print "removeEmbedded"

thres = 10

command= r'''perl -pe 's/>[^\$]*$/">Seg" . ++$n ."\n"/ge' ''' + folderName + "raw_reads.fasta > " + folderName + houseKeeper.globalReadName

os.system(command)

command= r'''perl -pe 's/>[^\$]*$/">Seg" . ++$n ."\n"/ge' ''' + folderName + "contigs.fasta > " + folderName + houseKeeper.globalContigName

os.system(command)

if True:

alignerRobot.useMummerAlignBatch(mummerLink, folderName, [["self", houseKeeper.globalContigName, houseKeeper.globalContigName, ""]], houseKeeper.globalParallel)

# alignerRobot.useMummerAlign(mummerLink, folderName, "self", "contigs.fasta", "contigs.fasta")

# outputName, referenceName, queryName, specialName

dataList = alignerRobot.extractMumData(folderName, "selfOut")

dataList = alignerRobot.transformCoor(dataList)

lenDic = IORobot.obtainLength(folderName, houseKeeper.globalContigName)

removeList = []

for eachitem in dataList:

match1, match2, name1, name2 = eachitem[4], eachitem[5], eachitem[7], eachitem[8]

if name1 != name2:

l1, l2 = lenDic[name1], lenDic[name2]

if abs(l1 - match1) < thres and abs(l2 - match2) > thres:

removeList.append(name1)

elif abs(l1 - match1) > thres and abs(l2 - match2) < thres:

removeList.append(name2)

elif abs(l1 - match1) < thres and abs(l2 - match2) < thres:

print "Both shortembedd", eachitem

nameList = []

for eachitem in lenDic:

nameList.append(eachitem)

print len(nameList)

for eachitem in removeList:

if eachitem in nameList:

nameList.remove(eachitem)

print len(nameList)