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Clone Mass | Clones in CloneSet | Parameter Count | Clone Similarity | Syntax Category [Sequence Length] |
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32 | 2 | 0 | 1.000 | stmt_list[2] |
Clone Abstraction | Parameter Bindings |
Clone Instance (Click to see clone) | Line Count | Source Line | Source File |
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1 | 32 | 7 | Bio/AlignAce/Applications.py |
2 | 32 | 30 | Bio/Motif/Applications/_AlignAce.py |
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"""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) |
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"""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) |
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"""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) |
CloneAbstraction |
Parameter Index | Clone Instance | Parameter Name | Value |
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None |