--- /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. #
+###########################################################################
+#
+# meme.py
+import os
+import time
+import string
+from cistematic.programs import Program
+from cistematic.core.motif import Motif
+from erange.commoncode import getConfigParser, getConfigOption
+
+SUPPORTED_MODELS = ["oops", "zoops", "tcm"]
+
+class Meme(Program):
+
+
+ def __init__(self):
+ parser = getConfigParser()
+ memeProgramName = getConfigOption(parser, "programs", "meme", default="meme.3.0.8")
+ self.memePath = string.join([Program.programRoot, memeProgramName], "/")
+ self.model = "zoops"
+ self.background = ""
+ self.numMotifs = 10
+ self.minWidth = 6
+ self.maxWidth = 15
+ self.bfile = ""
+ self.motifs = []
+ self.contents = []
+
+
+ def getSettings(self):
+ return (self.model, self.background, self.numMotifs, self.bfile)
+
+
+ def setSettings(self, settings):
+ self.clearMotifList()
+ try:
+ (self.model, self.background, self.numMotifs, self.bfile) = settings
+ except ValueError:
+ print "Error unpacking settings for Meme. No parameters changed."
+
+
+ def setGenExpOptions(self, optionArray):
+ for option in optionArray:
+ try:
+ (optionName, optionValue) = option.split(":")
+ except ValueError:
+ continue
+
+ if optionName == "model":
+ self.setModel(optionValue)
+
+ if optionName == "nmotifs":
+ self.setNumMotifs(optionValue)
+
+ if optionName == "maxwidth":
+ self.setMaxWidth(optionValue)
+
+
+ def buildCommand(self):
+ argList = ["%s/bin/meme" % self.memePath,
+ self.inputFilePath,
+ "-dna -maxsize 1000000",
+ "-maxw %d" % self.maxWidth,
+ "-minw %d" % self.minWidth,
+ "-mod %s" % self.model,
+ "-revcomp -nmotifs %d" % self.numMotifs
+ ]
+
+ if self.bfile != "":
+ argList.append("-bfile %s" % self.bfile)
+
+ cmd = string.join(argList, " ")
+
+ return cmd
+
+
+ def setModel(self, modelType):
+ if modelType in SUPPORTED_MODELS:
+ self.model = modelType
+
+
+ def setNumMotifs(self, motifNum):
+ self.numMotifs = motifNum
+
+
+ def setMinWidth(self, width):
+ self.minWidth = width
+
+
+ def setMaxWidth(self, width):
+ self.maxWidth = width
+
+
+ def setBackground(self, backgroundFileName):
+ self.bfile = backgroundFileName
+
+
+ def clearMotifList(self):
+ self.motifs = []
+
+
+ def setContents(self, motifFile):
+ self.contents = motifFile.readlines()
+
+
+ def run(self):
+ startTime = time.time()
+ memeResultFile = os.popen(Meme.buildCommand(self))
+ self.setContents(memeResultFile)
+ stopTime = time.time()
+
+ print "\nThis run took %.3f seconds and produced %d lines" % (stopTime - startTime, len(self.contents))
+
+
+ def getMotifs(self):
+ index = 0
+ self.clearMotifList()
+ try:
+ for motif in range(0, self.numMotifs):
+ PWM = []
+ seqList = []
+ index = self.locateMotifSeqs(index)
+ info = self.contents[index]
+ index += 1
+ while string.find(self.contents[index], "//") < 0:
+ fields = self.contents[index].split()
+ seqList.append(fields[-2])
+ index += 1
+
+ motifName = "%s-meme-%d" % (self.tagID, motif + 1)
+ self.motifs.append(Motif(motifName, "", PWM, seqList, 0.0, info))
+ except:
+ pass
+
+ return self.motifs
+
+
+ def locateMotif(self, startingLineNum):
+ return self.getDataLineNumberAfterHeader("pspm_doc", startingLineNum)
+
+
+ def locateMotifSeqs(self, startingLineNum):
+ return self.getDataLineNumberAfterHeader("BLOCKS_doc", startingLineNum)
+
+
+ def getDataLineNumberAfterHeader(self, headerText, startingLineNum):
+ currentLineNum = startingLineNum
+ numLines = len(self.contents)
+ while currentLineNum < numLines and string.find(self.contents[currentLineNum], headerText) < 0:
+ currentLineNum += 1
+
+ if currentLineNum < numLines:
+ return currentLineNum + 3
+
+ return -1
\ No newline at end of file
projects / erange.git / blobdiff