########################################################################### # # # 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"