# Path: xenoGI/parameters.py
# def createParametersD(baseParamStr,paramFN):
# def addParametersToD(paramL,paramD):
# def loadFileNameMapD(fileNameMapFN,genbankFileList=None):
# 
# Path: xenoGI/xenoGI.py
# def main():
# def parseGenbankWrapper(paramD):
# def writeStrainInfoFN(strainNamesT,paramD):
# def readStrainInfoFN(strainInfoFN):
# def runBlastWrapper(paramD):
# def loadGenomeRelatedData(paramD):
# def calcScoresWrapper(paramD,blastFnL):
# def makeSpeciesTreeWrapper(paramD):
# def loadTreeRelatedData(speciesTreeFN):
# def makeFamiliesWrapper(paramD):
# def makeIslandsWrapper(paramD):
# def refineWrapper(paramD):
# def printAnalysisWrapper(paramD,speciesTreeFN,rootFocalClade):
# def createIslandBedWrapper(paramD):
# def interactiveAnalysisWrapper(paramD):
#     def printFam(familyNum,familiesO,fileF=sys.stdout):
#     def findGene(searchStr,fileF=sys.stdout):
#     def printLocusIsland(locusIslandNum,synWSize,fileF=sys.stdout):
#     def printLocusIslandsAtNode(node,fileF=sys.stdout):
# def debugWrapper(paramD):
#         L=matchFamilyIsland(genesO,gene2FamIslandD,searchStr)


import sys,os
from xenoGI import parameters,xenoGI
sys.path.insert(0,os.path.join(sys.path[0],'..'))


if __name__ == "__main__":

    paramFN = sys.argv[1]
    speciesTreeFN = sys.argv[2] 


# Path: xenoGI/parameters.py
# def createParametersD(baseParamStr,paramFN):
# def addParametersToD(paramL,paramD):
# def loadFileNameMapD(fileNameMapFN,genbankFileList=None):
# 
# Path: xenoGI/xenoGI.py
# def main():
# def parseGenbankWrapper(paramD):
# def writeStrainInfoFN(strainNamesT,paramD):
# def readStrainInfoFN(strainInfoFN):
# def runBlastWrapper(paramD):
# def loadGenomeRelatedData(paramD):
# def calcScoresWrapper(paramD,blastFnL):
# def makeSpeciesTreeWrapper(paramD):
# def loadTreeRelatedData(speciesTreeFN):
# def makeFamiliesWrapper(paramD):
# def makeIslandsWrapper(paramD):
# def refineWrapper(paramD):
# def printAnalysisWrapper(paramD,speciesTreeFN,rootFocalClade):
# def createIslandBedWrapper(paramD):
# def interactiveAnalysisWrapper(paramD):
#     def printFam(familyNum,familiesO,fileF=sys.stdout):
#     def findGene(searchStr,fileF=sys.stdout):
#     def printLocusIsland(locusIslandNum,synWSize,fileF=sys.stdout):
#     def printLocusIslandsAtNode(node,fileF=sys.stdout):
# def debugWrapper(paramD):
#         L=matchFamilyIsland(genesO,gene2FamIslandD,searchStr)


# Path: misc/listTreeStrains.py
import sys,os
from xenoGI import parameters,xenoGI

sys.path.insert(0,os.path.join(sys.path[0],'..'))


if __name__ == "__main__":

    paramFN = sys.argv[1]
    speciesTreeFN = sys.argv[2] 


    paramD = parameters.createParametersD(parameters.baseParamStr,paramFN)