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
