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
