def RunGlobalAlphaTest(beginSeqNum, endSeqNum, firstTime, significantRepeatList, organism, prmPrefix, prmDirectory = 'prm_files/'):
"""
Runs all Global Alpha test calculations.
beginSeqNum: Beginning chromosome range.
endSeqNum: Ending chromosome range.
firstTime: Boolean if first time for all calculations.
significantRepeatList: List of significant transposable element family instances.
organism: Organism's name.
prmDirectory: Directory where all of the .prm files are located.
"""
print ("GLOBAL ALPHA")
# to find global alpha values for C and P
if firstTime == True:
AllRepObjs = list(itertools.chain.from_iterable(([unpickleRepeats(prmPrefix + "%d" % chrNum, prmDirectory) for chrNum in range(beginSeqNum, endSeqNum+1)])))
print (len(AllRepObjs))
sigReps = printAndParseFiles.SigTEs(AllRepObjs, significantRepeatList)
print len(sigReps)
CfamilyMats = FindCandP.combineMatrices(sigReps)
print ("done with C")
printAndParseFiles.printListToFile(CfamilyMats, "Calculations_" + organism + "\CFamilyMats.txt")
PfamilyMats = FindCandP.getPSymm(CfamilyMats)
printAndParseFiles.printListToFile(PfamilyMats, "Calculations_" + organism + "\PFamilyMats.txt")
print ("done with P")
else:
PfamilyMats = printAndParseFiles.parsePfamilyFile("Calculations_" + organism + "\PFamilyMats.txt")
# to find global alpha values for R*t
print ("R")
RmatDict = FindR.calculateR(PfamilyMats)
printAndParseFiles.printMatrixToFile(RmatDict, "Calculations_" + organism + "\RFamilyMats.txt" )
# to find global alpha values for m*t
matSize = 4
print ("mt")
mtDict = FindMT.calculateMt(RmatDict, matSize)
printAndParseFiles.printValuesToFile(mtDict, "Calculations_" + organism + "\MTFamilyVals.txt")
# to find global alpha values for Q
print ("Q")
QmatDict = FindQ.calculateQvalues(mtDict, RmatDict, matSize)
printAndParseFiles.printMatrixToFile(QmatDict, "Calculations_" + organism + "\QFamilyMats.txt" )
