temp_dir'] or tempfile.gettempdir())
 if (not temp_dir.endswith(os.sep)):
  temp_dir += os.sep
 qiime_config['temp_dir'] = temp_dir
 return qiime_config

def load_qiime_config ( ) : qiime_config_filepaths = [ ] qiime_project_dir = get_qiime_project_dir ( ) qiime_config_filepaths . append ( ( qiime_project_dir + '/qiime/support_files/qiime_config' ) ) qiime_config_env_filepath = getenv ( 'QIIME_CONFIG_FP' ) if qiime_config_env_filepath : qiime_config_filepaths . append ( qiime_config_env_filepath ) home_dir = getenv ( 'HOME' ) if home_dir : qiime_config_home_filepath = ( home_dir + '/.qiime_config' ) qiime_config_filepaths . append ( qiime_config_home_filepath ) qiime_config_files = [ ] for qiime_config_filepath in qiime_config_filepaths : if exists ( qiime_config_filepath ) : qiime_config_files . append ( open ( qiime_config_filepath ) ) qiime_config = parse_qiime_config_files ( qiime_config_files ) qiime_config [ 'pick_otus_reference_seqs_fp' ] = ( qiime_config [ 'pick_otus_reference_seqs_fp' ] or get_reference_sequences ( ) ) qiime_config [ 'pynast_template_alignment_fp' ] = ( qiime_config [ 'pynast_template_alignment_fp' ] or get_template_alignment ( ) ) qiime_config [ 'assign_taxonomy_reference_seqs_fp' ] = ( qiime_config [ 'assign_taxonomy_reference_seqs_fp' ] or get_reference_sequences ( ) ) qiime_config [ 'assign_taxonomy_id_to_taxonomy_fp' ] = ( qiime_config [ 'assign_taxonomy_id_to_taxonomy_fp' ] or get_reference_taxonomy ( ) ) temp_dir = ( qiime_config [ 'temp_dir' ] or tempfile . gettempdir ( ) ) if ( not temp_dir . endswith ( os . sep ) ) : temp_dir += os . sep qiime_config [ 'temp_dir' ] = temp_dir return qiime_config
return default parameters read in from file .