-# cmd = decorator +
-# ' -t -p -f=m ' + phylogeny_file + ' ' +
-# seqs_file_name + ' ' + TMP_FILE_1
-# puts cmd
-# begin
-# execute_cmd( cmd, log )
-# rescue Error
-# Util.fatal_error( PRG_NAME, 'error: ' + $! )
-# end
-#
-# cmd = decorator + ' ' + DECORATOR_OPTIONS_DOMAINS + ' ' +
-# '-f=d ' + TMP_FILE_1 + ' ' +
-# domains_mapfile_name + ' ' +TMP_FILE_2
-# puts cmd
-# begin
-# execute_cmd( cmd, log )
-# rescue Error
-# Util.fatal_error( PRG_NAME, 'error: ' + $! )
-# end
-
- cmd = decorator + ' ' + DECORATOR_OPTIONS_SEQ_NAMES + ' ' +
- '-f=n ' + seqs_file_name + ' ' +
- ids_mapfile_name + ' ' + outfile
- puts cmd
- begin
- execute_cmd( cmd, log )
- rescue Error
- Util.fatal_error( PRG_NAME, 'error: ' + $! )
+ 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 )