cistematic/programs/__init__.py

   1 ###########################################################################
   2 #                                                                         #
   3 # C O P Y R I G H T   N O T I C E                                         #
   4 #  Copyright (c) 2003-10 by:                                              #
   5 #    * California Institute of Technology                                 #
   6 #                                                                         #
   7 #    All Rights Reserved.                                                 #
   8 #                                                                         #
   9 # Permission is hereby granted, free of charge, to any person             #
  10 # obtaining a copy of this software and associated documentation files    #
  11 # (the "Software"), to deal in the Software without restriction,          #
  12 # including without limitation the rights to use, copy, modify, merge,    #
  13 # publish, distribute, sublicense, and/or sell copies of the Software,    #
  14 # and to permit persons to whom the Software is furnished to do so,       #
  15 # subject to the following conditions:                                    #
  16 #                                                                         #
  17 # The above copyright notice and this permission notice shall be          #
  18 # included in all copies or substantial portions of the Software.         #
  19 #                                                                         #
  20 # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,         #
  21 # EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF      #
  22 # MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND                   #
  23 # NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS     #
  24 # BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN      #
  25 # ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN       #
  26 # CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE        #
  27 # SOFTWARE.                                                               #
  28 ###########################################################################
  29 #
  30 __all__ = ["meme", "locator","mafft", "paircomp", "cisGreedy", "gibbs"]
  31
  32 from os import environ
  33
  34 supportedPrograms = [("locator" ,"Locator", {"consensus": "",
  35                                              "identifier": ""}),
  36                      ("meme" ,"Meme", {"model": "zoops",
  37                                        "nmotifs": 10,
  38                                        "maxwidth": 16}),
  39                      ("cisGreedy", "CisGreedy", {"model": "zoops",
  40                                                  "nmotifs": 10,
  41                                                  "maxwidth": 16,
  42                                                  "minwidth": 6,
  43                                                  "reverse": True,
  44                                                  "background": "None",
  45                                                  "iterations": 100,
  46                                                  "founder": False,
  47                                                  "percentID": 75,
  48                                                  "Markov size": 3}),
  49                      ("gibbs", "Gibbs", {"model": "zoops",
  50                                          "nmotifs": 10,
  51                                          "maxwidth":16,
  52                                          "minwidth": 6,
  53                                          "reverse": True,
  54                                          "background": "None",
  55                                          "percentID": 50,
  56                                          "Markov size": 3,
  57                                          "iterations": 100})
  58 ]
  59
  60
  61 class Program:
  62     """ Program is the Super class for all of the programs supported by cistematic and
  63         that are typically called by other classes in cistematic, such as the Experiments.
  64         Children will overide the methods that they need to instantiate.
  65     """
  66     if environ.get("CISTEMATIC_ROOT"):
  67         programRoot = "%s/programs" % environ.get("CISTEMATIC_ROOT")
  68     else:
  69         programRoot = "/proj/genome/programs"
  70
  71     contents = ""
  72     tagID = ""
  73
  74     def __init__(self, tagID="", inputFilePath="", outputFilePath=""):
  75         self.tagID = ""
  76         self.inputFilePath = inputFilePath
  77         self.outputFilePath = outputFilePath
  78
  79
  80     def setTagID(self, tid):
  81         self.tagID = tid
  82
  83
  84     def name(self):
  85         return self.__class__.__name__
  86
  87
  88     def inputFile(self, inputFilePath):
  89         self.inputFilePath = inputFilePath
  90
  91
  92     def outputFile(self, outputFilePath):
  93         self.outputFilePath = outputFilePath
  94
  95
  96     def setSeqLength(self, length):
  97         pass
  98
  99
 100     def setGenome(self, genome):
 101         pass
 102
 103
 104     def setGenExpOptions(self, optionArray):
 105         pass
 106
 107
 108     def run(self):
 109         pass
 110
 111
 112     def display(self):
 113         for line in self.contents:
 114             print line
 115
 116
 117     def load(self, inFilePath):
 118         inFile = open(inFilePath, "r")
 119         self.contents = inFile.readlines()
 120         inFile.close()
 121
 122
 123     def save(self):
 124         outFile = open(self.outputFilePath, "w")
 125         for line in self.contents:
 126             outFile.write(line)
 127
 128         outFile.close()