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)