CloneSet20

Bio/AlignAce/Applications.py

Bio/Motif/Applications/_AlignAce.py

    """Create a commandline for the AlignAce program.

    XXX This could use more checking for valid paramters to the program.
    """ 

    def __init__(self,cmd = "AlignACE", **kwargs):
                                                 
        self.parameters =
          [_Option(["-i","input"],["input"], lambda x:x.__class__==str,1,"Input Sequence file in FASTA format."),_Option(["-numcols","numcols"],["input"], lambda x:x.__class__==int,0,"Number of columns to align"),_Option(["-expect","expect"],["input"], lambda x:x.__class__==int,0,"number of sites expected in model "),_Option(["-gcback","gcback"],["input"], lambda x:x.__class__==float,0,"background fractional GC content of input sequence"),_Option(["-minpass","minpass"],["input"], lambda x:x.__class__==int,0,"minimum number of non-improved passes in phase 1"),_Option(["-seed","seed"],["input"], lambda x:x.__class__==int,0,"set seed for random number generator (time)"),_Option(["-undersample","undersample"],["input"], lambda x:x.__class__==int,0,"possible sites / (expect * numcols * seedings)"),_Option(["-oversample","oversample"],["input"], lambda x:x.__class__==int,0,"1/undersample"), ] 
























        AbstractCommandline.__init__(self,cmd,  **kwargs) 

    """Create a commandline for the AlignAce program.

    XXX This could use more checking for valid paramters to the program.
    """ 

    def __init__(self,cmd = "AlignACE", **kwargs):
                                                 
        self.parameters =
          [_Option(["-i","input"],["input"], lambda x:x.__class__==str,1,"Input Sequence file in FASTA format."),_Option(["-numcols","numcols"],["input"], lambda x:x.__class__==int,0,"Number of columns to align"),_Option(["-expect","expect"],["input"], lambda x:x.__class__==int,0,"number of sites expected in model "),_Option(["-gcback","gcback"],["input"], lambda x:x.__class__==float,0,"background fractional GC content of input sequence"),_Option(["-minpass","minpass"],["input"], lambda x:x.__class__==int,0,"minimum number of non-improved passes in phase 1"),_Option(["-seed","seed"],["input"], lambda x:x.__class__==int,0,"set seed for random number generator (time)"),_Option(["-undersample","undersample"],["input"], lambda x:x.__class__==int,0,"possible sites / (expect * numcols * seedings)"),_Option(["-oversample","oversample"],["input"], lambda x:x.__class__==int,0,"1/undersample"), ] 
























        AbstractCommandline.__init__(self,cmd,  **kwargs) 

"""Create a commandline for the AlignAce program.

    XXX This could use more checking for valid paramters to the program.
    """ 

def __init__(self,cmd = "AlignACE", **kwargs):
  self.parameters = [_Option(["-i","input"],["input"], lambda x:x.__class__==str,1,"Input Sequence file in FASTA format."),_Option(["-numcols","numcols"],["input"], lambda x:x.__class__==int,0,"Number of columns to align"),_Option(["-expect","expect"],["input"], lambda x:x.__class__==int,0,"number of sites expected in model "),_Option(["-gcback","gcback"],["input"], lambda x:x.__class__==float,0,"background fractional GC content of input sequence"),_Option(["-minpass","minpass"],["input"], lambda x:x.__class__==int,0,"minimum number of non-improved passes in phase 1"),_Option(["-seed","seed"],["input"], lambda x:x.__class__==int,0,"set seed for random number generator (time)"),_Option(["-undersample","undersample"],["input"], lambda x:x.__class__==int,0,"possible sites / (expect * numcols * seedings)"),_Option(["-oversample","oversample"],["input"], lambda x:x.__class__==int,0,"1/undersample"), ] 
  AbstractCommandline.__init__(self,cmd, **kwargs)