def multipleTesting(folderName, mummerLink, option):
print "Experiments : "
header = "/data/kakitone/May07-2015/workingMetaFinisherSC/"
os.system("mkdir "+ header + folderName )
os.system("cp "+header+"Apr10Test/* " + header + folderName )
if option == "1":
abunHouseKeeper.abunGlobalSplitParameterRobot.runGraphSurgery = True
abunHouseKeeper.abunGlobalSplitParameterRobot.runBResolve = True
abunHouseKeeper.abunGlobalSplitParameterRobot.runXResolve = True
abunHouseKeeper.abunGlobalSplitParameterRobot.RThres = 5
abunHouseKeeper.abunGlobalSplitParameterRobot.BRThresB = 2
#abunHouseKeeper.abunGlobalSplitParameterRobot.BRThresX = 1
abunHouseKeeper.abunGlobalSplitParameterRobot.AbunLowerB = 1.5
abunHouseKeeper.abunGlobalSplitParameterRobot.AbunUpperB = 1.5
#abunHouseKeeper.abunGlobalSplitParameterRobot.AbunLowerX = 0.5
#abunHouseKeeper.abunGlobalSplitParameterRobot.AbunUpperX = 1.5
elif option == "2" :
abunHouseKeeper.abunGlobalSplitParameterRobot.runGraphSurgery = True
abunHouseKeeper.abunGlobalSplitParameterRobot.runBResolve = True
abunHouseKeeper.abunGlobalSplitParameterRobot.runXResolve = True
abunHouseKeeper.abunGlobalSplitParameterRobot.RThres = 5
abunHouseKeeper.abunGlobalSplitParameterRobot.BRThres = 2
#abunHouseKeeper.abunGlobalSplitParameterRobot.AbunLowerB = 2
#abunHouseKeeper.abunGlobalSplitParameterRobot.AbunUpperB = 2
#abunHouseKeeper.abunGlobalSplitParameterRobot.AbunLowerX = 0.5
#abunHouseKeeper.abunGlobalSplitParameterRobot.AbunUpperX = 0.5
elif option == "3":
abunHouseKeeper.abunGlobalSplitParameterRobot.runGraphSurgery = True
abunHouseKeeper.abunGlobalSplitParameterRobot.runBResolve = True
abunHouseKeeper.abunGlobalSplitParameterRobot.runXResolve = True
abunHouseKeeper.abunGlobalSplitParameterRobot.RThres = 5
abunHouseKeeper.abunGlobalSplitParameterRobot.BRThresB = 3
abunHouseKeeper.abunGlobalSplitParameterRobot.BRThresX = 1
abunSplitter.mainFlow(folderName, mummerLink)
os.system("python /data/kakitone/download2/quast-2.3/quast.py " + header + folderName +"abun.fasta -o " + header + folderName + " -R "+ header + folderName + "reference.fasta")
for eachitem in settingDataCombo:
tmp = eachitem.split('=')
settingDic[tmp[0]] = tmp[1]
canLoad = abunHouseKeeper.abunGlobalSplitParameterRobot.loadData(
settingDic)
else:
canLoad = True
if canLoad:
settingDic = abunHouseKeeper.abunGlobalSplitParameterRobot.__dict__
with open(newFolderName + "option.json", 'w') as f:
json.dump(settingDic, f)
if pathExists and canLoad:
abunSplitter.mainFlow(newFolderName, newMummerLink)
else:
print "Sorry. The above folders or files are missing or options are not correct. If you continue to have problems, please contact me(Ka-Kit Lam) at [email protected]"
print "Time", time.time() - t0
if houseKeeper.globalRunMPI == True:
for i in range(1, nproc):
data = "endall"
comm.send(data, dest=i)
else:
while True:
data = comm.recv(source=0)
def test2():
import abunSplitter
abunSplitter.mainFlow("Apr10Test/", "/usr/bin/")
def continuousIntegration():
if False:
G = graphLib.seqGraph(10)
for i in range(5):
G.insertEdge(i,i+1,1997)
G.insertEdge(i,i+2, 1997)
resultList = abunGraphLib.BFS_revisit(1,3,G,1)
print "resultList", resultList
if False :
folderName, mummerPath, directPathList, indirectPathList, contigFile, readFile = \
"Apr10Test/", "/usr/bin/", [[1, 486, 217], [1, 8642, 217], [1, 13465, 217]], [[1, 486, 217]], "improved3_Double.fasta", "phasingSeedName_Double.fasta"
abunGraphLib.formPathSeq(folderName, mummerPath, directPathList, indirectPathList, contigFile, readFile)
if False:
lenDic = IORobot.obtainLength(folderName , contigFile)
N1 = len(lenDic)
print "N1", N1
G = graphLib.seqGraph(0)
G.loadFromFile(folderName, "phaseStringGraph1")
adj = [[] for i in range(N1)]
for i in range(N1):
adj[i] = abunGraphLib.findAllReachable(i, N1, G)
Gnew = abunGraphLib.seqGraphDynamic(N1)
for i in range(N1):
for j in adj[i]:
Gnew.insertEdge(i,j,1997)
Gnew.initAdv()
Gnew.doubleEdgeReduction()
contigPaths = abunGraphLib.findAllPathK(1, 217, Gnew, 3)
contigReadPaths = abunGraphLib.findAllPathK(1, 217, G, 5)
print "contigPaths", contigPaths
print "contigReadPaths", contigReadPaths
Gnew.transitiveReduction()
if False:
toDelete = abunGraphLib.decideCut("Apr10Test/", "/usr/bin/")
print toDelete
if False:
G = graphLib.seqGraph(0)
G.loadFromFile("Apr10TestA/", "xResolvedGraph")
if False:
for i in range(len(G.graphNodesList)):
v = G.graphNodesList[i]
if len(v.nodeIndexList) > 0:
print i , v.listOfPrevNodes , v.listOfNextNodes
G.reportEdge()
lenDic = IORobot.obtainLength("Apr10TestA/", "improved3_Double.fasta")
mylist = [401, 207, 405, 407, 344]
json_data = open("Apr10TestA/" + "myCountDic.json", 'r')
myCountDic = json.load(json_data)
for x in mylist:
print x, lenDic["Contig"+str(x/2)+"_p"], myCountDic["Segkk"+str(x/2)]
if False:
folderName = "Apr10TestA/"
G = graphLib.seqGraph(0)
G.loadFromFile(folderName , "xResolvedGraph")
json_data = open(folderName + "mapDummyToRealDic.json", 'r')
mapDummyToRealDic = json.load(json_data)
lenDic = IORobot.obtainLength(folderName, "improved3_Double.fasta")
print len(G.graphNodesList)
print len(mapDummyToRealDic)
print "fake N1 , real N1 ", len(G.graphNodesList) - len(mapDummyToRealDic), len(lenDic)
if False:
abunSplitter.mainFlow("Apr10TestB/", "/usr/bin/")
if False:
nonRedundantResolver.removeEmbedded("Apr10TestD/", "/usr/bin/")
if False:
folderName, contigReadGraph = "Apr10TestA/", "phaseStringGraph1"
G = graphLib.seqGraph(0)
kthres, edgeThres = 3, 1
G.loadFromFile(folderName, contigReadGraph)
lenDic = IORobot.obtainLength(folderName , "improved3_Double.fasta")
N1 = len(lenDic)
adj = [[] for i in range(N1)]
for i in range(N1):
tmpList = abunGraphLib.findAllReachable(i, N1, G)
for j in tmpList:
if len(abunGraphLib.findAllPathK(i,j,G,kthres)) >= edgeThres:
adj[i].append(j)
#print i, adj[i]
### Filter adaptor skipped case
adaptorPair = []
for i in range(len(adj)):
if i % 2 == 0:
if i + 1 in adj[i]:
adj[i].remove(i+1)
adaptorPair.append([i, i+1])
elif i % 2 ==1:
if i-1 in adj[i] :
adj[i].remove(i-1)
adaptorPair.append([i, i-1])
Gnew = abunGraphLib.seqGraphDynamic(N1)
for i in range(N1):
for j in adj[i]:
Gnew.insertEdge(i,j,1997)
for eachpair in adaptorPair:
u, v = eachpair[0], eachpair[1]
for x in Gnew.graphNodesList[u].listOfPrevNodes:
xIndex = x[0]
Gnew.removeEdge(xIndex, v)
for y in Gnew.graphNodesList[v].listOfNextNodes:
yIndex = y[0]
Gnew.removeEdge(u, yIndex)
#Gnew.reportEdge()
count2 = 0
for i in range(len(Gnew.graphNodesList)):
if len(Gnew.graphNodesList[i].listOfPrevNodes) == 2 and len(Gnew.graphNodesList[i].listOfNextNodes) == 2:
count2 = count2 + 1
print str(i)+"{color:red}"
print "count2, ", count2
### End filter adaptor skipped case
if True:
nonRedundantResolver.removeRedundantWithFile("May11TestB/" , "/usr/bin/", "abun", "abunDebug", "abunNoEmbed")
if args['avoidrefine'] == "True":
abunHouseKeeper.abunGlobalAvoidrefine = True
else:
abunHouseKeeper.abunGlobalAvoidrefine = False
if args['readsearch'] != None:
abunHouseKeeper.abunGlobalReadSearchDepth = int(args['readsearch'])
else:
abunHouseKeeper.abunGlobalReadSearchDepth = 1
if args['replace'] != None :
replacedName = args['replace']
abunHouseKeeper.replaceFiles( newFolderName, replacedName)
if args['RRDisable'] == "True":
abunHouseKeeper.abunGlobalRRDisable = True
else:
abunHouseKeeper.abunGlobalRRDisable = False
if pathExists:
abunSplitter.mainFlow(newFolderName, newMummerLink)
else:
print "Sorry. The above folders or files are missing. If you continue to have problems, please contact me(Ka-Kit Lam) at [email protected]"
print "Time", time.time() - t0