<s> '''<STR_LIT>''' <EOL> import sys <EOL> import CGAT . Experiment as E <EOL> import CGAT . Timeseries as TS <EOL> def main ( argv = None ) : <EOL> """<STR_LIT>""" <EOL> if argv is None : <EOL> argv = sys . argv <EOL> parser = E . OptionParser ( version = "<STR_LIT>" , <EOL> usage = globals ( ) [ "<STR_LIT>" ] ) <EOL> parser . add_option ( "<STR_LIT>" , "<STR_LIT>" , dest = "<STR_LIT:test>" , type = "<STR_LIT:string>" , <EOL> help = "<STR_LIT>" ) <EOL> parser . add_option ( "<STR_LIT>" , dest = "<STR_LIT>" , type = "<STR_LIT:string>" , <EOL> help = "<STR_LIT>" ) <EOL> parser . add_option ( "<STR_LIT>" , dest = "<STR_LIT>" , type = "<STR_LIT:string>" , <EOL> help = "<STR_LIT>" ) <EOL> parser . add_option ( "<STR_LIT>" , dest = "<STR_LIT>" , type = "<STR_LIT:string>" , <EOL> help = "<STR_LIT>" ) <EOL> parser . add_option ( "<STR_LIT>" , dest = "<STR_LIT>" , type = "<STR_LIT:int>" , <EOL> help = "<STR_LIT>" <EOL> "<STR_LIT>" ) <EOL> parser . add_option ( "<STR_LIT>" , dest = "<STR_LIT>" , type = "<STR_LIT:string>" , <EOL> help = "<STR_LIT>" ) <EOL> parser . add_option ( "<STR_LIT>" , dest = "<STR_LIT>" , type = "<STR_LIT:string>" , <EOL> help = "<STR_LIT>" <EOL> "<STR_LIT>" ) <EOL> parser . add_option ( "<STR_LIT>" , dest = "<STR_LIT>" , type = "<STR_LIT:string>" , <EOL> help = "<STR_LIT>" ) <EOL> parser . add_option ( "<STR_LIT>" , dest = "<STR_LIT>" , type = "<STR_LIT:string>" , <EOL> help = "<STR_LIT>" ) <EOL> parser . add_option ( "<STR_LIT>" , dest = "<STR_LIT>" , type = "<STR_LIT:string>" , <EOL> help = "<STR_LIT>" ) <EOL> parser . add_option ( "<STR_LIT>" , dest = "<STR_LIT>" , type = "<STR_LIT:string>" , <EOL> help = "<STR_LIT>" <EOL> "<STR_LIT>" ) <EOL> parser . add_option ( "<STR_LIT>" , dest = "<STR_LIT>" , type = "<STR_LIT:string>" , <EOL> help = "<STR_LIT>" ) <EOL> parser . add_option ( "<STR_LIT>" , dest = "<STR_LIT>" , type = "<STR_LIT:string>" , <EOL> help = "<STR_LIT>" ) <EOL> parser . add_option ( "<STR_LIT>" , dest = "<STR_LIT>" , type = "<STR_LIT:int>" , <EOL> help = "<STR_LIT>" ) <EOL> ( options , args ) = E . Start ( parser , argv = argv ) <EOL> infile = argv [ - <NUM_LIT:1> ] <EOL> parser . set_defaults ( cutHeight = <NUM_LIT:0> , <EOL> conditions = None , <EOL> split = False , <EOL> cluster_size = <NUM_LIT:30> ) <EOL> if options . task == "<STR_LIT>" : <EOL> timepoints = [ int ( x ) for x in options . timepoints . split ( "<STR_LIT:U+002C>" ) ] <EOL> timepoints . sort ( ) <EOL> reps = [ x for x in options . reps . split ( "<STR_LIT:U+002C>" ) ] <EOL> if not options . conditions : <EOL> conditions = None <EOL> else : <EOL> conditions = [ x for x in options . conditions . split ( "<STR_LIT:U+002C>" ) ] <EOL> data_frame = TS . deseqNormalize ( infile = infile , <EOL> time_points = timepoints , <EOL> reps = reps , <EOL> conditions = conditions ) <EOL> elif options . task == "<STR_LIT>" : <EOL> data_frame = TS . maSigPro ( infile = infile , <EOL> order_terms = int ( options . orders ) , <EOL> fdr = float ( options . fdr ) , <EOL> adjust = options . padjust , <EOL> stepwise = options . stepwise , <EOL> include_p = float ( options . pinclude ) , <EOL> rsq = float ( options . rsquared ) , <EOL> var_group = options . vargroup ) <EOL> elif options . task == "<STR_LIT>" : <EOL> timepoints = [ int ( x ) for x in options . timepoints . split ( "<STR_LIT:U+002C>" ) ] <EOL> reps = [ x for x in options . reps . split ( "<STR_LIT:U+002C>" ) ] <EOL> data_frame = TS . covarFilter ( infile = infile , <EOL> time_points = timepoints , <EOL> replicates = reps , <EOL> quantile = int ( options . quantile ) ) <EOL> elif options . task == "<STR_LIT>" : <EOL> data_frame = TS . avTimeExpression ( infile ) <EOL> else : <EOL> pass <EOL> data_frame . to_csv ( options . stdout , <EOL> sep = "<STR_LIT:\t>" , <EOL> header = True , <EOL> index_label = "<STR_LIT>" ) <EOL> E . Stop ( ) <EOL> if __name__ == "<STR_LIT:__main__>" : <EOL> sys . exit ( main ( sys . argv ) ) </s>
