erange 4.0a dev release with integrated cistematic

[erange.git] / cistematic / programs / __init__.py

diff --git a/cistematic/programs/__init__.py b/cistematic/programs/__init__.py
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+###########################################################################
+#                                                                         #
+# C O P Y R I G H T   N O T I C E                                         #
+#  Copyright (c) 2003-10 by:                                              #
+#    * California Institute of Technology                                 #
+#                                                                         #
+#    All Rights Reserved.                                                 #
+#                                                                         #
+# Permission is hereby granted, free of charge, to any person             #
+# obtaining a copy of this software and associated documentation files    #
+# (the "Software"), to deal in the Software without restriction,          #
+# including without limitation the rights to use, copy, modify, merge,    #
+# publish, distribute, sublicense, and/or sell copies of the Software,    #
+# and to permit persons to whom the Software is furnished to do so,       #
+# subject to the following conditions:                                    #
+#                                                                         #
+# The above copyright notice and this permission notice shall be          #
+# included in all copies or substantial portions of the Software.         #
+#                                                                         #
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,         #
+# EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF      #
+# MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND                   #
+# NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS     #
+# BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN      #
+# ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN       #
+# CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE        #
+# SOFTWARE.                                                               #
+###########################################################################
+#
+__all__ = ["meme", "locator","mafft", "paircomp", "cisGreedy", "gibbs"]
+
+from os import environ
+
+supportedPrograms = [("locator" ,"Locator", {"consensus": "",
+                                             "identifier": ""}),
+                     ("meme" ,"Meme", {"model": "zoops",
+                                       "nmotifs": 10,
+                                       "maxwidth": 16}),
+                     ("cisGreedy", "CisGreedy", {"model": "zoops",
+                                                 "nmotifs": 10,
+                                                 "maxwidth": 16,
+                                                 "minwidth": 6,
+                                                 "reverse": True,
+                                                 "background": "None",
+                                                 "iterations": 100,
+                                                 "founder": False,
+                                                 "percentID": 75,
+                                                 "Markov size": 3}),
+                     ("gibbs", "Gibbs", {"model": "zoops",
+                                         "nmotifs": 10,
+                                         "maxwidth":16,
+                                         "minwidth": 6,
+                                         "reverse": True,
+                                         "background": "None",
+                                         "percentID": 50,
+                                         "Markov size": 3,
+                                         "iterations": 100})
+]
+
+
+class Program:
+    """ Program is the Super class for all of the programs supported by cistematic and 
+        that are typically called by other classes in cistematic, such as the Experiments.
+        Children will overide the methods that they need to instantiate. 
+    """
+    if environ.get("CISTEMATIC_ROOT"):
+        programRoot = "%s/programs" % environ.get("CISTEMATIC_ROOT")
+    else:
+        programRoot = "/proj/genome/programs"
+
+    contents = ""
+    tagID = ""
+
+    def __init__(self, tagID="", inputFilePath="", outputFilePath=""):
+        self.tagID = ""
+        self.inputFilePath = inputFilePath
+        self.outputFilePath = outputFilePath
+
+
+    def setTagID(self, tid):
+        self.tagID = tid
+
+
+    def name(self):
+        return self.__class__.__name__
+
+
+    def inputFile(self, inputFilePath):
+        self.inputFilePath = inputFilePath
+
+
+    def outputFile(self, outputFilePath):
+        self.outputFilePath = outputFilePath
+
+
+    def setSeqLength(self, length):
+        pass
+
+
+    def setGenome(self, genome):
+        pass
+
+
+    def setGenExpOptions(self, optionArray):
+        pass
+
+
+    def run(self):
+        pass
+
+
+    def display(self):
+        for line in self.contents:
+            print line
+
+
+    def load(self, inFilePath):
+        inFile = open(inFilePath, "r")
+        self.contents = inFile.readlines()
+        inFile.close()
+
+
+    def save(self):
+        outFile = open(self.outputFilePath, "w")
+        for line in self.contents:
+            outFile.write(line)
+
+        outFile.close()
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