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)
else:
value = L[1]
D[gene] = value
return D
## main
#TODO: proper CLI
if __name__ == "__main__":
speciesTreeFN = sys.argv[1]
geneTreeFN = sys.argv[2]
# load stuff
speciesTree = trees.readTree(speciesTreeFN)
geneTree = trees.loadOneGeneTree(geneTreeFN)
bigTipMapD = loadD("tipMap.tsv")
tipMapD = {} # cut down to those in this gene tree
for leaf in trees.leafList(geneTree):
tipMapD[leaf] = bigTipMapD[leaf]
locusMapD = loadD("locusMap.tsv")
gtLocusMapD = familiesDTLORstuff.reduceLocusMap(geneTree, locusMapD)
locusMapForRootingD = trees.createLocusMapForRootingD(
geneTree, copy.deepcopy(gtLocusMapD))
argT = (speciesTree, geneTree, tipMapD, gtLocusMapD, locusMapForRootingD,
D, T, L, O, R)
for strain in s.split('\t')[1].split(','):
nodes.append(int(strainStr2NumD[strain]))
if strain not in uniqueStrains: uniqueStrains.append(strain)
nodesLL.append(nodes)
return nodesLL,uniqueStrains
if __name__ == "__main__":
#loading parameters from command line that will be used below
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)
}, {
'no surfacing': {
0: 'no',
1: {
'flippers': {
0: {
'head': {
0: 'no',
1: 'yes'
}
},
1: 'no'
}
}
}
}]
return listOfTrees[i]
if __name__ == "__main__":
# createNode()
dataSet = [[1, 1, 2, 'y'], [1, 1, 3, 'y'], [0, 1, 2, 'n'], [1, 0, 3, 'n'],
[1, 0, 2, 'n'], [1, 1, 0, 'm']]
# tree = trees.createTree(dataSet, ['A', 'B', 'C'])
# 将构建的树直接放在这里, 减少测试时间
# tree = {'C': {0: 'm', 2: {'A': {0: 'n', 1: {'B': {0: 'n', 1: 'y'}}}}, 3: {'B': {0: 'n', 1: 'y'}}}}
# print(getTreeDepth(tree))
# print(tree)
tree = trees.readTree('forshow')
createPlot(tree)