- cmd = decorator +
- ' -p -f=m ' + phylogeny_file + ' ' +
- seqs_file_name + ' ' + TMP_FILE_1
- puts cmd
- execute_cmd( cmd, log )
-
- cmd = decorator + ' ' + DECORATOR_OPTIONS_DOMAINS + ' ' +
- '-f=d ' + TMP_FILE_1 + ' ' +
- domains_mapfile_name + ' ' +TMP_FILE_2
- puts cmd
- execute_cmd( cmd, log )
-
- cmd = decorator + ' ' + DECORATOR_OPTIONS_SEQ_NAMES + ' ' +
- '-f=n ' + TMP_FILE_2 + ' ' +
- ids_mapfile_name + ' ' + outfile
- puts cmd
- execute_cmd( cmd, log )
-
- File.delete( TMP_FILE_1 )
- File.delete( TMP_FILE_2 )
-
+ if IDS_ONLY
+ cmd = decorator + ' ' + DECORATOR_OPTIONS_SEQ_NAMES + ' ' +
+ '-f=n ' + phylogeny_file + ' ' +
+ ids_mapfile_name + ' ' + outfile
+ puts cmd
+ begin
+ execute_cmd( cmd, log )
+ rescue Error
+ Util.fatal_error( PRG_NAME, 'error: ' + $! )
+ end
+ else
+ cmd = decorator + ' ' + DECORATOR_OPTIONS_SEQ_NAMES + ' ' +
+ '-f=n ' + TMP_FILE_2 + ' ' +
+ ids_mapfile_name + ' ' + outfile
+ puts cmd
+ begin
+ execute_cmd( cmd, log )
+ rescue Error
+ Util.fatal_error( PRG_NAME, 'error: ' + $! )
+ end
+ File.delete( TMP_FILE_1 )
+ File.delete( TMP_FILE_2 )
+ end