from shutil import copyfile import Util import PredictionToolExecuter import PredictionToolWriter import PredictionToolReader import FileReader paramToValue = Util.readConfigFile(Util.TOOL_CONFIG, "General") nonphospho = bool(paramToValue["nonphospho"]) Util.cleanUp() # create RMatrix with matches of modified phosphosites FileReader.modifyPeptides() # read matches (modified) or all files in dir allRefMat = PredictionToolWriter.readReference(Util.PATH_TO_TRAIN_REF) # take MATCHES.txt and create train & test files if PATH_TO_TEST+empty) #if matches are aktivated, zur zeit nicht # create random_trainset and testset with RT PredictionToolWriter.createSampleFile(Util.PATH_TO_TRAIN_REF) # create matrix out of file; HEADER! oder mit writeMatrix, dann header weg trainMatrix = PredictionToolWriter.readReference(Util.PATH_TRAIN_TMP) trainMatrix = PredictionToolReader.modifyRetentionTimes(trainMatrix) tools = ["Elude", "SSRCalc", "BioLCCC"] for tool in tools: PredictionToolWriter.writeTrainInput(trainMatrix, Util.PATH_TO_TMP, tool) #neue spalte einfuegen mit ID als sseq mit RT (toolinputseq zeigt auf modifi.Seq) #problem: ssrcalc nur unmodifizierte seq, rest mit -1