Package Bio :: Package AlignAce :: Module Applications
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Source Code for Module Bio.AlignAce.Applications

 1  """Definitions for interacting with AlignAce. 
 2  """ 
 3  from Bio import Application 
 4  from Bio.Application import _Option,_Argument 
 5   
6 -class AlignAceCommandline(Application.AbstractCommandline):
7 """Create a commandline for the AlignAce program. 8 9 XXX This could use more checking for valid paramters to the program. 10 """
11 - def __init__(self, cmd = "AlignACE"):
12 13 Application.AbstractCommandline.__init__(self) 14 self.program_name = cmd 15 16 self.parameters = \ 17 [ 18 _Option(["-i","input","Sequence File"],["input"],lambda x : x.__class__== str,1, 19 "Input Sequence file in FASTA format."), 20 21 _Option(["-numcols","numcols","number of columns to align"],["input"],lambda x : x.__class__== int,0, 22 "Number of columns to align"), 23 24 _Option(["-expect","expect","number of sites expected in model "],["input"],lambda x : x.__class__== int,0, 25 "number of sites expected in model "), 26 27 _Option(["-gcback","gcback","background fractional GC content of input sequence"],["input"],lambda x : x.__class__== float,0, 28 "background fractional GC content of input sequence"), 29 30 _Option(["-minpass","minpass","minimum number of non-improved passes in phase 1"],["input"],lambda x : x.__class__== int,0, 31 "minimum number of non-improved passes in phase 1"), 32 33 _Option(["-seed","seed","set seed for random number generator (time)"],["input"],lambda x : x.__class__== int,0, 34 "set seed for random number generator (time)"), 35 36 _Option(["-undersample","undersample","possible sites / (expect * numcols * seedings)"],["input"],lambda x : x.__class__== int,0, 37 "possible sites / (expect * numcols * seedings)"), 38 39 _Option(["-oversample","oversample","1/undersample"],["input"],lambda x : x.__class__== int,0, 40 "1/undersample"), 41 ]
42
43 - def run(self):
44 return Application.generic_run(self)
45 46 47
48 -class CompareAceCommandline(Application.AbstractCommandline):
49 """Create a commandline for the CompareAce program. 50 51 XXX This could use more checking for valid paramters to the program. 52 """
53 - def __init__(self, cmd = "CompareACE"):
54 55 import os.path 56 Application.AbstractCommandline.__init__(self) 57 self.program_name = cmd 58 59 self.parameters = \ 60 [ 61 _Argument(["motif1"],["input","file"], os.path.exists,1,"name of file containing motif 1"), 62 _Argument(["motif2"],["input","file"], os.path.exists,1,"name of file containing motif 2"), 63 ]
64
65 - def run(self):
66 return Application.generic_run(self)
67