def main_function():
parser = OptionParser()
parser.add_option("-v", "--verbose", action="store_true", dest="verbose", default=False, help="set verbose mode")
parser.add_option(
"--config",
type="string",
metavar="FILE",
dest="config",
default="redirector.config",
help="Master configuration file that provides most setting for the Flux Balanace Analysis. Extra variable settings will be ingnored. Hence the same config can be used for multiple analysis functions",
)
parser.add_option(
"-c",
"--modelConfig",
type="string",
metavar="FILE",
dest="configFileName",
default="model_config.txt",
help="Configuration file which sets model files",
)
parser.add_option(
"-n",
"--configNames",
type="string",
metavar="String",
dest="configNames",
default="Default",
help="A comma separated list of the names of configurations to use, as set out in the configuration file",
)
parser.add_option(
"-m",
"--modelname",
type="string",
metavar="String",
dest="modelName",
default="",
help="Name of model(s) from the modelconfiguration file",
)
parser.add_option(
"-b",
"--bioObjective",
type="string",
dest="bioObj",
default="Biomass",
help="Name / ID of biological objective reaction",
metavar="String",
)
parser.add_option(
"-o",
"--outputfile",
dest="outputFileName",
default=None,
help="Name of report file to be generated",
metavar="FILE",
)
parser.add_option(
"-r",
"--result_directory",
type="string",
metavar="directory",
dest="resultDirectory",
default="../../results/",
help="Directory where results are stored",
)
parser.add_option(
"--targets",
type="string",
metavar="String",
dest="targets",
default="",
help="List of valid reaction target, if left blank will be automatically filled in from metabolic network file",
)
parser.add_option(
"--report",
action="store_true",
dest="isReport",
default=False,
help="When this tag is used a report will be generated when the analysis is finished",
metavar="boolean",
)
parser.add_option("--debug", action="store_true", dest="debug", default=False, help="turn on debug mode")
parser.add_option("--gm", "--GeneMap", action="store_true", dest="useGeneMap", default=False, help="Use Gene Map")
parser.add_option(
"--section",
type="string",
metavar="String",
dest="subSections",
default="",
help="Comma separated list of sections of the model files to use",
)
# -------------------------------
# Parse options
# -------------------------------
(options, args) = parser.parse_args()
config = ReflectionConfig()
config.readfp(open("Redirector.config"))
# ---------------------------
# configure preset analysis
# ---------------------------
configNames = options.configNames.split(",")
configNames.insert(0, "Redirector Model")
for name in configNames:
config.merge(name, "Redirector", append=True)
# ----------------------------------------
# reflect options from configuration
# ----------------------------------------
config.reflect("Redirector", options)
config.load("Redirector", options.__dict__, override=False)
# -----------------------------------------
# Check and Build Storage Directories
# -----------------------------------------
dataDirectory = config.getValue("Redirector", "dataDirectory", classType="".__class__)
resultsDirectory = config.getValue("Redirector", "resultDirectory", classType="".__class__)
analysisDirectory = config.getValue("Redirector", "analysisDirectory", classType="".__class__)
if not os.path.exists(dataDirectory):
raise IOError("unable to find required data directory" % dataDirectory)
if not os.path.exists(resultsDirectory):
os.makedirs(resultsDirectory)
if not os.path.exists(analysisDirectory):
os.makedirs(analysisDirectory)
# ----------------------------
# Parse Inputs
# ----------------------------
verbose = options.verbose
modelName = options.modelName
objectiveName = options.bioObj
outputFileName = options.outputFileName
"""
#----------------------------------------------------
# Initialize and set values for tools and factories
#----------------------------------------------------
"""
naturalObjective = {objectiveName: -1.0}
if verbose:
print "Flux Balanace Analysis Version 1.6"
if verbose:
print "Model names: [%s]" % (modelName)
if verbose:
print "Parsing data files for [%s]" % (modelName)
"""
I. Parse data files and configuration settings
"""
if verbose:
print "----------------Loading Metabolic Models---------------"
modelNames = modelName.split(",")
modelFactory = ModelFactory()
config.reflect("Redirector", modelFactory)
(fluxModel, modelMatrix, reducer, geneReduction) = modelFactory.loadModel(modelNames)
model = modelMatrix
if verbose:
print "removing objectives from target set"
targets = modelMatrix.targets
if verbose:
print "Targets List Size [%s]" % len(targets)
lps = LPSolver()
predictions = lps.run(model, naturalObjective)
objectiveValue = predictions[objectiveName]
lps.clear()
if verbose:
print "Optimized Objective [%s] Value [%s]" % (objectiveName, objectiveValue)
report = fluxModel.getReport()
report.addColumnHash("Flux", predictions)
if outputFileName == None or outputFileName == "":
outputFileName = resultsDirectory + "FBA_%s_%s.txt" % (modelName, strftime("%Y%m%dT%H%M%S"))
writer = ReportWriter()
writer.setFile(outputFileName)
writer.write(report)
writer.closeFile()
if verbose:
print "Report Written [%s]" % (outputFileName)
dest="targetSeq",
default="",
help="fasta formated file of recombination target regions",
metavar="FILE")
parser.add_option("-r", "--recombination_seq",
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
dest="targetFileObjectives",
default = "",
help="List of objectives to get target count information for",
metavar="FILE")
parser.add_option("-o","--outputfile",
dest="outputFileName",
default = "rd_output.csv",
help="name of report FILE",
metavar="FILE")
# Parse options
(options,args) = parser.parse_args()
# Parse main configuration file
config = ReflectionConfig()
config.readfp(open("Redirector.config"))
#---------------------------
# configure preset analysis
#---------------------------
#options.configNames = "Default"
#options.configNames = "iAF1260 Export"
#options.configNames = "Test iAF1260"
#options.configNames = "Test Simple Model"
#options.configNames = "iAF1260 Export"
configNames = options.configNames.split(",")
configNames.append("Redirector Model")
for name in configNames:
help="melting temperature of suggested primers",
metavar="FILE")
parser.add_option("--minDeltaG",
dest="minDeltaG",
default=-13.0,
help="minimum folding energy of oligos",
metavar="FILE")
#parse command line arguments
(options,args) = parser.parse_args()
configFileName = options.config
configName = options.configName
# Parse main configuration and reflect into options
config = ReflectionConfig()
config.readfp(open(configFileName))
config.reflect(configName,options)
#----------------------------
#load command line
#----------------------------
verbose = options.verbose
mode = options.mode
locationFile = options.locationFile
targetFile = options.targetFile
oligoFileName = options.oligoFile
blastDB = options.databaseFile
