gvanno.py 文件源码

def read_config_options(configuration_file, gvanno_dir, logger):

   ## read default options
   gvanno_config_options = {}
   gvanno_configuration_file_default = os.path.join(gvanno_dir,'data','gvanno_configuration_default.toml')
   if not os.path.exists(gvanno_configuration_file_default):
      err_msg = "Default gvanno configuration file " + str(gvanno_configuration_file_default) + " does not exist - exiting"
      gvanno_error_message(err_msg,logger)
   try:
      gvanno_config_options = toml.load(gvanno_configuration_file_default)
   except IndexError,TypeError:
      err_msg = 'Configuration file ' + str(configuration_file) + ' is not formatted correctly'
      gvanno_error_message(err_msg, logger)

   ## override with options set by the users
   try:
      toml_options = toml.load(configuration_file)
   except IndexError,TypeError:
      err_msg = 'Configuration file ' + str(configuration_file) + ' is not formatted correctly'
      gvanno_error_message(err_msg, logger)

   #float_tags = ['maf_onekg_eur','maf_onekg_amr','maf_onekg_afr','maf_onekg_sas','maf_onekg_eas','maf_onekg_global','maf_gnomad_nfe','maf_gnomad_amr','maf_gnomad_fin','maf_gnomad_oth','maf_gnomad_afr','maf_gnomad_sas','maf_gnomad_eas','maf_gnomad_global']
   boolean_tags = ['vep_skip_intergenic']
   integer_tags = ['n_vcfanno_proc','n_vep_forks']
   for section in ['other']:
      if toml_options.has_key(section):
         # for t in float_tags:
         #    if toml_options[section].has_key(t):
         #       if not isinstance(toml_options[section][t],float) and not isinstance(toml_options[section][t],int):
         #          err_msg = 'Configuration value ' + str(toml_options[section][t]) + ' for ' + str(t) + ' cannot be parsed properly (expecting float)'
         #          gvanno_error_message(err_msg, logger)
         #       gvanno_config_options[section][t] = toml_options[section][t]
         for t in boolean_tags:
            if toml_options[section].has_key(t):
               if not isinstance(toml_options[section][t],bool):
                  err_msg = 'Configuration value ' + str(toml_options[section][t]) + ' for ' + str(t) + ' cannot be parsed properly (expecting true/false)'
                  gvanno_error_message(err_msg, logger)
               gvanno_config_options[section][t] = int(toml_options[section][t])
         for t in integer_tags:
            if toml_options[section].has_key(t):
               if not isinstance(toml_options[section][t],int):
                  err_msg = 'Configuration value ' + str(toml_options[section][t]) + ' for ' + str(t) + ' cannot be parsed properly (expecting integer)'
                  gvanno_error_message(err_msg, logger)
               gvanno_config_options[section][t] = toml_options[section][t]

   # for t in float_tags:
   #    if t.startswith('maf_'):
   #       if gvanno_config_options['variant_filter'][t] < 0 or gvanno_config_options['variant_filter'][t] > 1:
   #          err_msg = "MAF value: " + str(t) + " must be within the [0,1] range, current value is " + str(gvanno_config_options['variant_filter'][t]) + ")"
   #          gvanno_error_message(err_msg,logger)

   return gvanno_config_options