--- /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. #
+###########################################################################
+#
+import os
+import string
+from cistematic.programs import supportedPrograms
+from cistematic.experiments import experimentTypes, loadExperiment
+from os import environ
+
+if environ.get("CISTEMATIC_ROOT"):
+ cisRoot = environ.get("CISTEMATIC_ROOT")
+else:
+ cisRoot = "/proj/genome"
+
+
+class GenExp:
+ dataPath = ""
+ dbFilePath = ""
+ expFilePath = ""
+ expName = ""
+ expType = ""
+ dataset = []
+ expProgs = []
+ expSettings = {}
+ analysisName = ""
+
+
+ def __init__(self, path, dbPath, newexp, type="", dset="", progs="", analysis="", createExp=False):
+ self.dataPath = path
+ self.dbFilePath = dbPath
+ self.expName = newexp
+ self.expFilePath = string.replace(dbPath, ".db", "-db.py")
+ self.expType = type
+ self.dataset = dset
+ self.expProgs = progs
+ self.analysisName = newexp + analysis
+
+ if createExp:
+ self.createExpDB()
+
+ if len(self.expProgs) == 0:
+ exp = loadExperiment( self.expName , self.dbFilePath)
+ self.expType = exp.experimentType
+ self.expProgs = exp.getSetting("expProgs")
+
+ if len(dset) == 0:
+ exp = loadExperiment( self.expName , self.dbFilePath)
+ self.expType = exp.experimentType
+ self.dataset = exp.getDataset()
+
+ self.createExpRunFile()
+
+
+ def run(self):
+ exp = loadExperiment( self.expName , self.dbFilePath)
+ exp.setExternalStatus("QUEUED")
+ del exp
+ os.system("cd %s ; nohup /usr/bin/python %s & " % (self.dataPath, self.expFilePath))
+
+
+ def createExpDB():
+ strexec = 'from cistematic.experiments.' + modName + ' import ' + self.expType + '\n'
+ exec strexec
+ strexec = 'exp = ' + self.expType + '("' + self.expName + '", "' + self.dbFilePath + '")\n'
+ exec strexec
+
+
+ def createExpRunFile(self):
+ outFile = open(self.expFilePath, "w")
+ outFile.write(self.expHead())
+ outFile.write(self.expInit())
+ outFile.write(self.expPrograms())
+ outFile.write(self.expRun())
+ outFile.write(self.expAnalysis())
+ outFile.write(self.expStatus())
+ outFile.close()
+
+
+ def expHead(self):
+ strHead = ["# Experiment: %s autogenerated by Cistematic GenExp 0.9.9b\n" % self.expName]
+ strHead.append("from sys import path\n")
+ strHead.append("cisPath = '%s'\n" % cisRoot)
+ strHead.append("if cisPath not in path:\n\tpath.append(cisPath)\n\n")
+ for oneProg in supportedPrograms:
+ strHead.append("from cistematic.programs.%s import %s\n" % (oneProg[0], oneProg[1]))
+
+ strHead.append("\n")
+
+ return string.join(strHead, "")
+
+
+ def expInit(self):
+ useMussa = False
+ useSeqcomp = False
+ startingGenome = ""
+ targetGenomes = []
+ consGene = []
+ geneIDList = []
+
+ if self.expType in ["orthology", "phyloFoot", "phyloTest"]:
+ exp = loadExperiment( self.expName , self.dbFilePath)
+ consSettings = exp.getSetting("expConsConfig")
+ (window, threshold, numseq, homologs) = consSettings[0].split(":")
+ self.dataset.reverse()
+ if homologs != "1" and exp.settingsHasKey("gTargets"):
+ gTargets = exp.getSetting("gTargets")
+ if len(gTargets) > 0:
+ targetGenomes = gTargets[0].split(":")
+
+ del exp
+ for geneID in self.dataset:
+ (genome, gid) = geneID
+ if (genome not in targetGenomes) and homologs == "1":
+ targetGenomes.append(genome)
+
+ if startingGenome == "":
+ startingGenome = genome
+
+ gid = gid[0]
+ # we are assuming that all of these genes will be from the same
+ # genome - this is only true (or necessary) if these are not
+ # explicitely maked as "homologs" by the user
+ if gid not in consGene:
+ consGene.append(gid)
+
+ geneIDList.append((genome, gid))
+
+ preInitialize = ""
+ if homologs == "1":
+ preInitializeList = ["exp.createConservation()\n"]
+ preInitializeList.append("exp.loadConservation()\n")
+ preInitializeList.append("paralogs = %s\n" % str(geneIDList))
+ preInitializeList.append('exp.insertHomologs(paralogs, "genExp")\n\n')
+ preInitialize = string.join(preInitializeList, "")
+ del consGene[1:]
+
+ if int(numseq) > 0:
+ useSeqcomp = True
+ else:
+ useMussa = True
+ else:
+ initializeArguments = str(self.dataset)
+
+ strInit = ["# Initialize Experiment\n"]
+ strInit.append("from cistematic.experiments import loadExperiment\n\n")
+ strInit.append('exp = loadExperiment("%s", "%s")\n' % (self.expName, self.dbFilePath))
+ strInit.append('exp.setExternalStatus("INITIALIZING")\n')
+ strInit.append(preInitialize)
+ if useMussa or useSeqcomp:
+ if len(targetGenomes) > 0:
+ strInit.append('exp.initialize("%s", %s, %s)\n\n' % (startingGenome, str(consGene), str(targetGenomes)))
+ else:
+ strInit.append('exp.initialize("%s", %s)\n\n' % (startingGenome, str(consGene)))
+ strInit.append('exp.setExternalStatus("CONSERVATION")\n')
+ strInit.append("exp.computeAlignments()\n")
+ else:
+ strInit.append("exp.initialize(%s)\n\n" % initializeArguments)
+
+ if useMussa:
+ strInit.append("exp.mapMussaConservation(window=%s, threshold=%s)\n\n" % (window, threshold))
+
+ if useSeqcomp:
+ strInit.append("exp.mapSeqcompConservation(window=%s, threshold=%s, minSequences=%s)\n\n" % (window, threshold, numseq))
+
+ return string.join(strInit, "")
+
+
+ def expPrograms(self):
+ index = 1
+ genomes = []
+ for (genome, geneID) in self.dataset:
+ if genome not in genomes:
+ genomes.append(genome)
+
+ strProg = ["# Load individual programs and settings\n"]
+ for entry in self.expProgs:
+ progArray = entry[:-1].split(";")
+ (amod, aProg) = progArray[0].split(":")
+ strProg.append("prog%s = %s()\n" % (str(index), aProg))
+ if len(genomes) == 1 and self.expType == "Simple":
+ strProg.apend('prog%s.setGenome("%s")\n' % (str(index), genomes[0]))
+ if len(progArray) > 1:
+ strProg.append("prog%s.setGenExpOptions(%s)\n" % (str(index), str(progArray[1:])))
+ strProg.append("exp.appendProgram(prog%s)\n" % (str(index)))
+ index += 1
+
+ strProg.append("\n")
+
+ return string.join(strProg, "")
+
+
+ def expRun(self):
+ strRun = ["# Run experiment\n",
+ 'exp.setExternalStatus("MOTIF FINDING")\n',
+ "exp.run()\n",
+ "\n"
+ ]
+
+ return string.join(strRun, "")
+
+
+ def expAnalysis(self):
+ strAnalysis = ["# Analysis Section\n",
+ 'exp.setExternalStatus("ANALYZING")\n',
+ 'exp.loadAnalysis("consensus")\n',
+ "exp.annotateConsensus()\n",
+ "exp.mapConsensus()\n",
+ "exp.buildMotifSize()\n",
+ "\n",
+ 'exp.loadAnalysis("1 mismatch")\n',
+ "exp.annotateConsensus(numMismatches=1)\n",
+ "exp.mapConsensus(numMismatches=1)\n",
+ "exp.buildMotifSize()\n",
+ "\n",
+ 'exp.loadAnalysis("PWM - 90% threshold")\n',
+ "exp.annotateConsensus()\n",
+ "exp.mapMotifs(90.0)\n",
+ "exp.buildMotifSize()\n\n",
+ "\n"
+ ]
+
+ return string.join(strAnalysis, "")
+
+
+ def expStatus(self):
+ return "exp.resetExternalStatus()\n\n"
\ No newline at end of file
projects / erange.git / blobdiff