def rankAndMerge(folderName, contigsNamesList, contigsFilename, readsFilename,
scoreList, contigGapReadLookUpDic, mScoreThres, conScoreThres,
scoreListOutputName, outputContigsFilename,
dummyNodeDataRobot):
scoreList.sort(key=itemgetter(-1, -2), reverse=True)
houseKeeperLib.dumpDataToJson(folderName, scoreListOutputName, scoreList)
mergeList = cutOffToFormMergeList(scoreList, mScoreThres, conScoreThres)
dummyNodeDataRobot.removeUsedDummies(mergeList)
dummyNodeDataRobot.addAllContigs(contigsNamesList)
nameList = dummyNodeDataRobot.getNameList()
GCondensed = condenseEdgesOnlyGraph(nameList)
readingListWithDummy = GCondensed.mergeListToReadingList(mergeList)
readingList = dummyNodeDataRobot.mapReadingList(readingListWithDummy)
readContigGraphToContigs(folderName, contigsFilename, readsFilename,
contigGapReadLookUpDic, readingList,
outputContigsFilename)
def rankAndMerge(folderName, contigsNamesList, contigsFilename, readsFilename, scoreList, contigGapReadLookUpDic, mScoreThres, conScoreThres, scoreListOutputName, outputContigsFilename, dummyNodeDataRobot):
scoreList.sort(key = itemgetter(-1, -2), reverse = True)
houseKeeperLib.dumpDataToJson(folderName , scoreListOutputName, scoreList)
mergeList = cutOffToFormMergeList(scoreList, mScoreThres, conScoreThres )
dummyNodeDataRobot.removeUsedDummies(mergeList)
dummyNodeDataRobot.addAllContigs(contigsNamesList)
nameList = dummyNodeDataRobot.getNameList()
GCondensed = condenseEdgesOnlyGraph(nameList)
readingListWithDummy = GCondensed.mergeListToReadingList(mergeList)
readingList = dummyNodeDataRobot.mapReadingList(readingListWithDummy)
readContigGraphToContigs(folderName, contigsFilename, readsFilename, contigGapReadLookUpDic, readingList, outputContigsFilename)
def batchPostMe(folderName, mummerLink, contigsFilename, readsFilename, noAlignment):
commandsList, settingsList = [], []
if not noAlignment:
commandsList.append("python postme.py " \
+ " -o "+ folderName \
+ " -a " + mummerLink \
+ " -r " + readsFilename \
+ " -c " + contigsFilename \
+ " -s T -na F -sn scoreList.json -on improved.fasta -ms 2 -cs 0.95")
for i in range(1, 3):
for j in range(5):
mScoreThres, cScoreThres, = i, 0.95 - j*0.05
settingsList.append(["score_" + str(len(settingsList)) + ".fasta", \
"imp_" + str(len(settingsList)) + ".fasta", \
mScoreThres, cScoreThres])
commonHeader = "python postme.py " \
+ " -o "+ folderName \
+ " -a " + mummerLink \
+ " -r " + readsFilename \
+ " -c " + contigsFilename \
+ " -s T -na T "
for eachSetting in settingsList:
command = commonHeader \
+ " -sn " + str(eachSetting[0]) \
+ " -on " + str(eachSetting[1]) \
+ " -ms " + str(eachSetting[2]) \
+ " -cs " + str(eachSetting[3])
commandsList.append(command)
for eachCommand in commandsList:
os.system(eachCommand)
houseKeeperLib.dumpDataToJson(folderName, "settingsList.json" ,settingsList)
