Source Code for Module Bio.motifs.applications._alignace

  1  # Copyright 2003-2009 by Bartek Wilczynski.  All rights reserved. 
  2  # Revisions copyright 2009 by Peter Cock. 
  3  # This code is part of the Biopython distribution and governed by its 
  4  # license.  Please see the LICENSE file that should have been included 
  5  # as part of this package. 
  6  """This module provides code to work with the standalone version of AlignACE, 
  7  for motif search in DNA sequences. 
  8   
  9  AlignACE homepage: 
 10   
 11  http://arep.med.harvard.edu/mrnadata/mrnasoft.html 
 12   
 13  AlignACE Citations: 
 14   
 15  Computational identification of cis-regulatory elements associated with 
 16  groups of functionally related genes in Saccharomyces cerevisiae, 
 17  Hughes, JD, Estep, PW, Tavazoie S, & GM Church, Journal of Molecular 
 18  Biology 2000 Mar 10;296(5):1205-14. 
 19   
 20  Finding DNA Regulatory Motifs within Unaligned Non-Coding Sequences 
 21  Clustered by Whole-Genome mRNA Quantitation, 
 22  Roth, FR, Hughes, JD, Estep, PE & GM Church, Nature Biotechnology 
 23  1998 Oct;16(10):939-45. 
 24   
 25  """ 
 26  from Bio.Application import AbstractCommandline, _Option, _Argument 
 27   
 28   
 29 -class AlignAceCommandline(AbstractCommandline): 
 30      """Create a commandline for the AlignAce program. 
 31   
 32      Example: 
 33   
 34      >>> from Bio.Motif.Applications import AlignAceCommandline 
 35      >>> in_file = "sequences.fasta" 
 36      >>> alignace_cline = AlignAceCommandline(infile=in_file, gcback=0.55) 
 37      >>> print alignace_cline 
 38      AlignACE -i sequences.fasta -gcback 0.55 
 39   
 40      You would typically run the command line with alignace_cline() or via 
 41      the Python subprocess module, as described in the Biopython tutorial. 
 42      """ 
 43 -    def __init__(self, cmd="AlignACE", **kwargs): 
 44          self.parameters = \ 
 45            [ 
 46              _Option(["-i", "infile"], 
 47                      "Input Sequence file in FASTA format.", 
 48                      checker_function=lambda x: isinstance(x, str), 
 49                      equate=False, 
 50                      filename=True), 
 51   
 52              _Option(["-numcols", "numcols"], 
 53                      "Number of columns to align", 
 54                      equate=False, 
 55                      checker_function=lambda x: isinstance(x, int)), 
 56   
 57              _Option(["-expect", "expect"], 
 58                      "number of sites expected in model", 
 59                      equate=False, 
 60                      checker_function=lambda x: isinstance(x, int)), 
 61   
 62              _Option(["-gcback", "gcback"], 
 63                      "background fractional GC content of input sequence", 
 64                      equate=False, 
 65                      checker_function=lambda x: isinstance(x, float)), 
 66   
 67              _Option(["-minpass", "minpass"], 
 68                      "minimum number of non-improved passes in phase 1", 
 69                      equate=False, 
 70                      checker_function=lambda x: isinstance(x, int)), 
 71   
 72              _Option(["-seed", "seed"], 
 73                      "set seed for random number generator (time)", 
 74                      equate=False, 
 75                      checker_function=lambda x: isinstance(x, int)), 
 76   
 77              _Option(["-undersample", "undersample"], 
 78                      "possible sites / (expect * numcols * seedings)", 
 79                      equate=False, 
 80                      checker_function=lambda x: isinstance(x, int)), 
 81   
 82              _Option(["-oversample", "oversample"], 
 83                      "1/undersample", 
 84                      equate=False, 
 85                      checker_function=lambda x: isinstance(x, int)), 
 86            ] 
 87          AbstractCommandline.__init__(self, cmd, **kwargs) 
 88   
 89   
 90 -class CompareAceCommandline(AbstractCommandline): 
 91      """Create a commandline for the CompareAce program. 
 92   
 93      Example: 
 94   
 95      >>> from Bio.Motif.Applications import CompareAceCommandline 
 96      >>> m1_file = "sequences1.fasta" 
 97      >>> m2_file = "sequences2.fasta" 
 98      >>> compareace_cline = CompareAceCommandline(motif1=m1_file, motif2=m2_file) 
 99      >>> print compareace_cline 
100      CompareACE sequences1.fasta sequences2.fasta 
101   
102      You would typically run the command line with compareace_cline() or via 
103      the Python subprocess module, as described in the Biopython tutorial. 
104      """ 
105 -    def __init__(self, cmd="CompareACE", **kwargs): 
106          import os.path 
107   
108          self.parameters = \ 
109            [ 
110              _Argument(["motif1"], 
111                          "name of file containing motif 1", 
112                          checker_function=lambda x: isinstance(x, str), 
113                          filename=True), 
114              _Argument(["motif2"], 
115                          "name of file containing motif 2", 
116                          checker_function=lambda x: isinstance(x, str), 
117                          filename=True), 
118            ] 
119          AbstractCommandline.__init__(self, cmd, **kwargs) 
120   
121   
122 -def _test(): 
123      """Run the module's doctests (PRIVATE).""" 
124      print "Running AlignAce doctests..." 
125      import doctest 
126      doctest.testmod() 
127      print "Done" 
128   
129   
130  if __name__ == "__main__": 
131      _test() 
132