def alignWithName(leftSeg, rightSeg, folderName, mummerLink, nameOfOut):
overlap = [0, 0]
lLen = 0
f = open(folderName + nameOfOut + "leftSeg.fasta", 'w')
f.write(">SegL\n")
if len(leftSeg) < 50000:
f.write(leftSeg)
lLen = len(leftSeg)
else:
f.write(leftSeg[-50000:])
lLen = 50000
f.close()
rLen = 0
f = open(folderName + nameOfOut + "rightSeg.fasta", 'w')
f.write(">SegR\n")
if len(rightSeg) < 50000:
f.write(rightSeg)
rLen = len(rightSeg)
else:
f.write(rightSeg[0:50000])
rLen = 50000
f.close()
#alignerRobot.useMummerAlign(mummerLink, folderName, "overlap", "leftSeg.fasta", "rightSeg.fasta", False)
alignerRobot.useMummerAlign(mummerLink,
folderName,
nameOfOut,
nameOfOut + "leftSeg.fasta",
nameOfOut + "rightSeg.fasta",
specialForRaw=False,
specialName="",
refinedVersion=True)
dataList = alignerRobot.extractMumData(folderName, nameOfOut + "Out")
thres = 10
if len(dataList) == 0:
overlap = [0, 0]
else:
myMax = [0, 0]
for eachitem in dataList:
if eachitem[1] > lLen - thres and eachitem[2] < thres:
if eachitem[5] > myMax[1]:
myMax[0] = eachitem[4]
myMax[1] = eachitem[5]
overlap = myMax
return overlap
def alignWithName(leftSeg, rightSeg, folderName, mummerLink, nameOfOut):
overlap = [0, 0 ]
lLen = 0
f = open(folderName + nameOfOut+"leftSeg.fasta", 'w')
f.write(">SegL\n")
if len(leftSeg) < 50000:
f.write(leftSeg)
lLen = len(leftSeg)
else:
f.write(leftSeg[-50000:])
lLen = 50000
f.close()
rLen = 0
f = open(folderName + nameOfOut+"rightSeg.fasta", 'w')
f.write(">SegR\n")
if len(rightSeg) < 50000:
f.write(rightSeg)
rLen = len(rightSeg)
else:
f.write(rightSeg[0:50000])
rLen = 50000
f.close()
#alignerRobot.useMummerAlign(mummerLink, folderName, "overlap", "leftSeg.fasta", "rightSeg.fasta", False)
alignerRobot.useMummerAlign(mummerLink, folderName, nameOfOut, nameOfOut+"leftSeg.fasta", nameOfOut+"rightSeg.fasta", specialForRaw = False, specialName = "", refinedVersion= True)
dataList = alignerRobot.extractMumData(folderName , nameOfOut+"Out")
thres = 10
if len(dataList) == 0:
overlap = [0, 0 ]
else:
myMax = [0, 0]
for eachitem in dataList:
if eachitem[1] > lLen - thres and eachitem[2] < thres:
if eachitem[5] > myMax[1]:
myMax[0] = eachitem[4]
myMax[1] = eachitem[5]
overlap = myMax
return overlap
def align(leftSeg, rightSeg, folderName, mummerLink):
overlap = [0, 0]
lLen = 0
f = open(folderName + "leftSeg.fasta", "w")
f.write(">SegL\n")
if len(leftSeg) < 50000:
f.write(leftSeg)
lLen = len(leftSeg)
else:
f.write(leftSeg[-50000:])
lLen = 50000
f.close()
rLen = 0
f = open(folderName + "rightSeg.fasta", "w")
f.write(">SegR\n")
if len(rightSeg) < 50000:
f.write(rightSeg)
rLen = len(rightSeg)
else:
f.write(rightSeg[0:50000])
rLen = 50000
f.close()
alignerRobot.useMummerAlign(mummerLink, folderName, "overlap", "leftSeg.fasta", "rightSeg.fasta", False)
dataList = alignerRobot.extractMumData(folderName, "overlapOut")
thres = 10
if len(dataList) == 0:
overlap = [0, 0]
else:
myMax = [0, 0]
for eachitem in dataList:
if eachitem[1] > lLen - thres and eachitem[2] < thres:
if eachitem[5] > myMax[1]:
myMax[0] = eachitem[4]
myMax[1] = eachitem[5]
overlap = myMax
return overlap