#NEWLINE# def __main__( ) : #NEWLINE# #INDENT# args = Parser ( ) #NEWLINE# F = open ( args . output , 'w' ) #NEWLINE# if ( args . index_from == 'history' ) : #NEWLINE# #INDENT# ( tmp_dir , index_path ) = bowtie_squash ( args . index_source ) #NEWLINE# #UNINDENT# else : #NEWLINE# #INDENT# ( tmp_dir , index_path ) = ( 'dummy/dymmy' , args . index_source ) #NEWLINE# #UNINDENT# command_line = bowtieCommandLiner ( args . method , args . v_mismatches , args . output_format , args . aligned , args . unaligned , args . input_format , args . input , index_path , args . output , args . num_threads ) #NEWLINE# bowtie_alignment ( command_line , flyPreIndexed = tmp_dir ) #NEWLINE# F . close ( )