1 ###########################################################################
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 #
7 # All Rights Reserved. #
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: #
17 # The above copyright notice and this permission notice shall be #
18 # included in all copies or substantial portions of the Software. #
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 #
28 ###########################################################################
30 __all__ = ["meme", "locator","mafft", "paircomp", "cisGreedy", "gibbs"]
32 from os import environ
34 supportedPrograms = [("locator" ,"Locator", {"consensus": "",
36 ("meme" ,"Meme", {"model": "zoops",
39 ("cisGreedy", "CisGreedy", {"model": "zoops",
49 ("gibbs", "Gibbs", {"model": "zoops",
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.
66 if environ.get("CISTEMATIC_ROOT"):
67 programRoot = "%s/programs" % environ.get("CISTEMATIC_ROOT")
69 programRoot = "/proj/genome/programs"
74 def __init__(self, tagID="", inputFilePath="", outputFilePath=""):
76 self.inputFilePath = inputFilePath
77 self.outputFilePath = outputFilePath
80 def setTagID(self, tid):
85 return self.__class__.__name__
88 def inputFile(self, inputFilePath):
89 self.inputFilePath = inputFilePath
92 def outputFile(self, outputFilePath):
93 self.outputFilePath = outputFilePath
96 def setSeqLength(self, length):
100 def setGenome(self, genome):
104 def setGenExpOptions(self, optionArray):
113 for line in self.contents:
117 def load(self, inFilePath):
118 inFile = open(inFilePath, "r")
119 self.contents = inFile.readlines()
124 outFile = open(self.outputFilePath, "w")
125 for line in self.contents: