targetPercent = 0.40 usePersist=False #options.userControl = "T" #options.loadTargetFiles = True #options.controlFile = "T" ''' #---------------------------------------------------- # Initialize and set values for tools and tfactories #---------------------------------------------------- ''' verbose = True naturalObjective = {naturalObjectiveName:-1.0} syntheticObjective = {syntheticObjectiveName:-1.0} resultTag = config.get("Redirector", "resultTag") protectedTargets = set(naturalObjective.keys()).union(syntheticObjective.keys()) if verbose: print "Process Analysis Version 1.0" if verbose: print "Model names: [%s]" % (modelName) if verbose: print "Synthetic objective: [%s]" % (syntheticObjectiveName) if verbose: print "Parsing data files for [%s]" % (modelName) ''' * 0. Process target files into overview table ''' targetFileObjectives = options.targetFileObjectives if targetFileObjectives != '': findBestTargetSets(targetFileObjectives, k, n) '''
dest="recSeq", default="", help="VCF file format of recombination sequencing results", metavar="FILE") #Parse command line arguments, parse configuration, reflect into options (options,args) = parser.parse_args() configFileName = options.config configName = options.configName config = ReflectionConfig() config.readfp(open(configFileName)) config.reflect(configName,options) #Set variables verbose = options.verbose blastDB = config.get(configName, "databasefile") blastExe = config.get(configName, "blastExe") readFile = options.recSeq targetFile = options.targetSeq readRegx = 'Sample\.(.*)\.txt' rregx = re.search(readRegx,readFile) #temporary debugging variables #oligoReport = "20120709_FattyAcid_sequencing_colonies_primers.csv" #oligoSeqFile = "20120709_FA_recombination_oligos_v2.fasta" #! Make this something taken from the configuration file #oligoSeqFile = options.workFolder + oligoSeqFile #bTools = BlastTools() #bTools.verbose = verbose #bTools.blastDB = blastDB #bTools.blastExe = blastExe