--- /dev/null
+###########################################################################
+# #
+# 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. #
+###########################################################################
+#
+# covariance.py
+from cistematic.programs import Program
+import time, Consensus
+from cistematic.core.motif import Motif
+
+
+class CisGreedy(Program):
+
+
+ def getSettings(self):
+ return (self.model, self.nmotifs, self.minwidth, self.maxwidth, self.bON,
+ self.iterations, self.Founder, self.bfile, self.percID,
+ self.founderPercID, self.MarkovSize)
+
+
+ def setSettings(self, settings):
+ self.motifs = []
+ (self.model, self.nmotifs, self.minwidth, self.maxwidth, self.bON,
+ self.iterations, self.Founder, self.bfile, self.percID,
+ self.founderPercID, self.MarkovSize) = settings
+
+
+ def setGenExpOptions(self, optionArray):
+ self.setModel("zoops")
+ self.setNumMotifs("10")
+ self.setMaxWidth("15")
+ self.setMinWidth("6")
+ self.setBON(True)
+ self.setIterations("100")
+ self.bfile = "None"
+ self.TCM="All"
+ self.Founder = False
+ self.setPercID("75")
+ self.setMarkovSize("3")
+ self.setFounderPID("75")
+ self.setBackground("None")
+ for option in optionArray:
+ (optionTag, optionValue) = option.split(":")
+
+ if optionTag == "Markov size":
+ self.setMarkovSize(optionValue)
+
+ if optionTag == "percentID":
+ self.setPercID(optionValue)
+
+ if optionTag == "founderPercentID":
+ self.setFounderPID(optionValue)
+
+ if optionTag == "model":
+ self.setModel(optionValue)
+
+ if optionTag == "nmotifs":
+ self.setNumMotifs(optionValue)
+
+ if optionTag == "width":
+ self.setMinWidth(optionValue)
+ self.setMaxWidth(optionValue)
+
+ if optionTag == "minWidth":
+ self.setMinWidth(optionValue)
+
+ if optionTag == "maxWidth":
+ self.setMaxWidth(optionValue)
+
+ if optionTag == "reverse":
+ self.setBON(optionValue)
+
+ if optionTag == "iterations":
+ self.setIterations(optionValue)
+
+ if optionTag == "background":
+ self.setBackground(optionValue)
+
+ if optionTag == "founder":
+ self.setFounder(True)
+
+ #if no background file is provided the default setting
+ #is to use the input sequences as a background
+ print self.bfile
+ #set markovSize
+
+
+ def setMarkovSize(self, val):
+ self.MarkovSize = int(str(val))
+
+
+ def setFounderPID(self, val):
+ self.founderPercID = int(str(val))
+
+
+ def setFounder(self, boolVal):
+ if boolVal:
+ self.Founder = True
+ else:
+ self.Founder = False
+
+
+ def setPercID(self, percVal):
+ self.percID = int(str(percVal))
+
+
+ def setModel(self, modelType):
+ if modelType in ["oops", "zoops", "tcm"]:
+ self.model = str(modelType)
+ else:
+ self.model = "zoops";
+
+
+ def setIterations(self, number):
+ self.iterations = int(str(number))
+
+
+ def setNumMotifs(self, motifNum):
+ self.nmotifs = int(str(motifNum))
+
+
+ def setBON(self, B_val):
+ if str(B_val) == "False":
+ self.bON = False
+ else:
+ self.bON = True
+
+
+ def getSequences(self, infile):
+ seqFiles = open(infile, 'r')
+ Lines = seqFiles.readlines()
+ seqFiles.close()
+ self.sequences = []
+ for line in Lines:
+ if line[0] != ">":
+ self.sequences.append(line[:-1])
+
+
+ def setMinWidth(self, width):
+ self.minwidth = int(str(width))
+
+
+ def setMaxWidth(self, width):
+ self.maxwidth = int(str(width))
+
+
+ def setBackground(self, backFile):
+ self.bfile = str(backFile)
+
+
+ def run(self):
+ print self.nmotifs
+ startTime = time.time()
+ if self.bfile == "None":
+ self.bfile = Consensus.Markov(self.sequences, self.bON,self.MarkovSize)
+
+ print "geting consensus score"
+ self.contents = Consensus.MotifFinder(self.sequences, self.minwidth, self.maxwidth,
+ self.nmotifs, self.iterations, self.bfile,
+ self.bON, self.Founder,self.percID,
+ self.founderPercID, self.MarkovSize, self.model,
+ self.TCM)
+ stopTime = time.time()
+ print "\nThis run took %.3f - %.3f = %.3f seconds and produced %d motifs" % (startTime, stopTime, stopTime - startTime, len(self.contents[0]))
+
+
+ def getMotifs(self):
+ self.motifs = []
+ try:
+ (PWMs, Seqs) = self.contents
+ for index in range(len(Seqs)):
+ self.motifs.append(Motif("%s-cisGreedy-%s" % (self.tagID, str(index + 1)), seqs=Seqs[index]))
+ except:
+ print "error returning motifs"
+ pass
+
+ return self.motifs
\ No newline at end of file
projects / erange.git / blobdiff