def formPathSeq(folderName, mummerPath, directPathList, indirectPathList, contigFile, readFile):
'''
Input : directPathList, indirectPathList, contigFile, readFile
Output: directPath.fasta, indirectPath.fasta
'''
contigList = IORobot.readContigsFromFile(folderName,contigFile)
readList = IORobot.readContigsFromFile(folderName,readFile)
directPathSeqList = IORobot.pathListToSeqListTransform(directPathList, contigList, readList, mummerPath, folderName)
indirectPathSeqList = IORobot.pathListToSeqListTransform(indirectPathList, contigList, readList, mummerPath, folderName)
IORobot.writeSegOut(directPathSeqList,folderName,"directPath.fasta")
IORobot.writeSegOut(indirectPathSeqList,folderName,"indirectPath.fasta")
def formPathSeq(folderName, mummerPath, directPathList, indirectPathList, contigFile, readFile):
'''
Input : directPathList, indirectPathList, contigFile, readFile
Output: directPath.fasta, indirectPath.fasta
'''
contigList = IORobot.readContigsFromFile(folderName,contigFile)
readList = IORobot.readContigsFromFile(folderName,readFile)
directPathSeqList = IORobot.pathListToSeqListTransform(directPathList, contigList, readList, mummerPath, folderName)
indirectPathSeqList = IORobot.pathListToSeqListTransform(indirectPathList, contigList, readList, mummerPath, folderName)
IORobot.writeSegOut(directPathSeqList,folderName,"directPath.fasta")
IORobot.writeSegOut(indirectPathSeqList,folderName,"indirectPath.fasta")
def readContigForAbunSplit(folderName, mummerLink, contigFilename,
readsetFilename, N1, contigReadGraph):
json_data = open(folderName + "mapDummyToRealDic.json", 'r')
mapDummyToRealDic = json.load(json_data)
G = []
G = graphLib.seqGraph(0)
G.loadFromFile(folderName, "xResolvedGraph")
gapContentLookUpDic = {}
furtherGapList = []
for i in range(N1):
if len(G.graphNodesList[i].nodeIndexList) > 1:
for j in range(len(G.graphNodesList[i].nodeIndexList) - 1):
bk, fwd = G.graphNodesList[i].nodeIndexList[
j], G.graphNodesList[i].nodeIndexList[j + 1]
key = str(bk) + "_" + str(fwd)
if not key in gapContentLookUpDic:
furtherGapList.append([bk, fwd])
with open(folderName + "furtherGapList.json", 'w') as f:
json.dump(furtherGapList, f)
furtherGapContentLookUpList = generateGapContentLookup(
folderName, mummerLink, furtherGapList, contigReadGraph,
contigFilename, readsetFilename, mapDummyToRealDic)
for eachitem in furtherGapContentLookUpList:
gapContentLookUpDic[str(eachitem[0]) + "_" + str(eachitem[1])] = [
eachitem[2], eachitem[3], eachitem[4]
]
print eachitem[2:4], len(eachitem[4])
#segLookUp = IORobot.readContigsFromFile(folderName, "LC_n_Double.fasta")
print "Final step: really hacking a file"
os.system("cp " + folderName + contigFilename + "_Double.fasta " +
folderName + "tmpWithDummy.fasta")
contigList = IORobot.readContigsFromFile(folderName,
contigFilename + "_Double.fasta")
IORobot.extractGraphToContigs(G, folderName, mummerLink, "abunPre.fasta",
"tmpWithDummy.fasta", gapContentLookUpDic,
mapDummyToRealDic)
if True:
nonRedundantResolver.removeRedundantWithFile(folderName, mummerLink,
"abunPre", "abunMum",
"abun")
def readContigForAbunSplit(folderName, mummerLink, contigFilename, readsetFilename, N1, contigReadGraph):
json_data = open(folderName + "mapDummyToRealDic.json", "r")
mapDummyToRealDic = json.load(json_data)
G = []
G = graphLib.seqGraph(0)
G.loadFromFile(folderName, "xResolvedGraph")
gapContentLookUpDic = {}
furtherGapList = []
for i in range(N1):
if len(G.graphNodesList[i].nodeIndexList) > 1:
for j in range(len(G.graphNodesList[i].nodeIndexList) - 1):
bk, fwd = G.graphNodesList[i].nodeIndexList[j], G.graphNodesList[i].nodeIndexList[j + 1]
key = str(bk) + "_" + str(fwd)
if not key in gapContentLookUpDic:
furtherGapList.append([bk, fwd])
with open(folderName + "furtherGapList.json", "w") as f:
json.dump(furtherGapList, f)
furtherGapContentLookUpList = generateGapContentLookup(
folderName, mummerLink, furtherGapList, contigReadGraph, contigFilename, readsetFilename, mapDummyToRealDic
)
for eachitem in furtherGapContentLookUpList:
gapContentLookUpDic[str(eachitem[0]) + "_" + str(eachitem[1])] = [eachitem[2], eachitem[3], eachitem[4]]
print eachitem[2:4], len(eachitem[4])
# segLookUp = IORobot.readContigsFromFile(folderName, "LC_n_Double.fasta")
print "Final step: really hacking a file"
os.system("cp " + folderName + contigFilename + "_Double.fasta " + folderName + "tmpWithDummy.fasta")
contigList = IORobot.readContigsFromFile(folderName, contigFilename + "_Double.fasta")
IORobot.extractGraphToContigs(
G, folderName, mummerLink, "abunPre.fasta", "tmpWithDummy.fasta", gapContentLookUpDic, mapDummyToRealDic
)
if True:
nonRedundantResolver.removeRedundantWithFile(folderName, mummerLink, "abunPre", "abunMum", "abun")
def mapStrangePairs():
folderName = "Apr10Test/"
json_data = open(folderName + "furtherGapList.json", 'r')
furtherGapList = json.load(json_data)
segLookUp = IORobot.readContigsFromFile(folderName, "LC_n_Double.fasta")
f = open(folderName + "wrongCondense.fasta", 'w')
ctr = 0
for eachitem in furtherGapList:
beforeI, afterI = eachitem[0], eachitem[1]
f.write(">Segkk"+str(ctr)+"\n")
f.write(segLookUp[beforeI]+"\n")
ctr = ctr + 1
f.write(">Segkk"+str(ctr)+"\n")
f.write(segLookUp[afterI]+"\n")
ctr = ctr + 1
f.close()
if False:
alignerRobot.useMummerAlign("/usr/bin/", folderName, "wrongCondenseDebug", "reference.fasta", "wrongCondense.fasta")
dataList = alignerRobot.extractMumData(folderName, "wrongCondenseDebugOut")
dataList.sort(key = itemgetter(-1))
mappedDic = {}
for key, items in groupby(dataList, itemgetter(-1)):
print "key", key
matchLen = -1
for eachitem in items:
if eachitem[-4] > matchLen:
mappedDic[key] = eachitem
matchLen = eachitem[-4]
for eachitem in mappedDic:
print "results : ", eachitem, mappedDic[eachitem]
def abunSplitWithXResolve(folderName, mummerLink, myCountDic, contigReadGraph, contigFilename, readsetFilename):
N1 = len(myCountDic) * 2
print "N1", N1
# Debug
G = graphLib.seqGraph(0)
G.loadFromFile(folderName, contigReadGraph)
adj = [[] for i in range(N1)]
for i in range(N1):
adj[i] = abunGraphLib.findAllReachable(i, N1, G)
Gnew = graphLib.seqGraph(N1)
for i in range(N1):
for j in adj[i]:
Gnew.insertEdge(i, j, 1)
Gnew.reportEdge()
# End Debug
if False:
json_data = open(folderName + "phaseRepeat.txt", "r")
repeatPairs = json.load(json_data)
repeatPairs = obtainNonEmpty(repeatPairs)
biResolvedCombineList = []
for eachitem in repeatPairs:
inList, outList = eachitem[0], eachitem[1]
resolvedList = determindMatch(inList, outList, myCountDic, folderName, contigReadGraph, N1)
biResolvedCombineList += resolvedList
### Xnode repeatResolution
xResolvedList, mapDummyToRealDic = xNodeResolving(folderName, contigReadGraph)
### Combine resolution
resolvedList = xResolvedList + biResolvedCombineList
resolvedList = abunHouseKeeper.getDistinct(resolvedList)
print "resolvedList, len(resolvedList),len(xResolvedList), len(biResolvedCombineList) ", resolvedList, len(
resolvedList
), len(xResolvedList), len(biResolvedCombineList)
with open(folderName + "resolvedList.json", "w") as f:
json.dump(resolvedList, f)
with open(folderName + "mapDummyToRealDic.json", "w") as f:
json.dump(mapDummyToRealDic, f)
if False:
json_data = open(folderName + "resolvedList.json", "r")
resolvedList = json.load(json_data)
json_data = open(folderName + "mapDummyToRealDic.json", "r")
mapDummyToRealDic = json.load(json_data)
gapContentLookUpList = []
gapContentLookUpList = generateGapContentLookup(
folderName, mummerLink, resolvedList, contigReadGraph, contigFilename, readsetFilename, mapDummyToRealDic
)
gapContentLookUpDic = {}
gapContentLookUpList.sort()
for eachitem in gapContentLookUpList:
gapContentLookUpDic[str(eachitem[0]) + "_" + str(eachitem[1])] = [eachitem[2], eachitem[3], eachitem[4]]
print eachitem[2:4], len(eachitem[4])
with open(folderName + "gapContentLookUpDic.json", "w") as f:
json.dump(gapContentLookUpDic, f)
if False:
json_data = open(folderName + "resolvedList.json", "r")
resolvedList = json.load(json_data)
json_data = open(folderName + "mapDummyToRealDic.json", "r")
mapDummyToRealDic = json.load(json_data)
G = graphLib.seqGraph(N1 + len(mapDummyToRealDic))
addEdges(G, resolvedList)
G.condense()
G.saveToFile(folderName, "xResolvedGraph")
if False:
json_data = open(folderName + "mapDummyToRealDic.json", "r")
mapDummyToRealDic = json.load(json_data)
G = graphLib.seqGraph(0)
G.loadFromFile(folderName, "xResolvedGraph")
json_data = open(folderName + "gapContentLookUpDic.json", "r")
gapContentLookUpDic = json.load(json_data)
print "Final step: really hacking a file"
os.system("cp " + folderName + contigFilename + "_Double.fasta " + folderName + "tmpWithDummy.fasta")
contigList = IORobot.readContigsFromFile(folderName, contigFilename + "_Double.fasta")
f = open(folderName + "tmpWithDummy.fasta", "a")
for i in range(len(mapDummyToRealDic)):
id = mapDummyToRealDic[str(i)]
f.write(">SegDum" + str(i) + "\n")
f.write(contigList[id] + "\n")
f.close()
IORobot.extractGraphToContigs(
G, folderName, mummerLink, "abun.fasta", "tmpWithDummy.fasta", gapContentLookUpDic, mapDummyToRealDic
)
def abunSplitWithXResolve(folderName, mummerLink, myCountDic, contigReadGraph,
contigFilename, readsetFilename):
N1 = len(myCountDic) * 2
print "N1", N1
# Debug
G = graphLib.seqGraph(0)
G.loadFromFile(folderName, contigReadGraph)
adj = [[] for i in range(N1)]
for i in range(N1):
adj[i] = abunGraphLib.findAllReachable(i, N1, G)
Gnew = graphLib.seqGraph(N1)
for i in range(N1):
for j in adj[i]:
Gnew.insertEdge(i, j, 1)
Gnew.reportEdge()
# End Debug
if False:
json_data = open(folderName + "phaseRepeat.txt", 'r')
repeatPairs = json.load(json_data)
repeatPairs = obtainNonEmpty(repeatPairs)
biResolvedCombineList = []
for eachitem in repeatPairs:
inList, outList = eachitem[0], eachitem[1]
resolvedList = determindMatch(inList, outList, myCountDic,
folderName, contigReadGraph, N1)
biResolvedCombineList += resolvedList
### Xnode repeatResolution
xResolvedList, mapDummyToRealDic = xNodeResolving(
folderName, contigReadGraph)
### Combine resolution
resolvedList = xResolvedList + biResolvedCombineList
resolvedList = abunHouseKeeper.getDistinct(resolvedList)
print "resolvedList, len(resolvedList),len(xResolvedList), len(biResolvedCombineList) ", resolvedList, len(
resolvedList), len(xResolvedList), len(biResolvedCombineList)
with open(folderName + "resolvedList.json", 'w') as f:
json.dump(resolvedList, f)
with open(folderName + "mapDummyToRealDic.json", 'w') as f:
json.dump(mapDummyToRealDic, f)
if False:
json_data = open(folderName + "resolvedList.json", 'r')
resolvedList = json.load(json_data)
json_data = open(folderName + "mapDummyToRealDic.json", 'r')
mapDummyToRealDic = json.load(json_data)
gapContentLookUpList = []
gapContentLookUpList = generateGapContentLookup(
folderName, mummerLink, resolvedList, contigReadGraph,
contigFilename, readsetFilename, mapDummyToRealDic)
gapContentLookUpDic = {}
gapContentLookUpList.sort()
for eachitem in gapContentLookUpList:
gapContentLookUpDic[str(eachitem[0]) + "_" + str(eachitem[1])] = [
eachitem[2], eachitem[3], eachitem[4]
]
print eachitem[2:4], len(eachitem[4])
with open(folderName + "gapContentLookUpDic.json", 'w') as f:
json.dump(gapContentLookUpDic, f)
if False:
json_data = open(folderName + "resolvedList.json", 'r')
resolvedList = json.load(json_data)
json_data = open(folderName + "mapDummyToRealDic.json", 'r')
mapDummyToRealDic = json.load(json_data)
G = graphLib.seqGraph(N1 + len(mapDummyToRealDic))
addEdges(G, resolvedList)
G.condense()
G.saveToFile(folderName, "xResolvedGraph")
if False:
json_data = open(folderName + "mapDummyToRealDic.json", 'r')
mapDummyToRealDic = json.load(json_data)
G = graphLib.seqGraph(0)
G.loadFromFile(folderName, "xResolvedGraph")
json_data = open(folderName + "gapContentLookUpDic.json", 'r')
gapContentLookUpDic = json.load(json_data)
print "Final step: really hacking a file"
os.system("cp " + folderName + contigFilename + "_Double.fasta " +
folderName + "tmpWithDummy.fasta")
contigList = IORobot.readContigsFromFile(
folderName, contigFilename + "_Double.fasta")
f = open(folderName + "tmpWithDummy.fasta", 'a')
for i in range(len(mapDummyToRealDic)):
id = mapDummyToRealDic[str(i)]
f.write(">SegDum" + str(i) + "\n")
f.write(contigList[id] + "\n")
f.close()
IORobot.extractGraphToContigs(G, folderName, mummerLink, "abun.fasta",
"tmpWithDummy.fasta",
gapContentLookUpDic, mapDummyToRealDic)
