def RunGammaTest(chr, beginSeqName, globalOrLocalMts, organism):
"""
Runs all Gamma test calculations.
chr: Current chromosome number.
beginSeqName: Beginning of sequence names for query.
globalOrLocalMts: String identifying whether to use global or local Mt values.
organism: Organism's name.
"""
print ("GAMMA")
# to find P gamma
familyListAsym = printAndParseFiles.parsePalphaGamma("Calculations_" + organism + "\RSeqFamilyMats\RSeqFamilyMatsAsymmetric%d.txt" % (chr), beginSeqName)#change this to Rag, should be the final area of filtering
familyListSym = printAndParseFiles.parsePalphaGamma("Calculations_" + organism + "\RSeqFamilyMats\RSeqFamilyMatsSymmetric%d.txt" % (chr), beginSeqName)
QgammaAsym = printAndParseFiles.parseQgammaFile("Calculations_" + organism + "\Qgamma\QgammaAsymmetric%d.txt" % (chr))
QgammaSym = printAndParseFiles.parseQgammaFile("Calculations_" + organism + "\Qgamma\QgammaSymmetric%d.txt" % (chr))
mtDict = {}
if (globalOrLocalMts == "Global"):
mtDict = printAndParseFiles.parseValueFile("Calculations_" + organism + "\MTFamilyVals.txt")
PalphaGammaHatAsym = FindCandP.calculatePalphaGammaHatGlobal(QgammaAsym, familyListAsym, mtDict)
PalphaGammaHatSym = FindCandP.calculatePalphaGammaHatGlobal(QgammaSym, familyListSym, mtDict)
printAndParseFiles.printDictionaryMatrixToFile(PalphaGammaHatAsym, "Calculations_" + organism + "\PalphaGammaHat%s\PalphaGammaHatAsymmetric%d.txt" % (globalOrLocalMts,chr))
printAndParseFiles.printDictionaryMatrixToFile(PalphaGammaHatSym, "Calculations_" + organism + "\PalphaGammaHat%s\PalphaGammaHatSymmetric%d.txt" % (globalOrLocalMts,chr))
CalphaGamma = printAndParseFiles.parseCalphaGammaFile("Calculations_" + organism + "\CSeqFamilyMats\CSeqFamilyMats%d.txt" % (chr), beginSeqName)
# calculate this section's L gamma value
LgammaAsym = FindLg.findLgamma(CalphaGamma, PalphaGammaHatAsym)
LgammaSym = FindLg.findLgamma(CalphaGamma, PalphaGammaHatSym)
printAndParseFiles.printValuesToFile(LgammaAsym, "Calculations_" + organism + "\Lgamma%s\LgammaAsymmetric%d.txt" % (globalOrLocalMts,chr))
printAndParseFiles.printValuesToFile(LgammaSym, "Calculations_" + organism + "\Lgamma%s\LgammaSymmetric%d.txt" % (globalOrLocalMts,chr))
elif (globalOrLocalMts == "Local"):
mtDictAsym = printAndParseFiles.parseMtalphaGammaFile("Calculations_" + organism + "\MtSeqFamilyMats\MtSeqFamilyMatsAsymmetric%d.txt" % chr, beginSeqName) # create dictionary values for asymmetric and symmetric, perform gamma calculations using them
PalphaGammaHatAsym = FindCandP.calculatePalphaGammaHatLocal(QgammaAsym, familyListAsym, mtDictAsym)
mtDictSym = printAndParseFiles.parseMtalphaGammaFile("Calculations_" + organism + "\MtSeqFamilyMats\MtSeqFamilyMatsSymmetric%d.txt" % chr, beginSeqName)
PalphaGammaHatSym = FindCandP.calculatePalphaGammaHatLocal(QgammaSym, familyListSym, mtDictSym)
printAndParseFiles.printDictionaryMatrixToFile(PalphaGammaHatAsym, "Calculations_" + organism + "\PalphaGammaHat%s\PalphaGammaHatAsymmetric%d.txt" % (globalOrLocalMts,chr))
printAndParseFiles.printDictionaryMatrixToFile(PalphaGammaHatSym, "Calculations_" + organism + "\PalphaGammaHat%s\PalphaGammaHatSymmetric%d.txt" % (globalOrLocalMts,chr))
CalphaGamma = printAndParseFiles.parseCalphaGammaFile("Calculations_" + organism + "\CSeqFamilyMats\CSeqFamilyMats%d.txt" % (chr), beginSeqName)
# calculate this section's L gamma value
LgammaAsym = FindLg.findLgamma(CalphaGamma, PalphaGammaHatAsym)
LgammaSym = FindLg.findLgamma(CalphaGamma, PalphaGammaHatSym)
printAndParseFiles.printValuesToFile(LgammaAsym, "Calculations_" + organism + "\Lgamma%s\LgammaAsymmetric%d.txt" % (globalOrLocalMts,chr))
printAndParseFiles.printValuesToFile(LgammaSym, "Calculations_" + organism + "\Lgamma%s\LgammaSymmetric%d.txt" % (globalOrLocalMts,chr))
else:
print "Error with Global or Local choice. Please type 'Global' or 'Local'"
print ("DONE WITH CHR %d" % chr)
