import sys
import parameters, genbank, trees, genomes, scores, families, islands
if __name__ == "__main__":
paramFN = sys.argv[1]
paramD = parameters.loadParametersD(paramFN)
## load data structures we'll use below
tree, strainStr2NumD, strainNum2StrD = trees.readTree(paramD['treeFN'])
# an object for gene name conversions
geneNames = genomes.geneNames(paramD['geneOrderFN'], strainStr2NumD,
strainNum2StrD)
subtreeL = trees.createSubtreeL(tree)
subtreeL.sort()
geneOrderT = genomes.createGeneOrderTs(paramD['geneOrderFN'], geneNames,
subtreeL, strainStr2NumD)
## read scores
scoresO = scores.readScores(paramD['scoresFN'], geneNames)
## make gene families
familyIslandFormationSummaryF = open(
paramD['familyIslandFormationSummaryFN'], 'w')
familyL = families.families(
tree, subtreeL, geneNames, scoresO, paramD['minNormThresh'],
paramD['minCoreSynThresh'], paramD['minSynThresh'],
paramD['synAdjustThresh'], paramD['synAdjustExtent'],
paramD['familyFN'], strainNum2StrD, familyIslandFormationSummaryF)
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()