<s> '''<STR_LIT>''' <EOL> import sys <EOL> import CGAT . Experiment as E <EOL> import CGAT . VCF as VCF <EOL> def main ( argv = sys . argv ) : <EOL> parser = E . OptionParser ( version = "<STR_LIT>" , <EOL> usage = globals ( ) [ "<STR_LIT>" ] ) <EOL> parser . add_option ( <EOL> "<STR_LIT>" , dest = "<STR_LIT>" , type = "<STR_LIT>" , action = "<STR_LIT>" , <EOL> choices = ( "<STR_LIT>" , ) , <EOL> help = "<STR_LIT>" ) <EOL> parser . add_option ( <EOL> "<STR_LIT>" , dest = "<STR_LIT>" , <EOL> help = "<STR_LIT>" <EOL> "<STR_LIT>" <EOL> "<STR_LIT>" ) <EOL> parser . set_defaults ( <EOL> methods = [ ] , <EOL> sort_order = "<STR_LIT>" , <EOL> ) <EOL> ( options , args ) = E . Start ( parser , add_pipe_options = True ) <EOL> if not options . methods : <EOL> raise ValueError ( "<STR_LIT>" ) <EOL> infile = VCF . VCFFile ( options . stdin ) <EOL> sort_order = False <EOL> if "<STR_LIT>" in options . methods : <EOL> if options . sort_order : <EOL> sort_order = options . sort_order . split ( "<STR_LIT:U+002C>" ) <EOL> if "<STR_LIT>" in sort_order : <EOL> sort_order = sorted ( infile . samples ) <EOL> infile . writeHeader ( options . stdout , order = sort_order ) <EOL> for vcf in infile : <EOL> if sort_order : <EOL> vcf . order = sort_order <EOL> options . stdout . write ( str ( vcf ) + "<STR_LIT:\n>" ) <EOL> E . Stop ( ) <EOL> if __name__ == "<STR_LIT:__main__>" : <EOL> sys . exit ( main ( sys . argv ) ) </s>
