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