paramFN=sys.argv[1]
paramD = parameters.loadParametersD(paramFN)
strainStr = sys.argv[2]
validationFile = sys.argv[3]
minGenes = int(sys.argv[4])
tree,strainStr2NumD,strainNum2StrD = trees.readTree(paramD['treeFN'])
strainNum = strainStr2NumD[strainStr]
#node = strainStr2NumD[strainStr]
# load islands and genes
islandByNodeL=islands.readIslands(paramD['islandOutFN'],tree,strainStr2NumD)
geneNames = genomes.geneNames(paramD['geneOrderFN'],strainStr2NumD,strainNum2StrD)
subtreeL=trees.createSubtreeL(tree)
subtreeL.sort()
geneOrderT=genomes.createGeneOrderTs(paramD['geneOrderFN'],geneNames,subtreeL,strainStr2NumD)
familyL = families.readFamilies(paramD['familyFN'],tree,geneNames,strainStr2NumD)
geneInfoD = genomes.readGeneInfoD(paramD['geneInfoFN'])
totalBases, chromsL, allValRanges = readRanges(validationFile)
nodesLL,uniqueStrains = nodesPerRange()
islandsOfInterest()
paramFN = sys.argv[1]
paramD = parameters.loadParametersD(paramFN)
tree, strainStr2NumD, strainNum2StrD = trees.readTree(paramD['treeFN'])
# load islands
islandByNodeL = islands.readIslands(paramD['islandOutFN'], tree,
strainStr2NumD)
# get familyL etc.
geneNames = genomes.geneNames(paramD['geneOrderFN'], strainStr2NumD,
strainNum2StrD)
geneInfoD = genomes.readGeneInfoD(paramD['geneInfoFN'])
familyL = families.readFamilies(paramD['familyFN'], tree, geneNames,
strainStr2NumD)
gene2FamD = createGene2FamD(familyL)
fam2IslandD = createFam2IslandD(islandByNodeL)
# subtree list
subtreeL = trees.createSubtreeL(tree)
subtreeL.sort()
nodesL = trees.nodeList(tree)
geneOrderT = genomes.createGeneOrderTs(paramD['geneOrderFN'], geneNames,
subtreeL, strainStr2NumD)
# scores
scoresO = scores.readScores(paramD['scoresFN'], geneNames)
scoresO.createNodeConnectL(geneNames) # make nodeConnectL attribute