diff kinatestid_r/Kinatest-R.R @ 14:da1012f014bd draft

Uploaded
author jfb
date Thu, 08 Feb 2018 15:29:56 -0500
parents
children 15b5d4ae4480
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/kinatestid_r/Kinatest-R.R	Thu Feb 08 15:29:56 2018 -0500
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+
+ImportedSubstrateList<- read.csv("input1", stringsAsFactors=FALSE)
+NegativeSubstrateList<- read.csv("input2", stringsAsFactors=FALSE)
+SubstrateBackgroundFrequency<- read.csv("input3", stringsAsFactors=FALSE)
+
+ScreenerFilename<-"screener"
+
+
+
+FILENAME<-"output1.csv"
+FILENAME2<-"output2.csv"
+FILENAME3<-"output3.csv"
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+OutputMatrix<-"KinaseMatrix.csv"
+CharacterizationTable<-"CharacterizationTableForThisKinase.csv"
+SDtable<-"SDtableforthisKinase"
+SiteSelectivityTable<-"SiteSelectivityForThisKinase"
+
+
+
+substrates<-matrix(rep("A",times=((nrow(ImportedSubstrateList)-1)*15)),ncol = 15)
+#SeqsToBeScored<-"asdasd"
+  
+for (i in 2:nrow(ImportedSubstrateList))
+{
+  substratemotif<-ImportedSubstrateList[i,4:18]
+  substratemotif[8]<-"Y"
+  #substratemotif<-paste(substratemotif,sep = "",collapse = "")
+  j=i-1
+  substratemotif<-unlist(substratemotif)
+  substrates[j,1:15]<-substratemotif
+}
+
+# SpacesToOs<-c(""="O",)
+# substrates<-SpacesToOs[substrates]
+
+SubstrateBackgroundFrequency[nrow(SubstrateBackgroundFrequency),2]
+
+if(2==2){
+Amean<-mean(as.numeric(SubstrateBackgroundFrequency[1:(nrow(SubstrateBackgroundFrequency)),2]), na.rm=TRUE)
+Cmean<-mean(as.numeric(SubstrateBackgroundFrequency[1:(nrow(SubstrateBackgroundFrequency)),3]), na.rm=TRUE)
+Dmean<-mean(as.numeric(SubstrateBackgroundFrequency[1:(nrow(SubstrateBackgroundFrequency)),4]), na.rm=TRUE)
+Emean<-mean(as.numeric(SubstrateBackgroundFrequency[1:(nrow(SubstrateBackgroundFrequency)),5]), na.rm=TRUE)
+Fmean<-mean(as.numeric(SubstrateBackgroundFrequency[1:(nrow(SubstrateBackgroundFrequency)),6]), na.rm=TRUE)
+Gmean<-mean(as.numeric(SubstrateBackgroundFrequency[1:(nrow(SubstrateBackgroundFrequency)),7]), na.rm=TRUE)
+Hmean<-mean(as.numeric(SubstrateBackgroundFrequency[1:(nrow(SubstrateBackgroundFrequency)),8]), na.rm=TRUE)
+Imean<-mean(as.numeric(SubstrateBackgroundFrequency[1:(nrow(SubstrateBackgroundFrequency)),9]), na.rm=TRUE)
+Kmean<-mean(as.numeric(SubstrateBackgroundFrequency[1:(nrow(SubstrateBackgroundFrequency)),10]), na.rm=TRUE)
+Lmean<-mean(as.numeric(SubstrateBackgroundFrequency[1:(nrow(SubstrateBackgroundFrequency)),11]), na.rm=TRUE)
+Mmean<-mean(as.numeric(SubstrateBackgroundFrequency[1:(nrow(SubstrateBackgroundFrequency)),12]), na.rm=TRUE)
+Nmean<-mean(as.numeric(SubstrateBackgroundFrequency[1:(nrow(SubstrateBackgroundFrequency)),13]), na.rm=TRUE)
+Pmean<-mean(as.numeric(SubstrateBackgroundFrequency[1:(nrow(SubstrateBackgroundFrequency)),14]), na.rm=TRUE)
+Qmean<-mean(as.numeric(SubstrateBackgroundFrequency[1:(nrow(SubstrateBackgroundFrequency)),15]), na.rm=TRUE)
+Rmean<-mean(as.numeric(SubstrateBackgroundFrequency[1:(nrow(SubstrateBackgroundFrequency)),16]), na.rm=TRUE)
+Smean<-mean(as.numeric(SubstrateBackgroundFrequency[1:(nrow(SubstrateBackgroundFrequency)),17]), na.rm=TRUE)
+Tmean<-mean(as.numeric(SubstrateBackgroundFrequency[1:(nrow(SubstrateBackgroundFrequency)),18]), na.rm=TRUE)
+Vmean<-mean(as.numeric(SubstrateBackgroundFrequency[1:(nrow(SubstrateBackgroundFrequency)),19]), na.rm=TRUE)
+Wmean<-mean(as.numeric(SubstrateBackgroundFrequency[1:(nrow(SubstrateBackgroundFrequency)),20]), na.rm=TRUE)
+Ymean<-mean(as.numeric(SubstrateBackgroundFrequency[1:(nrow(SubstrateBackgroundFrequency)),21]), na.rm=TRUE)
+
+AllMeans<-c(Amean,Cmean,Dmean,Emean,Fmean,Gmean,Hmean,Imean,Kmean,Lmean,Mmean,Nmean,Pmean,Qmean,Rmean,Smean,Tmean,Vmean,Wmean,Ymean)
+
+Asd<-sd(as.numeric(SubstrateBackgroundFrequency[1:(nrow(SubstrateBackgroundFrequency)),2]), na.rm=TRUE)
+Csd<-sd(as.numeric(SubstrateBackgroundFrequency[1:(nrow(SubstrateBackgroundFrequency)),3]), na.rm=TRUE)
+Dsd<-sd(as.numeric(SubstrateBackgroundFrequency[1:(nrow(SubstrateBackgroundFrequency)),4]), na.rm=TRUE)
+Esd<-sd(as.numeric(SubstrateBackgroundFrequency[1:(nrow(SubstrateBackgroundFrequency)),5]), na.rm=TRUE)
+Fsd<-sd(as.numeric(SubstrateBackgroundFrequency[1:(nrow(SubstrateBackgroundFrequency)),6]), na.rm=TRUE)
+Gsd<-sd(as.numeric(SubstrateBackgroundFrequency[1:(nrow(SubstrateBackgroundFrequency)),7]), na.rm=TRUE)
+Hsd<-sd(as.numeric(SubstrateBackgroundFrequency[1:(nrow(SubstrateBackgroundFrequency)),8]), na.rm=TRUE)
+Isd<-sd(as.numeric(SubstrateBackgroundFrequency[1:(nrow(SubstrateBackgroundFrequency)),9]), na.rm=TRUE)
+Ksd<-sd(as.numeric(SubstrateBackgroundFrequency[1:(nrow(SubstrateBackgroundFrequency)),10]), na.rm=TRUE)
+Lsd<-sd(as.numeric(SubstrateBackgroundFrequency[1:(nrow(SubstrateBackgroundFrequency)),11]), na.rm=TRUE)
+Msd<-sd(as.numeric(SubstrateBackgroundFrequency[1:(nrow(SubstrateBackgroundFrequency)),12]), na.rm=TRUE)
+Nsd<-sd(as.numeric(SubstrateBackgroundFrequency[1:(nrow(SubstrateBackgroundFrequency)),13]), na.rm=TRUE)
+Psd<-sd(as.numeric(SubstrateBackgroundFrequency[1:(nrow(SubstrateBackgroundFrequency)),14]), na.rm=TRUE)
+Qsd<-sd(as.numeric(SubstrateBackgroundFrequency[1:(nrow(SubstrateBackgroundFrequency)),15]), na.rm=TRUE)
+Rsd<-sd(as.numeric(SubstrateBackgroundFrequency[1:(nrow(SubstrateBackgroundFrequency)),16]), na.rm=TRUE)
+Ssd<-sd(as.numeric(SubstrateBackgroundFrequency[1:(nrow(SubstrateBackgroundFrequency)),17]), na.rm=TRUE)
+Tsd<-sd(as.numeric(SubstrateBackgroundFrequency[1:(nrow(SubstrateBackgroundFrequency)),18]), na.rm=TRUE)
+Vsd<-sd(as.numeric(SubstrateBackgroundFrequency[1:(nrow(SubstrateBackgroundFrequency)),19]), na.rm=TRUE)
+Wsd<-sd(as.numeric(SubstrateBackgroundFrequency[1:(nrow(SubstrateBackgroundFrequency)),20]), na.rm=TRUE)
+Ysd<-sd(as.numeric(SubstrateBackgroundFrequency[1:(nrow(SubstrateBackgroundFrequency)),21]), na.rm=TRUE)
+}
+AllSDs<-c(Asd,Csd,Dsd,Esd,Fsd,Gsd,Hsd,Isd,Ksd,Lsd,Msd,Nsd,Psd,Qsd,Rsd,Ssd,Tsd,Vsd,Wsd,Ysd)
+#this is subbackfreq SDs
+
+SBF_statisticalvalues<-cbind(AllMeans,AllSDs)
+
+#create the percent table
+if (1==1){
+  Column1<-substrates[,1]
+  Column2<-substrates[,2]
+  Column3<-substrates[,3]
+  Column4<-substrates[,4]
+  Column5<-substrates[,5]
+  Column6<-substrates[,6]
+  Column7<-substrates[,7]
+  Column8<-substrates[,8]
+  Column9<-substrates[,9]
+  Column10<-substrates[,10]
+  Column11<-substrates[,11]
+  Column12<-substrates[,12]
+  Column13<-substrates[,13]
+  Column14<-substrates[,14]
+  Column15<-substrates[,15]
+  
+  spaces1<-sum((Column1%in% ""))
+  spaces2<-sum(Column2%in% "")
+  spaces3<-sum(Column3%in% "")
+  spaces4<-sum(Column4%in% "")
+  spaces5<-sum(Column5%in% "")
+  spaces6<-sum(Column6%in% "")
+  spaces7<-sum(Column7%in% "")
+  spaces8<-sum(Column8%in% "")
+  spaces9<-sum(Column9%in% "")
+  spaces10<-sum(Column10%in% "")
+  spaces11<-sum(Column11%in% "")
+  spaces12<-sum(Column12%in% "")
+  spaces13<-sum(Column13%in% "")
+  spaces14<-sum(Column14%in% "")
+  spaces15<-sum(Column15%in% "")
+  
+  A1<-sum(Column1 %in% "A")/(length(Column1)-spaces1)
+  A2<-sum(Column2 %in% "A")/(length(Column2)-spaces2)
+  A3<-sum(Column3 %in% "A")/(length(Column3)-spaces3)
+  A4<-sum(Column4 %in% "A")/(length(Column4)-spaces4)
+  A5<-sum(Column5 %in% "A")/(length(Column5)-spaces5)
+  A6<-sum(Column6 %in% "A")/(length(Column6)-spaces6)
+  A7<-sum(Column7 %in% "A")/(length(Column7)-spaces7)
+  A8<-sum(Column8 %in% "A")/(length(Column8)-spaces8)
+  A9<-sum(Column9 %in% "A")/(length(Column9)-spaces9)
+  A10<-sum(Column10 %in% "A")/(length(Column10)-spaces10)
+  A11<-sum(Column11 %in% "A")/(length(Column11)-spaces11)
+  A12<-sum(Column12 %in% "A")/(length(Column12)-spaces12)
+  A13<-sum(Column13 %in% "A")/(length(Column13)-spaces13)
+  A14<-sum(Column14 %in% "A")/(length(Column14)-spaces14)
+  A15<-sum(Column15 %in% "A")/(length(Column15)-spaces15)
+  AllAs<-cbind(A1,A2,A3,A4,A5,A6,A7,A8,A9,A10,A11,A12,A13,A14,A15)
+  
+  C1<-sum(Column1 %in% "C")/(length(Column1)-spaces1)
+  C2<-sum(Column2 %in% "C")/(length(Column2)-spaces2)
+  C3<-sum(Column3 %in% "C")/(length(Column3)-spaces3)
+  C4<-sum(Column4 %in% "C")/(length(Column4)-spaces4)
+  C5<-sum(Column5 %in% "C")/(length(Column5)-spaces5)
+  C6<-sum(Column6 %in% "C")/(length(Column6)-spaces6)
+  C7<-sum(Column7 %in% "C")/(length(Column7)-spaces7)
+  C8<-sum(Column8 %in% "C")/(length(Column8)-spaces8)
+  C9<-sum(Column9 %in% "C")/(length(Column9)-spaces9)
+  C10<-sum(Column10 %in% "C")/(length(Column10)-spaces10)
+  C11<-sum(Column11 %in% "C")/(length(Column11)-spaces11)
+  C12<-sum(Column12 %in% "C")/(length(Column12)-spaces12)
+  C13<-sum(Column13 %in% "C")/(length(Column13)-spaces13)
+  C14<-sum(Column14 %in% "C")/(length(Column14)-spaces14)
+  C15<-sum(Column15 %in% "C")/(length(Column15)-spaces15)
+  CllCs<-cbind(C1,C2,C3,C4,C5,C6,C7,C8,C9,C10,C11,C12,C13,C14,C15)
+  
+  D1<-sum(Column1 %in% "D")/(length(Column1)-spaces1)
+  D2<-sum(Column2 %in% "D")/(length(Column2)-spaces2)
+  D3<-sum(Column3 %in% "D")/(length(Column3)-spaces3)
+  D4<-sum(Column4 %in% "D")/(length(Column4)-spaces4)
+  D5<-sum(Column5 %in% "D")/(length(Column5)-spaces5)
+  D6<-sum(Column6 %in% "D")/(length(Column6)-spaces6)
+  D7<-sum(Column7 %in% "D")/(length(Column7)-spaces7)
+  D8<-sum(Column8 %in% "D")/(length(Column8)-spaces8)
+  D9<-sum(Column9 %in% "D")/(length(Column9)-spaces9)
+  D10<-sum(Column10 %in% "D")/(length(Column10)-spaces10)
+  D11<-sum(Column11 %in% "D")/(length(Column11)-spaces11)
+  D12<-sum(Column12 %in% "D")/(length(Column12)-spaces12)
+  D13<-sum(Column13 %in% "D")/(length(Column13)-spaces13)
+  D14<-sum(Column14 %in% "D")/(length(Column14)-spaces14)
+  D15<-sum(Column15 %in% "D")/(length(Column15)-spaces15)
+  DllDs<-cbind(D1,D2,D3,D4,D5,D6,D7,D8,D9,D10,D11,D12,D13,D14,D15)
+  
+  E1<-sum(Column1 %in% "E")/(length(Column1)-spaces1)
+  E2<-sum(Column2 %in% "E")/(length(Column2)-spaces2)
+  E3<-sum(Column3 %in% "E")/(length(Column3)-spaces3)
+  E4<-sum(Column4 %in% "E")/(length(Column4)-spaces4)
+  E5<-sum(Column5 %in% "E")/(length(Column5)-spaces5)
+  E6<-sum(Column6 %in% "E")/(length(Column6)-spaces6)
+  E7<-sum(Column7 %in% "E")/(length(Column7)-spaces7)
+  E8<-sum(Column8 %in% "E")/(length(Column8)-spaces8)
+  E9<-sum(Column9 %in% "E")/(length(Column9)-spaces9)
+  E10<-sum(Column10 %in% "E")/(length(Column10)-spaces10)
+  E11<-sum(Column11 %in% "E")/(length(Column11)-spaces11)
+  E12<-sum(Column12 %in% "E")/(length(Column12)-spaces12)
+  E13<-sum(Column13 %in% "E")/(length(Column13)-spaces13)
+  E14<-sum(Column14 %in% "E")/(length(Column14)-spaces14)
+  E15<-sum(Column15 %in% "E")/(length(Column15)-spaces15)
+  EllEs<-cbind(E1,E2,E3,E4,E5,E6,E7,E8,E9,E10,E11,E12,E13,E14,E15)
+  
+  
+  F1<-sum(Column1 %in% "F")/(length(Column1)-spaces1)
+  F2<-sum(Column2 %in% "F")/(length(Column2)-spaces2)
+  F3<-sum(Column3 %in% "F")/(length(Column3)-spaces3)
+  F4<-sum(Column4 %in% "F")/(length(Column4)-spaces4)
+  F5<-sum(Column5 %in% "F")/(length(Column5)-spaces5)
+  F6<-sum(Column6 %in% "F")/(length(Column6)-spaces6)
+  F7<-sum(Column7 %in% "F")/(length(Column7)-spaces7)
+  F8<-sum(Column8 %in% "F")/(length(Column8)-spaces8)
+  F9<-sum(Column9 %in% "F")/(length(Column9)-spaces9)
+  F10<-sum(Column10 %in% "F")/(length(Column10)-spaces10)
+  F11<-sum(Column11 %in% "F")/(length(Column11)-spaces11)
+  F12<-sum(Column12 %in% "F")/(length(Column12)-spaces12)
+  F13<-sum(Column13 %in% "F")/(length(Column13)-spaces13)
+  F14<-sum(Column14 %in% "F")/(length(Column14)-spaces14)
+  F15<-sum(Column15 %in% "F")/(length(Column15)-spaces15)
+  FllFs<-cbind(F1,F2,F3,F4,F5,F6,F7,F8,F9,F10,F11,F12,F13,F14,F15)
+  
+  
+  G1<-sum(Column1 %in% "G")/(length(Column1)-spaces1)
+  G2<-sum(Column2 %in% "G")/(length(Column2)-spaces2)
+  G3<-sum(Column3 %in% "G")/(length(Column3)-spaces3)
+  G4<-sum(Column4 %in% "G")/(length(Column4)-spaces4)
+  G5<-sum(Column5 %in% "G")/(length(Column5)-spaces5)
+  G6<-sum(Column6 %in% "G")/(length(Column6)-spaces6)
+  G7<-sum(Column7 %in% "G")/(length(Column7)-spaces7)
+  G8<-sum(Column8 %in% "G")/(length(Column8)-spaces8)
+  G9<-sum(Column9 %in% "G")/(length(Column9)-spaces9)
+  G10<-sum(Column10 %in% "G")/(length(Column10)-spaces10)
+  G11<-sum(Column11 %in% "G")/(length(Column11)-spaces11)
+  G12<-sum(Column12 %in% "G")/(length(Column12)-spaces12)
+  G13<-sum(Column13 %in% "G")/(length(Column13)-spaces13)
+  G14<-sum(Column14 %in% "G")/(length(Column14)-spaces14)
+  G15<-sum(Column15 %in% "G")/(length(Column15)-spaces15)
+  GllGs<-cbind(G1,G2,G3,G4,G5,G6,G7,G8,G9,G10,G11,G12,G13,G14,G15)
+  
+  
+  H1<-sum(Column1 %in% "H")/(length(Column1)-spaces1)
+  H2<-sum(Column2 %in% "H")/(length(Column2)-spaces2)
+  H3<-sum(Column3 %in% "H")/(length(Column3)-spaces3)
+  H4<-sum(Column4 %in% "H")/(length(Column4)-spaces4)
+  H5<-sum(Column5 %in% "H")/(length(Column5)-spaces5)
+  H6<-sum(Column6 %in% "H")/(length(Column6)-spaces6)
+  H7<-sum(Column7 %in% "H")/(length(Column7)-spaces7)
+  H8<-sum(Column8 %in% "H")/(length(Column8)-spaces8)
+  H9<-sum(Column9 %in% "H")/(length(Column9)-spaces9)
+  H10<-sum(Column10 %in% "H")/(length(Column10)-spaces10)
+  H11<-sum(Column11 %in% "H")/(length(Column11)-spaces11)
+  H12<-sum(Column12 %in% "H")/(length(Column12)-spaces12)
+  H13<-sum(Column13 %in% "H")/(length(Column13)-spaces13)
+  H14<-sum(Column14 %in% "H")/(length(Column14)-spaces14)
+  H15<-sum(Column15 %in% "H")/(length(Column15)-spaces15)
+  HllHs<-cbind(H1,H2,H3,H4,H5,H6,H7,H8,H9,H10,H11,H12,H13,H14,H15)
+  
+  
+  I1<-sum(Column1 %in% "I")/(length(Column1)-spaces1)
+  I2<-sum(Column2 %in% "I")/(length(Column2)-spaces2)
+  I3<-sum(Column3 %in% "I")/(length(Column3)-spaces3)
+  I4<-sum(Column4 %in% "I")/(length(Column4)-spaces4)
+  I5<-sum(Column5 %in% "I")/(length(Column5)-spaces5)
+  I6<-sum(Column6 %in% "I")/(length(Column6)-spaces6)
+  I7<-sum(Column7 %in% "I")/(length(Column7)-spaces7)
+  I8<-sum(Column8 %in% "I")/(length(Column8)-spaces8)
+  I9<-sum(Column9 %in% "I")/(length(Column9)-spaces9)
+  I10<-sum(Column10 %in% "I")/(length(Column10)-spaces10)
+  I11<-sum(Column11 %in% "I")/(length(Column11)-spaces11)
+  I12<-sum(Column12 %in% "I")/(length(Column12)-spaces12)
+  I13<-sum(Column13 %in% "I")/(length(Column13)-spaces13)
+  I14<-sum(Column14 %in% "I")/(length(Column14)-spaces14)
+  I15<-sum(Column15 %in% "I")/(length(Column15)-spaces15)
+  IllIs<-cbind(I1,I2,I3,I4,I5,I6,I7,I8,I9,I10,I11,I12,I13,I14,I15)
+  
+  
+  K1<-sum(Column1 %in% "K")/(length(Column1)-spaces1)
+  K2<-sum(Column2 %in% "K")/(length(Column2)-spaces2)
+  K3<-sum(Column3 %in% "K")/(length(Column3)-spaces3)
+  K4<-sum(Column4 %in% "K")/(length(Column4)-spaces4)
+  K5<-sum(Column5 %in% "K")/(length(Column5)-spaces5)
+  K6<-sum(Column6 %in% "K")/(length(Column6)-spaces6)
+  K7<-sum(Column7 %in% "K")/(length(Column7)-spaces7)
+  K8<-sum(Column8 %in% "K")/(length(Column8)-spaces8)
+  K9<-sum(Column9 %in% "K")/(length(Column9)-spaces9)
+  K10<-sum(Column10 %in% "K")/(length(Column10)-spaces10)
+  K11<-sum(Column11 %in% "K")/(length(Column11)-spaces11)
+  K12<-sum(Column12 %in% "K")/(length(Column12)-spaces12)
+  K13<-sum(Column13 %in% "K")/(length(Column13)-spaces13)
+  K14<-sum(Column14 %in% "K")/(length(Column14)-spaces14)
+  K15<-sum(Column15 %in% "K")/(length(Column15)-spaces15)
+  KllKs<-cbind(K1,K2,K3,K4,K5,K6,K7,K8,K9,K10,K11,K12,K13,K14,K15)
+  
+  
+  L1<-sum(Column1 %in% "L")/(length(Column1)-spaces1)
+  L2<-sum(Column2 %in% "L")/(length(Column2)-spaces2)
+  L3<-sum(Column3 %in% "L")/(length(Column3)-spaces3)
+  L4<-sum(Column4 %in% "L")/(length(Column4)-spaces4)
+  L5<-sum(Column5 %in% "L")/(length(Column5)-spaces5)
+  L6<-sum(Column6 %in% "L")/(length(Column6)-spaces6)
+  L7<-sum(Column7 %in% "L")/(length(Column7)-spaces7)
+  L8<-sum(Column8 %in% "L")/(length(Column8)-spaces8)
+  L9<-sum(Column9 %in% "L")/(length(Column9)-spaces9)
+  L10<-sum(Column10 %in% "L")/(length(Column10)-spaces10)
+  L11<-sum(Column11 %in% "L")/(length(Column11)-spaces11)
+  L12<-sum(Column12 %in% "L")/(length(Column12)-spaces12)
+  L13<-sum(Column13 %in% "L")/(length(Column13)-spaces13)
+  L14<-sum(Column14 %in% "L")/(length(Column14)-spaces14)
+  L15<-sum(Column15 %in% "L")/(length(Column15)-spaces15)
+  LllLs<-cbind(L1,L2,L3,L4,L5,L6,L7,L8,L9,L10,L11,L12,L13,L14,L15)
+  
+  
+  M1<-sum(Column1 %in% "M")/(length(Column1)-spaces1)
+  M2<-sum(Column2 %in% "M")/(length(Column2)-spaces2)
+  M3<-sum(Column3 %in% "M")/(length(Column3)-spaces3)
+  M4<-sum(Column4 %in% "M")/(length(Column4)-spaces4)
+  M5<-sum(Column5 %in% "M")/(length(Column5)-spaces5)
+  M6<-sum(Column6 %in% "M")/(length(Column6)-spaces6)
+  M7<-sum(Column7 %in% "M")/(length(Column7)-spaces7)
+  M8<-sum(Column8 %in% "M")/(length(Column8)-spaces8)
+  M9<-sum(Column9 %in% "M")/(length(Column9)-spaces9)
+  M10<-sum(Column10 %in% "M")/(length(Column10)-spaces10)
+  M11<-sum(Column11 %in% "M")/(length(Column11)-spaces11)
+  M12<-sum(Column12 %in% "M")/(length(Column12)-spaces12)
+  M13<-sum(Column13 %in% "M")/(length(Column13)-spaces13)
+  M14<-sum(Column14 %in% "M")/(length(Column14)-spaces14)
+  M15<-sum(Column15 %in% "M")/(length(Column15)-spaces15)
+  MllMs<-cbind(M1,M2,M3,M4,M5,M6,M7,M8,M9,M10,M11,M12,M13,M14,M15)
+  
+  
+  N1<-sum(Column1 %in% "N")/(length(Column1)-spaces1)
+  N2<-sum(Column2 %in% "N")/(length(Column2)-spaces2)
+  N3<-sum(Column3 %in% "N")/(length(Column3)-spaces3)
+  N4<-sum(Column4 %in% "N")/(length(Column4)-spaces4)
+  N5<-sum(Column5 %in% "N")/(length(Column5)-spaces5)
+  N6<-sum(Column6 %in% "N")/(length(Column6)-spaces6)
+  N7<-sum(Column7 %in% "N")/(length(Column7)-spaces7)
+  N8<-sum(Column8 %in% "N")/(length(Column8)-spaces8)
+  N9<-sum(Column9 %in% "N")/(length(Column9)-spaces9)
+  N10<-sum(Column10 %in% "N")/(length(Column10)-spaces10)
+  N11<-sum(Column11 %in% "N")/(length(Column11)-spaces11)
+  N12<-sum(Column12 %in% "N")/(length(Column12)-spaces12)
+  N13<-sum(Column13 %in% "N")/(length(Column13)-spaces13)
+  N14<-sum(Column14 %in% "N")/(length(Column14)-spaces14)
+  N15<-sum(Column15 %in% "N")/(length(Column15)-spaces15)
+  NllNs<-cbind(N1,N2,N3,N4,N5,N6,N7,N8,N9,N10,N11,N12,N13,N14,N15)
+  
+  
+  P1<-sum(Column1 %in% "P")/(length(Column1)-spaces1)
+  P2<-sum(Column2 %in% "P")/(length(Column2)-spaces2)
+  P3<-sum(Column3 %in% "P")/(length(Column3)-spaces3)
+  P4<-sum(Column4 %in% "P")/(length(Column4)-spaces4)
+  P5<-sum(Column5 %in% "P")/(length(Column5)-spaces5)
+  P6<-sum(Column6 %in% "P")/(length(Column6)-spaces6)
+  P7<-sum(Column7 %in% "P")/(length(Column7)-spaces7)
+  P8<-sum(Column8 %in% "P")/(length(Column8)-spaces8)
+  P9<-sum(Column9 %in% "P")/(length(Column9)-spaces9)
+  P10<-sum(Column10 %in% "P")/(length(Column10)-spaces10)
+  P11<-sum(Column11 %in% "P")/(length(Column11)-spaces11)
+  P12<-sum(Column12 %in% "P")/(length(Column12)-spaces12)
+  P13<-sum(Column13 %in% "P")/(length(Column13)-spaces13)
+  P14<-sum(Column14 %in% "P")/(length(Column14)-spaces14)
+  P15<-sum(Column15 %in% "P")/(length(Column15)-spaces15)
+  PllPs<-cbind(P1,P2,P3,P4,P5,P6,P7,P8,P9,P10,P11,P12,P13,P14,P15)
+  
+  
+  Q1<-sum(Column1 %in% "Q")/(length(Column1)-spaces1)
+  Q2<-sum(Column2 %in% "Q")/(length(Column2)-spaces2)
+  Q3<-sum(Column3 %in% "Q")/(length(Column3)-spaces3)
+  Q4<-sum(Column4 %in% "Q")/(length(Column4)-spaces4)
+  Q5<-sum(Column5 %in% "Q")/(length(Column5)-spaces5)
+  Q6<-sum(Column6 %in% "Q")/(length(Column6)-spaces6)
+  Q7<-sum(Column7 %in% "Q")/(length(Column7)-spaces7)
+  Q8<-sum(Column8 %in% "Q")/(length(Column8)-spaces8)
+  Q9<-sum(Column9 %in% "Q")/(length(Column9)-spaces9)
+  Q10<-sum(Column10 %in% "Q")/(length(Column10)-spaces10)
+  Q11<-sum(Column11 %in% "Q")/(length(Column11)-spaces11)
+  Q12<-sum(Column12 %in% "Q")/(length(Column12)-spaces12)
+  Q13<-sum(Column13 %in% "Q")/(length(Column13)-spaces13)
+  Q14<-sum(Column14 %in% "Q")/(length(Column14)-spaces14)
+  Q15<-sum(Column15 %in% "Q")/(length(Column15)-spaces15)
+  QllQs<-cbind(Q1,Q2,Q3,Q4,Q5,Q6,Q7,Q8,Q9,Q10,Q11,Q12,Q13,Q14,Q15)
+  
+  
+  R1<-sum(Column1 %in% "R")/(length(Column1)-spaces1)
+  R2<-sum(Column2 %in% "R")/(length(Column2)-spaces2)
+  R3<-sum(Column3 %in% "R")/(length(Column3)-spaces3)
+  R4<-sum(Column4 %in% "R")/(length(Column4)-spaces4)
+  R5<-sum(Column5 %in% "R")/(length(Column5)-spaces5)
+  R6<-sum(Column6 %in% "R")/(length(Column6)-spaces6)
+  R7<-sum(Column7 %in% "R")/(length(Column7)-spaces7)
+  R8<-sum(Column8 %in% "R")/(length(Column8)-spaces8)
+  R9<-sum(Column9 %in% "R")/(length(Column9)-spaces9)
+  R10<-sum(Column10 %in% "R")/(length(Column10)-spaces10)
+  R11<-sum(Column11 %in% "R")/(length(Column11)-spaces11)
+  R12<-sum(Column12 %in% "R")/(length(Column12)-spaces12)
+  R13<-sum(Column13 %in% "R")/(length(Column13)-spaces13)
+  R14<-sum(Column14 %in% "R")/(length(Column14)-spaces14)
+  R15<-sum(Column15 %in% "R")/(length(Column15)-spaces15)
+  RllRs<-cbind(R1,R2,R3,R4,R5,R6,R7,R8,R9,R10,R11,R12,R13,R14,R15)
+  
+  
+  S1<-sum(Column1 %in% "S")/(length(Column1)-spaces1)
+  S2<-sum(Column2 %in% "S")/(length(Column2)-spaces2)
+  S3<-sum(Column3 %in% "S")/(length(Column3)-spaces3)
+  S4<-sum(Column4 %in% "S")/(length(Column4)-spaces4)
+  S5<-sum(Column5 %in% "S")/(length(Column5)-spaces5)
+  S6<-sum(Column6 %in% "S")/(length(Column6)-spaces6)
+  S7<-sum(Column7 %in% "S")/(length(Column7)-spaces7)
+  S8<-sum(Column8 %in% "S")/(length(Column8)-spaces8)
+  S9<-sum(Column9 %in% "S")/(length(Column9)-spaces9)
+  S10<-sum(Column10 %in% "S")/(length(Column10)-spaces10)
+  S11<-sum(Column11 %in% "S")/(length(Column11)-spaces11)
+  S12<-sum(Column12 %in% "S")/(length(Column12)-spaces12)
+  S13<-sum(Column13 %in% "S")/(length(Column13)-spaces13)
+  S14<-sum(Column14 %in% "S")/(length(Column14)-spaces14)
+  S15<-sum(Column15 %in% "S")/(length(Column15)-spaces15)
+  SllSs<-cbind(S1,S2,S3,S4,S5,S6,S7,S8,S9,S10,S11,S12,S13,S14,S15)
+  
+  
+  T1<-sum(Column1 %in% "T")/(length(Column1)-spaces1)
+  T2<-sum(Column2 %in% "T")/(length(Column2)-spaces2)
+  T3<-sum(Column3 %in% "T")/(length(Column3)-spaces3)
+  T4<-sum(Column4 %in% "T")/(length(Column4)-spaces4)
+  T5<-sum(Column5 %in% "T")/(length(Column5)-spaces5)
+  T6<-sum(Column6 %in% "T")/(length(Column6)-spaces6)
+  T7<-sum(Column7 %in% "T")/(length(Column7)-spaces7)
+  T8<-sum(Column8 %in% "T")/(length(Column8)-spaces8)
+  T9<-sum(Column9 %in% "T")/(length(Column9)-spaces9)
+  T10<-sum(Column10 %in% "T")/(length(Column10)-spaces10)
+  T11<-sum(Column11 %in% "T")/(length(Column11)-spaces11)
+  T12<-sum(Column12 %in% "T")/(length(Column12)-spaces12)
+  T13<-sum(Column13 %in% "T")/(length(Column13)-spaces13)
+  T14<-sum(Column14 %in% "T")/(length(Column14)-spaces14)
+  T15<-sum(Column15 %in% "T")/(length(Column15)-spaces15)
+  TllTs<-cbind(T1,T2,T3,T4,T5,T6,T7,T8,T9,T10,T11,T12,T13,T14,T15)
+  
+  
+  V1<-sum(Column1 %in% "V")/(length(Column1)-spaces1)
+  V2<-sum(Column2 %in% "V")/(length(Column2)-spaces2)
+  V3<-sum(Column3 %in% "V")/(length(Column3)-spaces3)
+  V4<-sum(Column4 %in% "V")/(length(Column4)-spaces4)
+  V5<-sum(Column5 %in% "V")/(length(Column5)-spaces5)
+  V6<-sum(Column6 %in% "V")/(length(Column6)-spaces6)
+  V7<-sum(Column7 %in% "V")/(length(Column7)-spaces7)
+  V8<-sum(Column8 %in% "V")/(length(Column8)-spaces8)
+  V9<-sum(Column9 %in% "V")/(length(Column9)-spaces9)
+  V10<-sum(Column10 %in% "V")/(length(Column10)-spaces10)
+  V11<-sum(Column11 %in% "V")/(length(Column11)-spaces11)
+  V12<-sum(Column12 %in% "V")/(length(Column12)-spaces12)
+  V13<-sum(Column13 %in% "V")/(length(Column13)-spaces13)
+  V14<-sum(Column14 %in% "V")/(length(Column14)-spaces14)
+  V15<-sum(Column15 %in% "V")/(length(Column15)-spaces15)
+  VllVs<-cbind(V1,V2,V3,V4,V5,V6,V7,V8,V9,V10,V11,V12,V13,V14,V15)
+  
+  
+  W1<-sum(Column1 %in% "W")/(length(Column1)-spaces1)
+  W2<-sum(Column2 %in% "W")/(length(Column2)-spaces2)
+  W3<-sum(Column3 %in% "W")/(length(Column3)-spaces3)
+  W4<-sum(Column4 %in% "W")/(length(Column4)-spaces4)
+  W5<-sum(Column5 %in% "W")/(length(Column5)-spaces5)
+  W6<-sum(Column6 %in% "W")/(length(Column6)-spaces6)
+  W7<-sum(Column7 %in% "W")/(length(Column7)-spaces7)
+  W8<-sum(Column8 %in% "W")/(length(Column8)-spaces8)
+  W9<-sum(Column9 %in% "W")/(length(Column9)-spaces9)
+  W10<-sum(Column10 %in% "W")/(length(Column10)-spaces10)
+  W11<-sum(Column11 %in% "W")/(length(Column11)-spaces11)
+  W12<-sum(Column12 %in% "W")/(length(Column12)-spaces12)
+  W13<-sum(Column13 %in% "W")/(length(Column13)-spaces13)
+  W14<-sum(Column14 %in% "W")/(length(Column14)-spaces14)
+  W15<-sum(Column15 %in% "W")/(length(Column15)-spaces15)
+  WllWs<-cbind(W1,W2,W3,W4,W5,W6,W7,W8,W9,W10,W11,W12,W13,W14,W15)
+  
+  
+  Y1<-sum(Column1 %in% "Y")/(length(Column1)-spaces1)
+  Y2<-sum(Column2 %in% "Y")/(length(Column2)-spaces2)
+  Y3<-sum(Column3 %in% "Y")/(length(Column3)-spaces3)
+  Y4<-sum(Column4 %in% "Y")/(length(Column4)-spaces4)
+  Y5<-sum(Column5 %in% "Y")/(length(Column5)-spaces5)
+  Y6<-sum(Column6 %in% "Y")/(length(Column6)-spaces6)
+  Y7<-sum(Column7 %in% "Y")/(length(Column7)-spaces7)
+  Y8<-sum(Column8 %in% "Y")/(length(Column8)-spaces8)
+  Y9<-sum(Column9 %in% "Y")/(length(Column9)-spaces9)
+  Y10<-sum(Column10 %in% "Y")/(length(Column10)-spaces10)
+  Y11<-sum(Column11 %in% "Y")/(length(Column11)-spaces11)
+  Y12<-sum(Column12 %in% "Y")/(length(Column12)-spaces12)
+  Y13<-sum(Column13 %in% "Y")/(length(Column13)-spaces13)
+  Y14<-sum(Column14 %in% "Y")/(length(Column14)-spaces14)
+  Y15<-sum(Column15 %in% "Y")/(length(Column15)-spaces15)
+  YllYs<-cbind(Y1,Y2,Y3,Y4,Y5,Y6,Y7,Y8,Y9,Y10,Y11,Y12,Y13,Y14,Y15)
+}
+#this is substrate percents
+
+#A C D E F G H I K L N P Q R S T V W Y
+
+PercentTable<-rbind(AllAs,CllCs,DllDs,EllEs,FllFs,GllGs,HllHs,IllIs,KllKs,LllLs,MllMs,NllNs,PllPs,QllQs,RllRs,SllSs,TllTs,VllVs,WllWs,YllYs)
+PercentTable<-PercentTable*100
+
+#create the SD table
+SDtable<-matrix(data = rep(1,times=(nrow(PercentTable)*ncol(PercentTable))),nrow = nrow(PercentTable),ncol = ncol(PercentTable))
+#for every row, a percertage minus the same mean over the same SD
+if(1==1){
+  SDtable[1,]<-(PercentTable[1,]-Amean)/Asd
+  SDtable[2,]<-(PercentTable[2,]-Cmean)/Csd
+  SDtable[3,]<-(PercentTable[3,]-Dmean)/Dsd
+  SDtable[4,]<-(PercentTable[4,]-Emean)/Esd
+  SDtable[5,]<-(PercentTable[5,]-Fmean)/Fsd
+  SDtable[6,]<-(PercentTable[6,]-Gmean)/Gsd
+  SDtable[7,]<-(PercentTable[7,]-Hmean)/Hsd
+  SDtable[8,]<-(PercentTable[8,]-Imean)/Isd
+  SDtable[9,]<-(PercentTable[9,]-Kmean)/Ksd
+  SDtable[10,]<-(PercentTable[10,]-Lmean)/Lsd
+  SDtable[11,]<-(PercentTable[11,]-Mmean)/Msd
+  SDtable[12,]<-(PercentTable[12,]-Nmean)/Nsd
+  SDtable[13,]<-(PercentTable[13,]-Pmean)/Psd
+  SDtable[14,]<-(PercentTable[14,]-Qmean)/Qsd
+  SDtable[15,]<-(PercentTable[15,]-Rmean)/Rsd
+  SDtable[16,]<-(PercentTable[16,]-Smean)/Ssd
+  SDtable[17,]<-(PercentTable[17,]-Tmean)/Tsd
+  SDtable[18,]<-(PercentTable[18,]-Vmean)/Vsd
+  SDtable[19,]<-(PercentTable[19,]-Wmean)/Wsd
+  SDtable[20,]<-(PercentTable[20,]-Ymean)/Ysd
+}
+
+
+SetOfAAs<-c("Letter","A","C","D","E","F","G","H","I","K","L","M","N","P","Q","R","S","T","V","W","Y")
+
+
+SumOfSigmaAAs<-c(1:15)
+
+for (i in 1:15){
+  SumOfSigmasValue<-0
+  for (j in 1:20){
+        value<-0
+    if (SDtable[j,i]>2){
+      value<-sum(substrates[,i]==SetOfAAs[j])
+    }
+    SumOfSigmasValue<-SumOfSigmasValue+value
+  }
+  SumOfSigmaAAs[i]<-SumOfSigmasValue
+}
+
+# AAs1<-length(substrates[,1])-sum(substrates[,1]=="")
+# AAs2<-length(substrates[,2])-sum(substrates[,2]=="")
+# AAs3<-length(substrates[,3])-sum(substrates[,3]=="")
+# AAs4<-length(substrates[,4])-sum(substrates[,4]=="")
+# AAs5<-length(substrates[,5])-sum(substrates[,5]=="")
+# AAs6<-length(substrates[,6])-sum(substrates[,6]=="")
+# AAs7<-length(substrates[,7])-sum(substrates[,7]=="")
+# AAs8<-length(substrates[,8])-sum(substrates[,8]=="")
+# AAs9<-length(substrates[,9])-sum(substrates[,9]=="")
+# 
+# 
+# 
+# #AAsAtPositions<-c(AAs1,AAs2,AAs3,AAs4,AAs5,AAs6,AAs7,AAs8,AAs9)
+# AAsAtPositions<-c(length(substrates[,1]),length(substrates[,2]),length(substrates[,3]),length(substrates[,4]),
+#                   length(substrates[,5]),length(substrates[,6]),length(substrates[,7]),length(substrates[,8]),
+#                   length(substrates[,9]))
+
+SumOfExpectedSigmaAAs<-c(1:15)
+for (i in 1:15){
+  ExpectedValue<-0
+  for (j in 1:20){
+        value<-0
+    if (SDtable[j,i]>2){
+      value<-AllMeans[j]
+    }
+    ExpectedValue<-ExpectedValue+value
+  }
+  SumOfExpectedSigmaAAs[i]<-ExpectedValue*(length(substrates[,i])-sum(substrates[,i]%in% ""))/100
+}
+
+SelectivityRow<-SumOfSigmaAAs/SumOfExpectedSigmaAAs
+SelectivitySheet<-rbind(SumOfSigmaAAs,SumOfExpectedSigmaAAs,SelectivityRow)
+
+SetOfAAs<-matrix(data = SetOfAAs,ncol = 1)
+
+SDtableu<-SDtable
+HeaderSD<-c(-7:7)
+SDtable<-rbind(HeaderSD,SDtableu)
+row.names(SDtable)<-NULL
+SDtable<-data.frame(SetOfAAs,SDtable)
+
+PercentTable<-rbind(HeaderSD,PercentTable)
+row.names(PercentTable)<-NULL
+PercentTable<-data.frame(SetOfAAs,PercentTable)
+numberofY<-as.numeric(SubstrateBackgroundFrequency$Number.of.Y)
+numberofY<-numberofY[!is.na(numberofY)]
+
+numberofPY<-as.numeric(SubstrateBackgroundFrequency$Number.of.pY)
+numberofPY<-numberofPY[!is.na(numberofPY)]
+
+NormalizationScore<-sum(numberofPY)/sum(numberofY)
+
+# positions<-matrix(data = NA, nrow=20,ncol = 15)
+# 
+# #column1
+# 
+# for (q in 1:15) {
+#   sA<-sum(substrates[,i]=="A")
+#   positions[1,i]<-sA
+#   sC<-sum(substrates[,i]=="C")
+#   positions[2,i]<-sC
+#   sD<-sum(substrates[,i]=="D")
+#   positions[3,i]<-sD
+#   sE<-sum(substrates[,i]=="E")
+#   positions[4,i]<-sE
+#   sF<-sum(substrates[,i]=="F")
+#   sG<-sum(substrates[,i]=="G")
+#   sH<-sum(substrates[,i]=="H")
+#   sI<-sum(substrates[,i]=="I")
+#   sK<-sum(substrates[,i]=="K")
+#   sL<-sum(substrates[,i]=="L")
+#   sM<-sum(substrates[,i]=="M")
+#   sN<-sum(substrates[,i]=="N")
+#   sP<-sum(substrates[,i]=="P")
+#   sQ<-sum(substrates[,i]=="Q")
+#   sR<-sum(substrates[,i]=="R")
+#   sS<-sum(substrates[,i]=="S")
+#   sT<-sum(substrates[,i]=="T")
+#   sV<-sum(substrates[,i]=="V")
+#   sW<-sum(substrates[,i]=="W")
+#   sY<-sum(substrates[,i]=="Y")
+#   positions[5,i]<-sF
+#   positions[6,i]<-sG
+#   positions[7,i]<-sH
+#   positions[8,i]<-sI
+#   positions[9,i]<-sK
+#   positions[10,i]<-sL
+#   positions[11,i]<-sM
+#   positions[12,i]<-sN
+#   positions[13,i]<-sP
+#   positions[14,i]<-sQ
+#   positions[15,i]<-sR
+#   positions[16,i]<-sS
+#   positions[17,i]<-sT
+#   positions[18,i]<-sV
+#   positions[19,i]<-sW
+#   positions[20,i]<-sY
+# }
+
+#here I create the positions table which is needed for the endogenous prob matrix and is simply "how many times did an AA show up in this spot?
+if (6==6){
+  Column1<-substrates[,1]
+  Column2<-substrates[,2]
+  Column3<-substrates[,3]
+  Column4<-substrates[,4]
+  Column5<-substrates[,5]
+  Column6<-substrates[,6]
+  Column7<-substrates[,7]
+  Column8<-substrates[,8]
+  Column9<-substrates[,9]
+  Column10<-substrates[,10]
+  Column11<-substrates[,11]
+  Column12<-substrates[,12]
+  Column13<-substrates[,13]
+  Column14<-substrates[,14]
+  Column15<-substrates[,15]
+  
+  spaces1<-sum((Column1%in% ""))
+  spaces2<-sum(Column2%in% "")
+  spaces3<-sum(Column3%in% "")
+  spaces4<-sum(Column4%in% "")
+  spaces5<-sum(Column5%in% "")
+  spaces6<-sum(Column6%in% "")
+  spaces7<-sum(Column7%in% "")
+  spaces8<-sum(Column8%in% "")
+  spaces9<-sum(Column9%in% "")
+  spaces10<-sum(Column10%in% "")
+  spaces11<-sum(Column11%in% "")
+  spaces12<-sum(Column12%in% "")
+  spaces13<-sum(Column13%in% "")
+  spaces14<-sum(Column14%in% "")
+  spaces15<-sum(Column15%in% "")
+  
+  A1<-sum(Column1 %in% "A")
+  A2<-sum(Column2 %in% "A")
+  A3<-sum(Column3 %in% "A")
+  A4<-sum(Column4 %in% "A")
+  A5<-sum(Column5 %in% "A")
+  A6<-sum(Column6 %in% "A")
+  A7<-sum(Column7 %in% "A")
+  A8<-sum(Column8 %in% "A")
+  A9<-sum(Column9 %in% "A")
+  A10<-sum(Column10 %in% "A")
+  A11<-sum(Column11 %in% "A")
+  A12<-sum(Column12 %in% "A")
+  A13<-sum(Column13 %in% "A")
+  A14<-sum(Column14 %in% "A")
+  A15<-sum(Column15 %in% "A")
+  AllAs<-cbind(A1,A2,A3,A4,A5,A6,A7,A8,A9,A10,A11,A12,A13,A14,A15)
+  
+  C1<-sum(Column1 %in% "C")
+  C2<-sum(Column2 %in% "C")
+  C3<-sum(Column3 %in% "C")
+  C4<-sum(Column4 %in% "C")
+  C5<-sum(Column5 %in% "C")
+  C6<-sum(Column6 %in% "C")
+  C7<-sum(Column7 %in% "C")
+  C8<-sum(Column8 %in% "C")
+  C9<-sum(Column9 %in% "C")  
+  C10<-sum(Column10 %in% "C")
+  C11<-sum(Column11 %in% "C")
+  C12<-sum(Column12 %in% "C")
+  C13<-sum(Column13 %in% "C")
+  C14<-sum(Column14 %in% "C")
+  C15<-sum(Column15 %in% "C")
+  CllCs<-cbind(C1,C2,C3,C4,C5,C6,C7,C8,C9,C10,C11,C12,C13,C14,C15)
+  
+  D1<-sum(Column1 %in% "D")
+  D2<-sum(Column2 %in% "D")
+  D3<-sum(Column3 %in% "D")
+  D4<-sum(Column4 %in% "D")
+  D5<-sum(Column5 %in% "D")
+  D6<-sum(Column6 %in% "D")
+  D7<-sum(Column7 %in% "D")
+  D8<-sum(Column8 %in% "D")
+  D9<-sum(Column9 %in% "D")
+  D10<-sum(Column10 %in% "D")
+  D11<-sum(Column11 %in% "D")
+  D12<-sum(Column12 %in% "D")
+  D13<-sum(Column13 %in% "D")
+  D14<-sum(Column14 %in% "D")
+  D15<-sum(Column15 %in% "D")
+  DllDs<-cbind(D1,D2,D3,D4,D5,D6,D7,D8,D9,D10,D11,D12,D13,D14,D15)
+  
+  E1<-sum(Column1 %in% "E")
+  E2<-sum(Column2 %in% "E")
+  E3<-sum(Column3 %in% "E")
+  E4<-sum(Column4 %in% "E")
+  E5<-sum(Column5 %in% "E")
+  E6<-sum(Column6 %in% "E")
+  E7<-sum(Column7 %in% "E")
+  E8<-sum(Column8 %in% "E")
+  E9<-sum(Column9 %in% "E")
+  E10<-sum(Column10 %in% "E")
+  E11<-sum(Column11 %in% "E")
+  E12<-sum(Column12 %in% "E")
+  E13<-sum(Column13 %in% "E")
+  E14<-sum(Column14 %in% "E")
+  E15<-sum(Column15 %in% "E")
+  EllEs<-cbind(E1,E2,E3,E4,E5,E6,E7,E8,E9,E10,E11,E12,E13,E14,E15)
+  
+  F1<-sum(Column1 %in% "F")
+  F2<-sum(Column2 %in% "F")
+  F3<-sum(Column3 %in% "F")
+  F4<-sum(Column4 %in% "F")
+  F5<-sum(Column5 %in% "F")
+  F6<-sum(Column6 %in% "F")
+  F7<-sum(Column7 %in% "F")
+  F8<-sum(Column8 %in% "F")
+  F9<-sum(Column9 %in% "F")
+  F10<-sum(Column10 %in% "F")
+  F11<-sum(Column11 %in% "F")
+  F12<-sum(Column12 %in% "F")
+  F13<-sum(Column13 %in% "F")
+  F14<-sum(Column14 %in% "F")
+  F15<-sum(Column15 %in% "F")
+  FllFs<-cbind(F1,F2,F3,F4,F5,F6,F7,F8,F9,F10,F11,F12,F13,F14,F15)
+  
+  G1<-sum(Column1 %in% "G")
+  G2<-sum(Column2 %in% "G")
+  G3<-sum(Column3 %in% "G")
+  G4<-sum(Column4 %in% "G")
+  G5<-sum(Column5 %in% "G")
+  G6<-sum(Column6 %in% "G")
+  G7<-sum(Column7 %in% "G")
+  G8<-sum(Column8 %in% "G")
+  G9<-sum(Column9 %in% "G")
+  G10<-sum(Column10 %in% "G")
+  G11<-sum(Column11 %in% "G")
+  G12<-sum(Column12 %in% "G")
+  G13<-sum(Column13 %in% "G")
+  G14<-sum(Column14 %in% "G")
+  G15<-sum(Column15 %in% "G")
+  GllGs<-cbind(G1,G2,G3,G4,G5,G6,G7,G8,G9,G10,G11,G12,G13,G14,G15)
+  
+  H1<-sum(Column1 %in% "H")
+  H2<-sum(Column2 %in% "H")
+  H3<-sum(Column3 %in% "H")
+  H4<-sum(Column4 %in% "H")
+  H5<-sum(Column5 %in% "H")
+  H6<-sum(Column6 %in% "H")
+  H7<-sum(Column7 %in% "H")
+  H8<-sum(Column8 %in% "H")
+  H9<-sum(Column9 %in% "H")
+  H10<-sum(Column10 %in% "H")
+  H11<-sum(Column11 %in% "H")
+  H12<-sum(Column12 %in% "H")
+  H13<-sum(Column13 %in% "H")
+  H14<-sum(Column14 %in% "H")
+  H15<-sum(Column15 %in% "H")
+  HllHs<-cbind(H1,H2,H3,H4,H5,H6,H7,H8,H9,H10,H11,H12,H13,H14,H15)
+  
+  I1<-sum(Column1 %in% "I")
+  I2<-sum(Column2 %in% "I")
+  I3<-sum(Column3 %in% "I")
+  I4<-sum(Column4 %in% "I")
+  I5<-sum(Column5 %in% "I")
+  I6<-sum(Column6 %in% "I")
+  I7<-sum(Column7 %in% "I")
+  I8<-sum(Column8 %in% "I")
+  I9<-sum(Column9 %in% "I")
+  I10<-sum(Column10 %in% "I")
+  I11<-sum(Column11 %in% "I")
+  I12<-sum(Column12 %in% "I")
+  I13<-sum(Column13 %in% "I")
+  I14<-sum(Column14 %in% "I")
+  I15<-sum(Column15 %in% "I")
+  IllIs<-cbind(I1,I2,I3,I4,I5,I6,I7,I8,I9,I10,I11,I12,I13,I14,I15)
+  
+  K1<-sum(Column1 %in% "K")
+  K2<-sum(Column2 %in% "K")
+  K3<-sum(Column3 %in% "K")
+  K4<-sum(Column4 %in% "K")
+  K5<-sum(Column5 %in% "K")
+  K6<-sum(Column6 %in% "K")
+  K7<-sum(Column7 %in% "K")
+  K8<-sum(Column8 %in% "K")
+  K9<-sum(Column9 %in% "K")
+  K10<-sum(Column10 %in% "K")
+  K11<-sum(Column11 %in% "K")
+  K12<-sum(Column12 %in% "K")
+  K13<-sum(Column13 %in% "K")
+  K14<-sum(Column14 %in% "K")
+  K15<-sum(Column15 %in% "K")
+  KllKs<-cbind(K1,K2,K3,K4,K5,K6,K7,K8,K9,K10,K11,K12,K13,K14,K15)
+  
+  L1<-sum(Column1 %in% "L")
+  L2<-sum(Column2 %in% "L")
+  L3<-sum(Column3 %in% "L")
+  L4<-sum(Column4 %in% "L")
+  L5<-sum(Column5 %in% "L")
+  L6<-sum(Column6 %in% "L")
+  L7<-sum(Column7 %in% "L")
+  L8<-sum(Column8 %in% "L")
+  L9<-sum(Column9 %in% "L")
+  L10<-sum(Column10 %in% "L")
+  L11<-sum(Column11 %in% "L")
+  L12<-sum(Column12 %in% "L")
+  L13<-sum(Column13 %in% "L")
+  L14<-sum(Column14 %in% "L")
+  L15<-sum(Column15 %in% "L")
+  LllLs<-cbind(L1,L2,L3,L4,L5,L6,L7,L8,L9,L10,L11,L12,L13,L14,L15)
+  
+  M1<-sum(Column1 %in% "M")
+  M2<-sum(Column2 %in% "M")
+  M3<-sum(Column3 %in% "M")
+  M4<-sum(Column4 %in% "M")
+  M5<-sum(Column5 %in% "M")
+  M6<-sum(Column6 %in% "M")
+  M7<-sum(Column7 %in% "M")
+  M8<-sum(Column8 %in% "M")
+  M9<-sum(Column9 %in% "M")
+  M10<-sum(Column10 %in% "M")
+  M11<-sum(Column11 %in% "M")
+  M12<-sum(Column12 %in% "M")
+  M13<-sum(Column13 %in% "M")
+  M14<-sum(Column14 %in% "M")
+  M15<-sum(Column15 %in% "M")
+  MllMs<-cbind(M1,M2,M3,M4,M5,M6,M7,M8,M9,M10,M11,M12,M13,M14,M15)
+  
+  N1<-sum(Column1 %in% "N")
+  N2<-sum(Column2 %in% "N")
+  N3<-sum(Column3 %in% "N")
+  N4<-sum(Column4 %in% "N")
+  N5<-sum(Column5 %in% "N")
+  N6<-sum(Column6 %in% "N")
+  N7<-sum(Column7 %in% "N")
+  N8<-sum(Column8 %in% "N")
+  N9<-sum(Column9 %in% "N")
+  N10<-sum(Column10 %in% "N")
+  N11<-sum(Column11 %in% "N")
+  N12<-sum(Column12 %in% "N")
+  N13<-sum(Column13 %in% "N")
+  N14<-sum(Column14 %in% "N")
+  N15<-sum(Column15 %in% "N")
+  NllNs<-cbind(N1,N2,N3,N4,N5,N6,N7,N8,N9,N10,N11,N12,N13,N14,N15)
+  
+  P1<-sum(Column1 %in% "P")
+  P2<-sum(Column2 %in% "P")
+  P3<-sum(Column3 %in% "P")
+  P4<-sum(Column4 %in% "P")
+  P5<-sum(Column5 %in% "P")
+  P6<-sum(Column6 %in% "P")
+  P7<-sum(Column7 %in% "P")
+  P8<-sum(Column8 %in% "P")
+  P9<-sum(Column9 %in% "P")
+  P10<-sum(Column10 %in% "P")
+  P11<-sum(Column11 %in% "P")
+  P12<-sum(Column12 %in% "P")
+  P13<-sum(Column13 %in% "P")
+  P14<-sum(Column14 %in% "P")
+  P15<-sum(Column15 %in% "P")
+  PllPs<-cbind(P1,P2,P3,P4,P5,P6,P7,P8,P9,P10,P11,P12,P13,P14,P15)
+  
+  Q1<-sum(Column1 %in% "Q")
+  Q2<-sum(Column2 %in% "Q")
+  Q3<-sum(Column3 %in% "Q")
+  Q4<-sum(Column4 %in% "Q")
+  Q5<-sum(Column5 %in% "Q")
+  Q6<-sum(Column6 %in% "Q")
+  Q7<-sum(Column7 %in% "Q")
+  Q8<-sum(Column8 %in% "Q")
+  Q9<-sum(Column9 %in% "Q")
+  Q10<-sum(Column10 %in% "Q")
+  Q11<-sum(Column11 %in% "Q")
+  Q12<-sum(Column12 %in% "Q")
+  Q13<-sum(Column13 %in% "Q")
+  Q14<-sum(Column14 %in% "Q")
+  Q15<-sum(Column15 %in% "Q")
+  QllQs<-cbind(Q1,Q2,Q3,Q4,Q5,Q6,Q7,Q8,Q9,Q10,Q11,Q12,Q13,Q14,Q15)
+  
+  R1<-sum(Column1 %in% "R")
+  R2<-sum(Column2 %in% "R")
+  R3<-sum(Column3 %in% "R")
+  R4<-sum(Column4 %in% "R")
+  R5<-sum(Column5 %in% "R")
+  R6<-sum(Column6 %in% "R")
+  R7<-sum(Column7 %in% "R")
+  R8<-sum(Column8 %in% "R")
+  R9<-sum(Column9 %in% "R")
+  R10<-sum(Column10 %in% "R")
+  R11<-sum(Column11 %in% "R")
+  R12<-sum(Column12 %in% "R")
+  R13<-sum(Column13 %in% "R")
+  R14<-sum(Column14 %in% "R")
+  R15<-sum(Column15 %in% "R")
+  RllRs<-cbind(R1,R2,R3,R4,R5,R6,R7,R8,R9,R10,R11,R12,R13,R14,R15)
+  
+  S1<-sum(Column1 %in% "S")
+  S2<-sum(Column2 %in% "S")
+  S3<-sum(Column3 %in% "S")
+  S4<-sum(Column4 %in% "S")
+  S5<-sum(Column5 %in% "S")
+  S6<-sum(Column6 %in% "S")
+  S7<-sum(Column7 %in% "S")
+  S8<-sum(Column8 %in% "S")
+  S9<-sum(Column9 %in% "S")
+  S10<-sum(Column10 %in% "S")
+  S11<-sum(Column11 %in% "S")
+  S12<-sum(Column12 %in% "S")
+  S13<-sum(Column13 %in% "S")
+  S14<-sum(Column14 %in% "S")
+  S15<-sum(Column15 %in% "S")
+  SllSs<-cbind(S1,S2,S3,S4,S5,S6,S7,S8,S9,S10,S11,S12,S13,S14,S15)
+  
+  T1<-sum(Column1 %in% "T")
+  T2<-sum(Column2 %in% "T")
+  T3<-sum(Column3 %in% "T")
+  T4<-sum(Column4 %in% "T")
+  T5<-sum(Column5 %in% "T")
+  T6<-sum(Column6 %in% "T")
+  T7<-sum(Column7 %in% "T")
+  T8<-sum(Column8 %in% "T")
+  T9<-sum(Column9 %in% "T")
+  T10<-sum(Column10 %in% "T")
+  T11<-sum(Column11 %in% "T")
+  T12<-sum(Column12 %in% "T")
+  T13<-sum(Column13 %in% "T")
+  T14<-sum(Column14 %in% "T")
+  T15<-sum(Column15 %in% "T")
+  TllTs<-cbind(T1,T2,T3,T4,T5,T6,T7,T8,T9,T10,T11,T12,T13,T14,T15)
+  
+  V1<-sum(Column1 %in% "V")
+  V2<-sum(Column2 %in% "V")
+  V3<-sum(Column3 %in% "V")
+  V4<-sum(Column4 %in% "V")
+  V5<-sum(Column5 %in% "V")
+  V6<-sum(Column6 %in% "V")
+  V7<-sum(Column7 %in% "V")
+  V8<-sum(Column8 %in% "V")
+  V9<-sum(Column9 %in% "V")
+  V10<-sum(Column10 %in% "V")
+  V11<-sum(Column11 %in% "V")
+  V12<-sum(Column12 %in% "V")
+  V13<-sum(Column13 %in% "V")
+  V14<-sum(Column14 %in% "V")
+  V15<-sum(Column15 %in% "V")
+  VllVs<-cbind(V1,V2,V3,V4,V5,V6,V7,V8,V9,V10,V11,V12,V13,V14,V15)
+  
+  W1<-sum(Column1 %in% "W")
+  W2<-sum(Column2 %in% "W")
+  W3<-sum(Column3 %in% "W")
+  W4<-sum(Column4 %in% "W")
+  W5<-sum(Column5 %in% "W")
+  W6<-sum(Column6 %in% "W")
+  W7<-sum(Column7 %in% "W")
+  W8<-sum(Column8 %in% "W")
+  W9<-sum(Column9 %in% "W")
+  W10<-sum(Column10 %in% "W")
+  W11<-sum(Column11 %in% "W")
+  W12<-sum(Column12 %in% "W")
+  W13<-sum(Column13 %in% "W")
+  W14<-sum(Column14 %in% "W")
+  W15<-sum(Column15 %in% "W")
+  WllWs<-cbind(W1,W2,W3,W4,W5,W6,W7,W8,W9,W10,W11,W12,W13,W14,W15)
+  
+  Y1<-sum(Column1 %in% "Y")
+  Y2<-sum(Column2 %in% "Y")
+  Y3<-sum(Column3 %in% "Y")
+  Y4<-sum(Column4 %in% "Y")
+  Y5<-sum(Column5 %in% "Y")
+  Y6<-sum(Column6 %in% "Y")
+  Y7<-sum(Column7 %in% "Y")
+  Y8<-sum(Column8 %in% "Y")
+  Y9<-sum(Column9 %in% "Y")
+  Y10<-sum(Column10 %in% "Y")
+  Y11<-sum(Column11 %in% "Y")
+  Y12<-sum(Column12 %in% "Y")
+  Y13<-sum(Column13 %in% "Y")
+  Y14<-sum(Column14 %in% "Y")
+  Y15<-sum(Column15 %in% "Y")
+  YllYs<-cbind(Y1,Y2,Y3,Y4,Y5,Y6,Y7,Y8,Y9,Y10,Y11,Y12,Y13,Y14,Y15)
+  PositionTable<-rbind(AllAs,CllCs,DllDs,EllEs,FllFs,GllGs,HllHs,IllIs,KllKs,LllLs,MllMs,NllNs,PllPs,QllQs,RllRs,SllSs,TllTs,VllVs,WllWs,YllYs)
+}
+#endogenous prob matrix is AA position over subbackfreqmean
+dim(PositionTable)
+EPMtable<-PositionTable
+# EPMtable[1,]<-(PositionTable[1,]/(PositionTable[1,]*.01*Amean))
+# EPMtable[2,]<-(PositionTable[2,]/(PositionTable[2,]*.01*Cmean))
+# EPMtable[3,]<-(PositionTable[3,]/(PositionTable[3,]*.01*Dmean))
+# EPMtable[4,]<-(PositionTable[4,]/(PositionTable[4,]*.01*Emean))
+# EPMtable[5,]<-(PositionTable[5,]/(PositionTable[5,]*.01*Fmean))
+# EPMtable[6,]<-(PositionTable[6,]/(PositionTable[6,]*.01*Gmean))
+# EPMtable[7,]<-(PositionTable[7,]/(PositionTable[7,]*.01*Hmean))
+# EPMtable[8,]<-(PositionTable[8,]/(PositionTable[8,]*.01*Imean))
+# EPMtable[9,]<-(PositionTable[9,]/(PositionTable[9,]*.01*Kmean))
+# EPMtable[10,]<-(PositionTable[10,]/(PositionTable[10,]*.01*Lmean))
+# EPMtable[11,]<-(PositionTable[11,]/(PositionTable[11,]*.01*Mmean))
+# EPMtable[12,]<-(PositionTable[12,]/(PositionTable[12,]*.01*Nmean))
+# EPMtable[13,]<-(PositionTable[13,]/(PositionTable[13,]*.01*Pmean))
+# EPMtable[14,]<-(PositionTable[14,]/(PositionTable[14,]*.01*Qmean))
+# EPMtable[15,]<-(PositionTable[15,]/(PositionTable[15,]*.01*Rmean))
+# EPMtable[16,]<-(PositionTable[16,]/(PositionTable[16,]*.01*Smean))
+# EPMtable[17,]<-(PositionTable[17,]/(PositionTable[17,]*.01*Tmean))
+# EPMtable[18,]<-(PositionTable[18,]/(PositionTable[18,]*.01*Vmean))
+# EPMtable[19,]<-(PositionTable[19,]/(PositionTable[19,]*.01*Wmean))
+# EPMtable[20,]<-(PositionTable[20,]/(PositionTable[20,]*.01*Ymean))
+
+columns<-c(length(Column1)-sum(Column1==""),
+           length(Column2)-sum(Column2==""),
+           length(Column3)-sum(Column3==""),
+           length(Column4)-sum(Column4==""),
+           length(Column5)-sum(Column5==""),
+           length(Column6)-sum(Column6==""),
+           length(Column7)-sum(Column7==""),
+           length(Column8)-sum(Column8==""),
+           length(Column9)-sum(Column9==""),
+           length(Column10)-sum(Column10==""),
+           length(Column11)-sum(Column11==""),
+           length(Column12)-sum(Column12==""),
+           length(Column13)-sum(Column13==""),
+           length(Column14)-sum(Column14==""),
+           length(Column15)-sum(Column15==""))
+
+for (z in 1:15) {
+  for (y in 1:20) {
+    if (PositionTable[y,z]>0){
+      EPMtable[y,z]<-PositionTable[y,z]/((columns[z]*.01*AllMeans[y]))
+    }
+    if (PositionTable[y,z]==0){
+      EPMtable[y,z]<-(1/columns[z])/((columns[z]*.01*AllMeans[y]))
+    }
+  }
+}
+#here I created the endogenous probability matrix
+#now all I need to do is make the program automatically determine which SDs are >2, and then make it perform screener and sorter on those SDs
+
+
+
+
+
+# write.xlsx(SDtable,file=FILENAME, sheetName = "Standard Deviation Table",col.names = FALSE,row.names = FALSE,append = TRUE)
+# write.xlsx(PercentTable,file = FILENAME,sheetName = "Percent Table",col.names = FALSE,row.names = FALSE,append = TRUE)
+# write.xlsx(SelectivitySheet,file = FILENAME,sheetName = "Site Selectivity",col.names = FALSE,row.names = FALSE,append = TRUE)
+# write.xlsx(EPMtable,file=FILENAME,sheetName = "Endogenous Probability Matrix",col.names = FALSE,row.names = FALSE,append = TRUE)
+# write.xlsx(NormalizationScore,file = FILENAME,sheetName = "Normalization Score",col.names = FALSE,row.names = FALSE,append = TRUE)
+
+NormalizationScore<-c("Normalization Score",NormalizationScore)
+
+write.table(x=c("SD Table"),file=FILENAME,append = TRUE,sep=",", row.names = FALSE, col.names = FALSE)
+write.table(SDtable,file=FILENAME,append = TRUE,sep=",", row.names = FALSE, col.names = FALSE)
+write.table(x=c("Percent Table"),file=FILENAME,append = TRUE,sep=",", row.names = FALSE, col.names = FALSE)
+write.table(PercentTable,file=FILENAME, append = TRUE,sep=",",row.names = FALSE, col.names = FALSE)
+
+EPMtableu<-EPMtable
+HeaderSD<-c(-7:7)
+EPMtableu<-rbind(HeaderSD,EPMtableu)
+row.names(EPMtableu)<-NULL
+EPMtableu<-data.frame(SetOfAAs,EPMtableu)
+
+write.table("Site Selectivity Matrix", file = FILENAME2, append = TRUE, sep = ",", row.names = FALSE, col.names = FALSE)
+SelectivityHeader=matrix(data = c("Position",-7,-6,-5,-4,-3,-2,-1,0,1,2,3,4,5,6,7),nrow = 1)
+head<-matrix(data=rep(" ",times=16),nrow = 1)
+SelectivityHeader<-rbind(head,SelectivityHeader)
+
+write.table(SelectivityHeader, file = FILENAME2, append = TRUE, sep = ",", row.names = FALSE, col.names = FALSE)
+#colnames(SelectivitySheet)<-c("-7","-6","-5","-4","-3","-2","-1","0","1","2","3","4","5","6","7")
+write.table(SelectivitySheet,file = FILENAME2, append = TRUE,sep = ",",row.names = TRUE, col.names = FALSE)
+write.table(x=c("Endogenous Probability Matrix"),file=FILENAME2,append = TRUE,sep=",", row.names = FALSE, col.names = FALSE)
+write.table(EPMtableu,file = FILENAME2, append = TRUE,sep = ",",row.names = FALSE, col.names = FALSE)
+write.table(NormalizationScore, file = FILENAME2, append = TRUE,sep = ",",row.names = FALSE, col.names = FALSE)
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+#test myself: this script should take in  amino acids for each of the 9 positions and give out every single combination of those AAs
+
+#need to do following: fix it so that the accession numbers stay with the substrates,
+#also the neg false constant is totaly unphos'd Ys found by FASTA-2-CSV system# uniprot
+
+#HOW MANY: IF THERE'S two aas in each position you get 2^9, so I assume the numbers are:
+#(number in position-4)*(number in position -3)*(number in position -2)...=total
+# require(rJava)
+# require(xlsxjars)
+# require(xlsx)
+# # require(readxl)
+
+#View(SDtable)
+bareSDs<-SDtable[2:21,2:16]
+goodones<-bareSDs>2
+
+Positionm7<-which(goodones[,1] %in% TRUE)
+if (length(Positionm7)<1){Positionm7<-which(bareSDs[,1]==max(bareSDs[,1]))}
+Positionm6<-which(goodones[,2] %in% TRUE)
+if (length(Positionm6)<1){Positionm6<-which(bareSDs[,2]==max(bareSDs[,2]))}
+Positionm5<-which(goodones[,3] %in% TRUE)
+if (length(Positionm5)<1){Positionm5<-which(bareSDs[,3]==max(bareSDs[,3]))}
+Positionm4<-which(goodones[,4] %in% TRUE)
+if (length(Positionm4)<1){Positionm4<-which(bareSDs[,4]==max(bareSDs[,4]))}
+Positionm3<-which(goodones[,5] %in% TRUE)
+if (length(Positionm3)<1){Positionm3<-which(bareSDs[,5]==max(bareSDs[,5]))}
+Positionm2<-which(goodones[,6] %in% TRUE)
+if (length(Positionm2)<1){Positionm2<-which(bareSDs[,6]==max(bareSDs[,6]))}
+Positionm1<-which(goodones[,7] %in% TRUE)
+if (length(Positionm1)<1){Positionm1<-which(bareSDs[,7]==max(bareSDs[,7]))}
+
+Positiond0<-which(goodones[,8] %in% TRUE)
+if (length(Positiond0)<1){Positiond0<-which(bareSDs[,8]==max(bareSDs[,8]))}
+
+Positionp1<-which(goodones[,9] %in% TRUE)
+if (length(Positionp1)<1){Positionp1<-which(bareSDs[,9]==max(bareSDs[,9]))}
+Positionp2<-which(goodones[,10] %in% TRUE)
+if (length(Positionp2)<1){Positionp2<-which(bareSDs[,10]==max(bareSDs[,10]))}
+Positionp3<-which(goodones[,11] %in% TRUE)
+if (length(Positionp3)<1){Positionp3<-which(bareSDs[,11]==max(bareSDs[,11]))}
+Positionp4<-which(goodones[,12] %in% TRUE)
+if (length(Positionp4)<1){Positionp4<-which(bareSDs[,12]==max(bareSDs[,12]))}
+Positionp5<-which(goodones[,13] %in% TRUE)
+if (length(Positionp5)<1){Positionp5<-which(bareSDs[,13]==max(bareSDs[,13]))}
+Positionp6<-which(goodones[,14] %in% TRUE)
+if (length(Positionp6)<1){Positionp6<-which(bareSDs[,14]==max(bareSDs[,14]))}
+Positionp7<-which(goodones[,15] %in% TRUE)
+if (length(Positionp7)<1){Positionp7<-which(bareSDs[,15]==max(bareSDs[,15]))}
+
+aa_props2 <- c("1"="A", "2"="C", "3"="D", "4"="E", "5"="F", "6"="G", "7"="H", "8"="I", "9"="K", "10"="L", "11"="M", "12"="N",
+               "13"="P", "14"="Q", "15"="R", "16"="S", "17"="T", "18"="V", "19"="W", "20"="Y")
+
+Positionm7<-sapply(Positionm7, function (x) aa_props2[x])
+Positionm6<-sapply(Positionm6, function (x) aa_props2[x])
+Positionm5<-sapply(Positionm5, function (x) aa_props2[x])
+Positionm4<-sapply(Positionm4, function (x) aa_props2[x])
+Positionm3<-sapply(Positionm3, function (x) aa_props2[x])
+Positionm2<-sapply(Positionm2, function (x) aa_props2[x])
+Positionm1<-sapply(Positionm1, function (x) aa_props2[x])
+Positiond0<-sapply(Positiond0, function (x) aa_props2[x])
+Positionp1<-sapply(Positionp1, function (x) aa_props2[x])
+Positionp2<-sapply(Positionp2, function (x) aa_props2[x])
+Positionp3<-sapply(Positionp3, function (x) aa_props2[x])
+Positionp4<-sapply(Positionp4, function (x) aa_props2[x])
+Positionp5<-sapply(Positionp5, function (x) aa_props2[x])
+Positionp6<-sapply(Positionp6, function (x) aa_props2[x])
+Positionp7<-sapply(Positionp7, function (x) aa_props2[x])
+
+
+# Positionm7<-c("D","H","N","V")
+# Positionm6<-c("E","V")
+# Positionm5<-c("D","H")
+# Positionm4<-c("D","N")
+# Positionm3<-c("D","E","F","Q")
+# Positionm2<-c("D","N","Q","S")
+# Positionm1<-c("F","I","L")
+# Positiond0<-c("Y")
+# Positionp1<-c("A","E")
+# Positionp2<-c("T","S","Q","E")
+# Positionp3<-c("V")
+# Positionp4<-c("K")
+# Positionp5<-c("K")
+# Positionp6<-c("K")
+# Positionp7<-c("R")
+#this is where the amino acids for each position are given.  m means minus, p mean plus
+########################################
+# ScreenerFilename<-"C:/Users/User Name/Desktop/UMN 2017 Spring/Parker Lab/Kinatest ID/Screener.xls"
+
+
+
+
+
+
+
+
+
+
+
+screaner<-read.csv(ScreenerFilename, header = FALSE, stringsAsFactors = FALSE)
+
+
+Abl<-screaner[2:25,]
+Arg<-screaner[27:50,]
+Btk<-screaner[52:75,]
+Csk<-screaner[77:100,]
+Fyn<-screaner[102:125,]
+Hck<-screaner[127:150,]
+JAK2<-screaner[152:175,]
+Lck<-screaner[177:200,]
+Lyn<-screaner[202:225,]
+Pyk2<-screaner[227:250,]
+Src<-screaner[252:275,]
+Syk<-screaner[277:300,]
+Yes<-screaner[302:325,]
+
+#two questions: why are we doing BTK when we already have a bioninformatics page about it?
+#two I reran everything and only get 96 positions of interest in the SD table
+
+
+
+
+
+
+
+
+
+#Do_You_want_An_Excel_Output_Questionmark<-"NO"
+GeneratedPeptidesFile<-"GeneratedPeptidesFile.csv"
+
+
+# Abl<-read.xlsx("C:/Users/User Name/Desktop/UMN 2017 Spring/Parker Lab/Kinatest ID/Screener.xls", sheetIndex = 4)
+# Arg<-read.xlsx("C:/Users/User Name/Desktop/UMN 2017 Spring/Parker Lab/Kinatest ID/Screener.xls", sheetIndex = 5)
+# Btk<-read.xlsx("C:/Users/User Name/Desktop/UMN 2017 Spring/Parker Lab/Kinatest ID/Screener.xls", sheetIndex = 6)
+# Csk<-read.xlsx("C:/Users/User Name/Desktop/UMN 2017 Spring/Parker Lab/Kinatest ID/Screener.xls", sheetIndex = 7)
+# Fyn<-read.xlsx("C:/Users/User Name/Desktop/UMN 2017 Spring/Parker Lab/Kinatest ID/Screener.xls", sheetIndex = 8)
+# Hck<-read.xlsx("C:/Users/User Name/Desktop/UMN 2017 Spring/Parker Lab/Kinatest ID/Screener.xls", sheetIndex = 9)
+# JAK2<-read.xlsx("C:/Users/User Name/Desktop/UMN 2017 Spring/Parker Lab/Kinatest ID/Screener.xls", sheetIndex = 10)
+# Lck<-read.xlsx("C:/Users/User Name/Desktop/UMN 2017 Spring/Parker Lab/Kinatest ID/Screener.xls", sheetIndex = 11)
+# Lyn<-read.xlsx("C:/Users/User Name/Desktop/UMN 2017 Spring/Parker Lab/Kinatest ID/Screener.xls", sheetIndex = 12)
+# Pyk2<-read.xlsx("C:/Users/User Name/Desktop/UMN 2017 Spring/Parker Lab/Kinatest ID/Screener.xls", sheetIndex = 13)
+# Src<-read.xlsx("C:/Users/User Name/Desktop/UMN 2017 Spring/Parker Lab/Kinatest ID/Screener.xls", sheetIndex = 14)
+# Syk<-read.xlsx("C:/Users/User Name/Desktop/UMN 2017 Spring/Parker Lab/Kinatest ID/Screener.xls", sheetIndex = 15)
+# Yes<-read.xlsx("C:/Users/User Name/Desktop/UMN 2017 Spring/Parker Lab/Kinatest ID/Screener.xls", sheetIndex = 16)
+# 
+
+
+"A"=1
+"C"=2
+"D"=3
+"E"=4
+"F"=5
+"G"=6
+"H"=7
+"I"=8
+"K"=9
+"L"=10
+"M"=11
+"N"=12
+"P"=13
+"Q"=14
+"R"=15
+"S"=16
+"T"=17
+"V"=18
+"W"=19
+"Y"=20
+
+aa_props <- c("A"=A, "C"=C, "D"=D, "E"=E, "F"=F,"G"=G,"H"=H,"I"=I,"K"=K,"L"=L,"M"=M,"N"=N,"P"=P,"Q"=Q,"R"=R,
+              "S"=S,"T"=T,"V"=V,"W"=W,"Y"=Y,"xY"=Y,"O"=21)
+
+number15<-sapply(Positionm7, function (x) aa_props[x])
+number14<-sapply(Positionm6, function (x) aa_props[x])
+number13<-sapply(Positionm5, function (x) aa_props[x])
+number1 <- sapply(Positionm4, function (x) aa_props[x])
+number2 <- sapply(Positionm3, function (x) aa_props[x])
+number3 <- sapply(Positionm2, function (x) aa_props[x])
+number4 <- sapply(Positionm1, function (x) aa_props[x])
+number5 <- sapply(Positiond0, function (x) aa_props[x])
+number6 <- sapply(Positionp1, function (x) aa_props[x])
+number7 <- sapply(Positionp2, function (x) aa_props[x])
+number8 <- sapply(Positionp3, function (x) aa_props[x])
+number9 <- sapply(Positionp4, function (x) aa_props[x])
+number10<-sapply(Positionp5, function (x) aa_props[x])
+number11<-sapply(Positionp6, function (x) aa_props[x])
+number12<-sapply(Positionp7, function (x) aa_props[x])
+
+# number1<-Positionm4
+# number2<-Positionm3
+# number3<-Positionm2
+# number4<-Positionm1
+# number5<-Positiond0
+# number6<-Positionp1
+# number7<-Positionp2
+# number8<-Positionp3
+# number9<-Positionp4
+
+#############################
+#here I create the Abl seqs with proper value for each number
+if (1==0){
+  Ablnumber1<- gsub("A",A,Ablnumber1,perl = TRUE)
+  Ablnumber1<- gsub("C",C,Ablnumber1,perl = TRUE)
+  Ablnumber1<- gsub("D",D,Ablnumber1,perl = TRUE)
+  Ablnumber1<- gsub("E",E,Ablnumber1,perl = TRUE)
+  Ablnumber1<- gsub("F",F,Ablnumber1,perl = TRUE)
+  Ablnumber1<- gsub("G",G,Ablnumber1,perl = TRUE)
+  Ablnumber1<- gsub("H",H,Ablnumber1,perl = TRUE)
+  Ablnumber1<- gsub("I",I,Ablnumber1,perl = TRUE)
+  Ablnumber1<- gsub("K",K,Ablnumber1,perl = TRUE)
+  Ablnumber1<- gsub("L",L,Ablnumber1,perl = TRUE)
+  Ablnumber1<- gsub("M",M,Ablnumber1,perl = TRUE)
+  Ablnumber1<- gsub("N",N,Ablnumber1,perl = TRUE)
+  Ablnumber1<- gsub("P",P,Ablnumber1,perl = TRUE)
+  Ablnumber1<- gsub("Q",Q,Ablnumber1,perl = TRUE)
+  Ablnumber1<- gsub("R",R,Ablnumber1,perl = TRUE)
+  Ablnumber1<- gsub("S",S,Ablnumber1,perl = TRUE)
+  Ablnumber1<- gsub("T",T,Ablnumber1,perl = TRUE)
+  Ablnumber1<- gsub("V",V,Ablnumber1,perl = TRUE)
+  Ablnumber1<- gsub("W",W,Ablnumber1,perl = TRUE)
+  Ablnumber1<- gsub("Y",Y,Ablnumber1,perl = TRUE)
+  
+  Ablnumber2<- gsub("A",A,Ablnumber2,perl = TRUE)
+  Ablnumber2<- gsub("C",C,Ablnumber2,perl = TRUE)
+  Ablnumber2<- gsub("D",D,Ablnumber2,perl = TRUE)
+  Ablnumber2<- gsub("E",E,Ablnumber2,perl = TRUE)
+  Ablnumber2<- gsub("F",F,Ablnumber2,perl = TRUE)
+  Ablnumber2<- gsub("G",G,Ablnumber2,perl = TRUE)
+  Ablnumber2<- gsub("H",H,Ablnumber2,perl = TRUE)
+  Ablnumber2<- gsub("I",I,Ablnumber2,perl = TRUE)
+  Ablnumber2<- gsub("K",K,Ablnumber2,perl = TRUE)
+  Ablnumber2<- gsub("L",L,Ablnumber2,perl = TRUE)
+  Ablnumber2<- gsub("M",M,Ablnumber2,perl = TRUE)
+  Ablnumber2<- gsub("N",N,Ablnumber2,perl = TRUE)
+  Ablnumber2<- gsub("P",P,Ablnumber2,perl = TRUE)
+  Ablnumber2<- gsub("Q",Q,Ablnumber2,perl = TRUE)
+  Ablnumber2<- gsub("R",R,Ablnumber2,perl = TRUE)
+  Ablnumber2<- gsub("S",S,Ablnumber2,perl = TRUE)
+  Ablnumber2<- gsub("T",T,Ablnumber2,perl = TRUE)
+  Ablnumber2<- gsub("V",V,Ablnumber2,perl = TRUE)
+  Ablnumber2<- gsub("W",W,Ablnumber2,perl = TRUE)
+  Ablnumber2<- gsub("Y",Y,Ablnumber2,perl = TRUE)
+  
+  Ablnumber3<- gsub("A",A,Ablnumber3,perl = TRUE)
+  Ablnumber3<- gsub("C",C,Ablnumber3,perl = TRUE)
+  Ablnumber3<- gsub("D",D,Ablnumber3,perl = TRUE)
+  Ablnumber3<- gsub("E",E,Ablnumber3,perl = TRUE)
+  Ablnumber3<- gsub("F",F,Ablnumber3,perl = TRUE)
+  Ablnumber3<- gsub("G",G,Ablnumber3,perl = TRUE)
+  Ablnumber3<- gsub("H",H,Ablnumber3,perl = TRUE)
+  Ablnumber3<- gsub("I",I,Ablnumber3,perl = TRUE)
+  Ablnumber3<- gsub("K",K,Ablnumber3,perl = TRUE)
+  Ablnumber3<- gsub("L",L,Ablnumber3,perl = TRUE)
+  Ablnumber3<- gsub("M",M,Ablnumber3,perl = TRUE)
+  Ablnumber3<- gsub("N",N,Ablnumber3,perl = TRUE)
+  Ablnumber3<- gsub("P",P,Ablnumber3,perl = TRUE)
+  Ablnumber3<- gsub("Q",Q,Ablnumber3,perl = TRUE)
+  Ablnumber3<- gsub("R",R,Ablnumber3,perl = TRUE)
+  Ablnumber3<- gsub("S",S,Ablnumber3,perl = TRUE)
+  Ablnumber3<- gsub("T",T,Ablnumber3,perl = TRUE)
+  Ablnumber3<- gsub("V",V,Ablnumber3,perl = TRUE)
+  Ablnumber3<- gsub("W",W,Ablnumber3,perl = TRUE)
+  Ablnumber3<- gsub("Y",Y,Ablnumber3,perl = TRUE)
+  
+  Ablnumber4<- gsub("A",A,Ablnumber4,perl = TRUE)
+  Ablnumber4<- gsub("C",C,Ablnumber4,perl = TRUE)
+  Ablnumber4<- gsub("D",D,Ablnumber4,perl = TRUE)
+  Ablnumber4<- gsub("E",E,Ablnumber4,perl = TRUE)
+  Ablnumber4<- gsub("F",F,Ablnumber4,perl = TRUE)
+  Ablnumber4<- gsub("G",G,Ablnumber4,perl = TRUE)
+  Ablnumber4<- gsub("H",H,Ablnumber4,perl = TRUE)
+  Ablnumber4<- gsub("I",I,Ablnumber4,perl = TRUE)
+  Ablnumber4<- gsub("K",K,Ablnumber4,perl = TRUE)
+  Ablnumber4<- gsub("L",L,Ablnumber4,perl = TRUE)
+  Ablnumber4<- gsub("M",M,Ablnumber4,perl = TRUE)
+  Ablnumber4<- gsub("N",N,Ablnumber4,perl = TRUE)
+  Ablnumber4<- gsub("P",P,Ablnumber4,perl = TRUE)
+  Ablnumber4<- gsub("Q",Q,Ablnumber4,perl = TRUE)
+  Ablnumber4<- gsub("R",R,Ablnumber4,perl = TRUE)
+  Ablnumber4<- gsub("S",S,Ablnumber4,perl = TRUE)
+  Ablnumber4<- gsub("T",T,Ablnumber4,perl = TRUE)
+  Ablnumber4<- gsub("V",V,Ablnumber4,perl = TRUE)
+  Ablnumber4<- gsub("W",W,Ablnumber4,perl = TRUE)
+  Ablnumber4<- gsub("Y",Y,Ablnumber4,perl = TRUE)
+  
+  Ablnumber5<- gsub("A",A,Ablnumber5,perl = TRUE)
+  Ablnumber5<- gsub("C",C,Ablnumber5,perl = TRUE)
+  Ablnumber5<- gsub("D",D,Ablnumber5,perl = TRUE)
+  Ablnumber5<- gsub("E",E,Ablnumber5,perl = TRUE)
+  Ablnumber5<- gsub("F",F,Ablnumber5,perl = TRUE)
+  Ablnumber5<- gsub("G",G,Ablnumber5,perl = TRUE)
+  Ablnumber5<- gsub("H",H,Ablnumber5,perl = TRUE)
+  Ablnumber5<- gsub("I",I,Ablnumber5,perl = TRUE)
+  Ablnumber5<- gsub("K",K,Ablnumber5,perl = TRUE)
+  Ablnumber5<- gsub("L",L,Ablnumber5,perl = TRUE)
+  Ablnumber5<- gsub("M",M,Ablnumber5,perl = TRUE)
+  Ablnumber5<- gsub("N",N,Ablnumber5,perl = TRUE)
+  Ablnumber5<- gsub("P",P,Ablnumber5,perl = TRUE)
+  Ablnumber5<- gsub("Q",Q,Ablnumber5,perl = TRUE)
+  Ablnumber5<- gsub("R",R,Ablnumber5,perl = TRUE)
+  Ablnumber5<- gsub("S",S,Ablnumber5,perl = TRUE)
+  Ablnumber5<- gsub("T",T,Ablnumber5,perl = TRUE)
+  Ablnumber5<- gsub("V",V,Ablnumber5,perl = TRUE)
+  Ablnumber5<- gsub("W",W,Ablnumber5,perl = TRUE)
+  Ablnumber5<- gsub("Y",Y,Ablnumber5,perl = TRUE)
+  
+  Ablnumber6<- gsub("A",A,Ablnumber6,perl = TRUE)
+  Ablnumber6<- gsub("C",C,Ablnumber6,perl = TRUE)
+  Ablnumber6<- gsub("D",D,Ablnumber6,perl = TRUE)
+  Ablnumber6<- gsub("E",E,Ablnumber6,perl = TRUE)
+  Ablnumber6<- gsub("F",F,Ablnumber6,perl = TRUE)
+  Ablnumber6<- gsub("G",G,Ablnumber6,perl = TRUE)
+  Ablnumber6<- gsub("H",H,Ablnumber6,perl = TRUE)
+  Ablnumber6<- gsub("I",I,Ablnumber6,perl = TRUE)
+  Ablnumber6<- gsub("K",K,Ablnumber6,perl = TRUE)
+  Ablnumber6<- gsub("L",L,Ablnumber6,perl = TRUE)
+  Ablnumber6<- gsub("M",M,Ablnumber6,perl = TRUE)
+  Ablnumber6<- gsub("N",N,Ablnumber6,perl = TRUE)
+  Ablnumber6<- gsub("P",P,Ablnumber6,perl = TRUE)
+  Ablnumber6<- gsub("Q",Q,Ablnumber6,perl = TRUE)
+  Ablnumber6<- gsub("R",R,Ablnumber6,perl = TRUE)
+  Ablnumber6<- gsub("S",S,Ablnumber6,perl = TRUE)
+  Ablnumber6<- gsub("T",T,Ablnumber6,perl = TRUE)
+  Ablnumber6<- gsub("V",V,Ablnumber6,perl = TRUE)
+  Ablnumber6<- gsub("W",W,Ablnumber6,perl = TRUE)
+  Ablnumber6<- gsub("Y",Y,Ablnumber6,perl = TRUE)
+  
+  Ablnumber7<- gsub("A",A,Ablnumber7,perl = TRUE)
+  Ablnumber7<- gsub("C",C,Ablnumber7,perl = TRUE)
+  Ablnumber7<- gsub("D",D,Ablnumber7,perl = TRUE)
+  Ablnumber7<- gsub("E",E,Ablnumber7,perl = TRUE)
+  Ablnumber7<- gsub("F",F,Ablnumber7,perl = TRUE)
+  Ablnumber7<- gsub("G",G,Ablnumber7,perl = TRUE)
+  Ablnumber7<- gsub("H",H,Ablnumber7,perl = TRUE)
+  Ablnumber7<- gsub("I",I,Ablnumber7,perl = TRUE)
+  Ablnumber7<- gsub("K",K,Ablnumber7,perl = TRUE)
+  Ablnumber7<- gsub("L",L,Ablnumber7,perl = TRUE)
+  Ablnumber7<- gsub("M",M,Ablnumber7,perl = TRUE)
+  Ablnumber7<- gsub("N",N,Ablnumber7,perl = TRUE)
+  Ablnumber7<- gsub("P",P,Ablnumber7,perl = TRUE)
+  Ablnumber7<- gsub("Q",Q,Ablnumber7,perl = TRUE)
+  Ablnumber7<- gsub("R",R,Ablnumber7,perl = TRUE)
+  Ablnumber7<- gsub("S",S,Ablnumber7,perl = TRUE)
+  Ablnumber7<- gsub("T",T,Ablnumber7,perl = TRUE)
+  Ablnumber7<- gsub("V",V,Ablnumber7,perl = TRUE)
+  Ablnumber7<- gsub("W",W,Ablnumber7,perl = TRUE)
+  Ablnumber7<- gsub("Y",Y,Ablnumber7,perl = TRUE)
+  
+  Ablnumber8<- gsub("A",A,Ablnumber8,perl = TRUE)
+  Ablnumber8<- gsub("C",C,Ablnumber8,perl = TRUE)
+  Ablnumber8<- gsub("D",D,Ablnumber8,perl = TRUE)
+  Ablnumber8<- gsub("E",E,Ablnumber8,perl = TRUE)
+  Ablnumber8<- gsub("F",F,Ablnumber8,perl = TRUE)
+  Ablnumber8<- gsub("G",G,Ablnumber8,perl = TRUE)
+  Ablnumber8<- gsub("H",H,Ablnumber8,perl = TRUE)
+  Ablnumber8<- gsub("I",I,Ablnumber8,perl = TRUE)
+  Ablnumber8<- gsub("K",K,Ablnumber8,perl = TRUE)
+  Ablnumber8<- gsub("L",L,Ablnumber8,perl = TRUE)
+  Ablnumber8<- gsub("M",M,Ablnumber8,perl = TRUE)
+  Ablnumber8<- gsub("N",N,Ablnumber8,perl = TRUE)
+  Ablnumber8<- gsub("P",P,Ablnumber8,perl = TRUE)
+  Ablnumber8<- gsub("Q",Q,Ablnumber8,perl = TRUE)
+  Ablnumber8<- gsub("R",R,Ablnumber8,perl = TRUE)
+  Ablnumber8<- gsub("S",S,Ablnumber8,perl = TRUE)
+  Ablnumber8<- gsub("T",T,Ablnumber8,perl = TRUE)
+  Ablnumber8<- gsub("V",V,Ablnumber8,perl = TRUE)
+  Ablnumber8<- gsub("W",W,Ablnumber8,perl = TRUE)
+  Ablnumber8<- gsub("Y",Y,Ablnumber8,perl = TRUE)
+  
+  Ablnumber9<- gsub("A",A,Ablnumber9,perl = TRUE)
+  Ablnumber9<- gsub("C",C,Ablnumber9,perl = TRUE)
+  Ablnumber9<- gsub("D",D,Ablnumber9,perl = TRUE)
+  Ablnumber9<- gsub("E",E,Ablnumber9,perl = TRUE)
+  Ablnumber9<- gsub("F",F,Ablnumber9,perl = TRUE)
+  Ablnumber9<- gsub("G",G,Ablnumber9,perl = TRUE)
+  Ablnumber9<- gsub("H",H,Ablnumber9,perl = TRUE)
+  Ablnumber9<- gsub("I",I,Ablnumber9,perl = TRUE)
+  Ablnumber9<- gsub("K",K,Ablnumber9,perl = TRUE)
+  Ablnumber9<- gsub("L",L,Ablnumber9,perl = TRUE)
+  Ablnumber9<- gsub("M",M,Ablnumber9,perl = TRUE)
+  Ablnumber9<- gsub("N",N,Ablnumber9,perl = TRUE)
+  Ablnumber9<- gsub("P",P,Ablnumber9,perl = TRUE)
+  Ablnumber9<- gsub("Q",Q,Ablnumber9,perl = TRUE)
+  Ablnumber9<- gsub("R",R,Ablnumber9,perl = TRUE)
+  Ablnumber9<- gsub("S",S,Ablnumber9,perl = TRUE)
+  Ablnumber9<- gsub("T",T,Ablnumber9,perl = TRUE)
+  Ablnumber9<- gsub("V",V,Ablnumber9,perl = TRUE)
+  Ablnumber9<- gsub("W",W,Ablnumber9,perl = TRUE)
+  Ablnumber9<- gsub("Y",Y,Ablnumber9,perl = TRUE)
+}
+########################################
+
+
+total=length(Positionp7)*length(Positionp6)*length(Positionp5)*length(Positionp4)*length(Positionp3)*(length(Positionp2))*length(Positionp1)*
+  length(Positiond0)*length(Positionm1)*length(Positionm2)*length(Positionm3)*length(Positionm4)*length(Positionm5)*length(Positionm6)*length(Positionm7)
+#this is just a way to doublecheck that the length of the generated peptides vector is correct
+
+GeneratedPeptides<-rep(NA, times=total*15)
+GeneratedPeptides<-matrix(data = GeneratedPeptides,ncol = 15)
+
+NumeratedPeptides<-GeneratedPeptides
+#create an empty vector of correct length by finding the number of each AAs per position and multiplying them
+count<-0
+for (t in 1:length(Positionm7)) {
+  for (s in 1:length(Positionm6)) {
+    for (r in 1:length(Positionm5)) {
+      for (i in 1:length(Positionm4)) {
+        for (j in 1:length(Positionm3)) {
+          for (k in 1:length(Positionm2)) {
+            for (l in 1:length(Positionm1)) {
+              for (m in 1:length(Positiond0)) {
+                for (n in 1:length(Positionp1)) {
+                  for (o in 1:length(Positionp2)) {
+                    for (p in 1:length(Positionp3)) {
+                      for (q in 1:length(Positionp4)) {
+                        for (u in 1:length(Positionp5)) {
+                          for (v in 1:length(Positionp6)) {
+                            for (w in 1:length(Positionp7)) {
+                              # i=1
+                              # j=1
+                              # k=1
+                              # l=1
+                              # m=1
+                              # n=1
+                              # o=1
+                              # p=1
+                              # q=1
+                              # 
+                              #for every single position, increment the count number, create a peptide using the AAs at that position
+                              #then put them together into the generated peptides sequencex
+                              count<-count+1
+                              tabulation<-c(Positionm7[t],Positionm6[s],Positionm5[r],Positionm4[i],Positionm3[j],Positionm2[k],Positionm1[l],Positiond0[m],Positionp1[n],
+                                            Positionp2[o],Positionp3[p],Positionp4[q],Positionp5[u],Positionp6[v],Positionp7[w])
+                              numeration<-c(number15[t],number14[s],number13[r],number1[i],number2[j],number3[k],number4[l],number5[m],number6[n],number7[o],number8[p],number9[q],number10[u],number11[v],
+                                            number12[w])
+                              #tabulation<-paste(tabulation, sep="", collapse="")
+                              GeneratedPeptides[count,1:15]<-tabulation
+                              NumeratedPeptides[count,1:15]<-numeration
+                            }
+                          }
+                        }
+                      }
+                    }
+                  }
+                }
+              }
+            }
+          }
+        }
+      }
+    }
+  }
+}
+####################################################################
+#now here I use the Endogenous Probabilty matrix from the previous script, which is called EMPtable
+#to score the created peptides
+ThisKinTable<-EPMtableu#[1:nrow(SDtable),]
+TKTcolumn<-c(data=rep(1,times=21))
+TKTcolumn<-as.matrix(TKTcolumn,ncol=1)
+ThisKinTable<-cbind(TKTcolumn,ThisKinTable)
+
+ThisKinGeneratedScores<-rep(NA,times=nrow(GeneratedPeptides))
+ThisKinGenWeirdScore<-rep(NA,times=nrow(GeneratedPeptides))
+
+for (x in 1:nrow(GeneratedPeptides)){
+  Scoringpeptide<-NumeratedPeptides[x,1:15]
+  Scoringpeptide<-Scoringpeptide+1
+  ThisKinTableScore<-as.numeric(ThisKinTable[Scoringpeptide[1],3])*ThisKinTable[as.numeric(Scoringpeptide[2]),4]*ThisKinTable[as.numeric(Scoringpeptide[3]),5]*
+    ThisKinTable[as.numeric(Scoringpeptide[4]),6]*ThisKinTable[as.numeric(Scoringpeptide[5]),7]*ThisKinTable[as.numeric(Scoringpeptide[6]),8]*ThisKinTable[as.numeric(Scoringpeptide[7]),9]*
+    #ThisKinTable[as.numeric(Scoringpeptide[8]),10]*
+    ThisKinTable[as.numeric(Scoringpeptide[9]),11]*ThisKinTable[as.numeric(Scoringpeptide[10]),12]*ThisKinTable[as.numeric(Scoringpeptide[11]),13]*
+    ThisKinTable[as.numeric(Scoringpeptide[12]),14]*ThisKinTable[as.numeric(Scoringpeptide[13]),15]*ThisKinTable[as.numeric(Scoringpeptide[14]),16]*ThisKinTable[as.numeric(Scoringpeptide[15]),17]
+  ThisKinGeneratedScores[x]<-ThisKinTableScore
+  ThisKinTableScore<-(ThisKinTableScore/(ThisKinTableScore+1/as.numeric(NormalizationScore[2])))
+  ThisKinGenWeirdScore[x]<-ThisKinTableScore
+}
+
+AblGeneratedScores<-rep(NA,times=nrow(GeneratedPeptides))
+ArgGeneratedScores<-rep(NA,times=nrow(GeneratedPeptides))
+BtkGeneratedScores<-rep(NA,times=nrow(GeneratedPeptides))
+CskGeneratedScores<-rep(NA,times=nrow(GeneratedPeptides))
+FynGeneratedScores<-rep(NA,times=nrow(GeneratedPeptides))
+HckGeneratedScores<-rep(NA,times=nrow(GeneratedPeptides))
+JAK2GeneratedScores<-rep(NA,times=nrow(GeneratedPeptides))
+LckGeneratedScores<-rep(NA,times=nrow(GeneratedPeptides))
+LynGeneratedScores<-rep(NA,times=nrow(GeneratedPeptides))
+Pyk2GeneratedScores<-rep(NA,times=nrow(GeneratedPeptides))
+SrcGeneratedScores<-rep(NA,times=nrow(GeneratedPeptides))
+SykGeneratedScores<-rep(NA,times=nrow(GeneratedPeptides))
+YesGeneratedScores<-rep(NA,times=nrow(GeneratedPeptides))
+
+
+for (x in 1:nrow(GeneratedPeptides)){
+  Scoringpeptide<-NumeratedPeptides[x,1:15]
+  AblScore<-Abl[Scoringpeptide[1],2]*Abl[Scoringpeptide[2],3]*Abl[Scoringpeptide[3],4]*Abl[Scoringpeptide[4],5]*Abl[Scoringpeptide[5],6]*Abl[Scoringpeptide[6],7]*
+    Abl[Scoringpeptide[7],8]*Abl[Scoringpeptide[9],10]*Abl[Scoringpeptide[10],11]*Abl[Scoringpeptide[11],12]*Abl[Scoringpeptide[12],13]*
+    Abl[Scoringpeptide[13],14]*Abl[Scoringpeptide[14],15]*Abl[Scoringpeptide[15],16]
+  AblGeneratedScores[x]<-AblScore
+  
+  ArgScore<-Arg[Scoringpeptide[1],2]*Arg[Scoringpeptide[2],3]*Arg[Scoringpeptide[3],4]*Arg[Scoringpeptide[4],5]*Arg[Scoringpeptide[5],6]*Arg[Scoringpeptide[6],7]*
+    Arg[Scoringpeptide[7],8]*Arg[Scoringpeptide[9],10]*Arg[Scoringpeptide[10],11]*Arg[Scoringpeptide[11],12]*Arg[Scoringpeptide[12],13]*
+    Arg[Scoringpeptide[13],14]*Arg[Scoringpeptide[14],15]*Arg[Scoringpeptide[15],16]
+  ArgGeneratedScores[x]<-ArgScore
+  
+  BtkScore<-Btk[Scoringpeptide[1],2]*Btk[Scoringpeptide[2],3]*Btk[Scoringpeptide[3],4]*Btk[Scoringpeptide[4],5]*Btk[Scoringpeptide[5],6]*Btk[Scoringpeptide[6],7]*
+    Btk[Scoringpeptide[7],8]*Btk[Scoringpeptide[9],10]*Btk[Scoringpeptide[10],11]*Btk[Scoringpeptide[11],12]*Btk[Scoringpeptide[12],13]*
+    Btk[Scoringpeptide[13],14]*Btk[Scoringpeptide[14],15]*Btk[Scoringpeptide[15],16]
+  BtkGeneratedScores[x]<-BtkScore
+  
+  CskScore<-Csk[Scoringpeptide[1],2]*Csk[Scoringpeptide[2],3]*Csk[Scoringpeptide[3],4]*Csk[Scoringpeptide[4],5]*Csk[Scoringpeptide[5],6]*Csk[Scoringpeptide[6],7]*
+    Csk[Scoringpeptide[7],8]*Csk[Scoringpeptide[9],10]*Csk[Scoringpeptide[10],11]*Csk[Scoringpeptide[11],12]*Csk[Scoringpeptide[12],13]*
+    Csk[Scoringpeptide[13],14]*Csk[Scoringpeptide[14],15]*Csk[Scoringpeptide[15],16]
+  CskGeneratedScores[x]<-CskScore
+  
+  FynScore<-Fyn[Scoringpeptide[1],2]*Fyn[Scoringpeptide[2],3]*Fyn[Scoringpeptide[3],4]*Fyn[Scoringpeptide[4],5]*Fyn[Scoringpeptide[5],6]*Fyn[Scoringpeptide[6],7]*
+    Fyn[Scoringpeptide[7],8]*Fyn[Scoringpeptide[9],10]*Fyn[Scoringpeptide[10],11]*Fyn[Scoringpeptide[11],12]*Fyn[Scoringpeptide[12],13]*
+    Fyn[Scoringpeptide[13],14]*Fyn[Scoringpeptide[14],15]*Fyn[Scoringpeptide[15],16]
+  FynGeneratedScores[x]<-FynScore
+  
+  HckScore<-Hck[Scoringpeptide[1],2]*Hck[Scoringpeptide[2],3]*Hck[Scoringpeptide[3],4]*Hck[Scoringpeptide[4],5]*Hck[Scoringpeptide[5],6]*Hck[Scoringpeptide[6],7]*
+    Hck[Scoringpeptide[7],8]*Hck[Scoringpeptide[9],10]*Hck[Scoringpeptide[10],11]*Hck[Scoringpeptide[11],12]*Hck[Scoringpeptide[12],13]*
+    Hck[Scoringpeptide[13],14]*Hck[Scoringpeptide[14],15]*Hck[Scoringpeptide[15],16]
+  HckGeneratedScores[x]<-HckScore
+  
+  JAK2Score<-JAK2[Scoringpeptide[1],2]*JAK2[Scoringpeptide[2],3]*JAK2[Scoringpeptide[3],4]*JAK2[Scoringpeptide[4],5]*JAK2[Scoringpeptide[5],6]*JAK2[Scoringpeptide[6],7]*
+    JAK2[Scoringpeptide[7],8]*JAK2[Scoringpeptide[9],10]*JAK2[Scoringpeptide[10],11]*JAK2[Scoringpeptide[11],12]*JAK2[Scoringpeptide[12],13]*
+    JAK2[Scoringpeptide[13],14]*JAK2[Scoringpeptide[14],15]*JAK2[Scoringpeptide[15],16]
+  JAK2GeneratedScores[x]<-JAK2Score
+  
+  LckScore<-Lck[Scoringpeptide[1],2]*Lck[Scoringpeptide[2],3]*Lck[Scoringpeptide[3],4]*Lck[Scoringpeptide[4],5]*Lck[Scoringpeptide[5],6]*Lck[Scoringpeptide[6],7]*
+    Lck[Scoringpeptide[7],8]*Lck[Scoringpeptide[9],10]*Lck[Scoringpeptide[10],11]*Lck[Scoringpeptide[11],12]*Lck[Scoringpeptide[12],13]*
+    Lck[Scoringpeptide[13],14]*Lck[Scoringpeptide[14],15]*Lck[Scoringpeptide[15],16]
+  LckGeneratedScores[x]<-LckScore
+  
+  LynScore<-Lyn[Scoringpeptide[1],2]*Lyn[Scoringpeptide[2],3]*Lyn[Scoringpeptide[3],4]*Lyn[Scoringpeptide[4],5]*Lyn[Scoringpeptide[5],6]*Lyn[Scoringpeptide[6],7]*
+    Lyn[Scoringpeptide[7],8]*Lyn[Scoringpeptide[9],10]*Lyn[Scoringpeptide[10],11]*Lyn[Scoringpeptide[11],12]*Lyn[Scoringpeptide[12],13]*
+    Lyn[Scoringpeptide[13],14]*Lyn[Scoringpeptide[14],15]*Lyn[Scoringpeptide[15],16]
+  LynGeneratedScores[x]<-LynScore
+  
+  Pyk2Score<-Pyk2[Scoringpeptide[1],2]*Pyk2[Scoringpeptide[2],3]*Pyk2[Scoringpeptide[3],4]*Pyk2[Scoringpeptide[4],5]*Pyk2[Scoringpeptide[5],6]*Pyk2[Scoringpeptide[6],7]*
+    Pyk2[Scoringpeptide[7],8]*Pyk2[Scoringpeptide[9],10]*Pyk2[Scoringpeptide[10],11]*Pyk2[Scoringpeptide[11],12]*Pyk2[Scoringpeptide[12],13]*
+    Pyk2[Scoringpeptide[13],14]*Pyk2[Scoringpeptide[14],15]*Pyk2[Scoringpeptide[15],16]
+  Pyk2GeneratedScores[x]<-Pyk2Score
+  
+  SrcScore<-Src[Scoringpeptide[1],2]*Src[Scoringpeptide[2],3]*Src[Scoringpeptide[3],4]*Src[Scoringpeptide[4],5]*Src[Scoringpeptide[5],6]*Src[Scoringpeptide[6],7]*
+    Src[Scoringpeptide[7],8]*Src[Scoringpeptide[9],10]*Src[Scoringpeptide[10],11]*Src[Scoringpeptide[11],12]*Src[Scoringpeptide[12],13]*
+    Src[Scoringpeptide[13],14]*Src[Scoringpeptide[14],15]*Src[Scoringpeptide[15],16]
+  SrcGeneratedScores[x]<-SrcScore
+  
+  SykScore<-Syk[Scoringpeptide[1],2]*Syk[Scoringpeptide[2],3]*Syk[Scoringpeptide[3],4]*Syk[Scoringpeptide[4],5]*Syk[Scoringpeptide[5],6]*Syk[Scoringpeptide[6],7]*
+    Syk[Scoringpeptide[7],8]*Syk[Scoringpeptide[9],10]*Syk[Scoringpeptide[10],11]*Syk[Scoringpeptide[11],12]*Syk[Scoringpeptide[12],13]*
+    Syk[Scoringpeptide[13],14]*Syk[Scoringpeptide[14],15]*Syk[Scoringpeptide[15],16]
+  SykGeneratedScores[x]<-SykScore
+  
+  YesScore<-Yes[Scoringpeptide[1],2]*Yes[Scoringpeptide[2],3]*Yes[Scoringpeptide[3],4]*Yes[Scoringpeptide[4],5]*Yes[Scoringpeptide[5],6]*Yes[Scoringpeptide[6],7]*
+    Yes[Scoringpeptide[7],8]*Yes[Scoringpeptide[9],10]*Yes[Scoringpeptide[10],11]*Yes[Scoringpeptide[11],12]*Yes[Scoringpeptide[12],13]*
+    Yes[Scoringpeptide[13],14]*Yes[Scoringpeptide[14],15]*Yes[Scoringpeptide[15],16]
+  YesGeneratedScores[x]<-YesScore
+  
+  # ThisKinTableScore<-ThisKinTable[as.numeric(Scoringpeptide[1]),3]*ThisKinTable[as.numeric(Scoringpeptide[2]),4]*ThisKinTable[as.numeric(Scoringpeptide[3]),5]*
+  #   ThisKinTable[as.numeric(Scoringpeptide[4]),6]*ThisKinTable[as.numeric(Scoringpeptide[6]),8]*
+  #   ThisKinTable[as.numeric(Scoringpeptide[7]),9]*ThisKinTable[as.numeric(Scoringpeptide[8]),10]*ThisKinTable[as.numeric(Scoringpeptide[9]),11]
+  # ThisKinGeneratedScores[x]<-ThisKinTableScore
+}
+
+
+
+AblNorm<-1/as.numeric(Abl[22,1])
+AblThresh<-as.numeric(Abl[24,1])
+AblTrueThresh<-((AblThresh*AblNorm)/(100-AblThresh))
+AblActive<-unlist(AblGeneratedScores)>AblTrueThresh
+
+ArgNorm<-1/as.numeric(Arg[22,1])
+ArgThresh<-as.numeric(Arg[24,1])
+ArgTrueThresh<-((ArgThresh*ArgNorm)/(100-ArgThresh))
+ArgActive<-unlist(ArgGeneratedScores)>ArgTrueThresh
+
+BtkNorm<-1/as.numeric(Btk[22,1])
+BtkThresh<-as.numeric(Btk[24,1])
+BtkTrueThresh<-((BtkThresh*BtkNorm)/(100-BtkThresh))
+BtkActive<-unlist(BtkGeneratedScores)>BtkTrueThresh
+
+CskNorm<-1/as.numeric(Csk[22,1])
+CskThresh<-as.numeric(Csk[24,1])
+CskTrueThresh<-((CskThresh*CskNorm)/(100-CskThresh))
+CskActive<-(CskGeneratedScores)>CskTrueThresh
+
+FynNorm<-1/as.numeric(Fyn[22,1])
+FynThresh<-as.numeric(Fyn[24,1])
+FynTrueThresh<-((FynThresh*FynNorm)/(100-FynThresh))
+FynActive<-unlist(FynGeneratedScores)>FynTrueThresh
+
+HckNorm<-1/as.numeric(Hck[22,1])
+HckThresh<-as.numeric(Hck[24,1])
+HckTrueThresh<-((HckThresh*HckNorm)/(100-HckThresh))
+HckActive<-unlist(HckGeneratedScores)>HckTrueThresh
+
+JAK2Norm<-1/as.numeric(JAK2[22,1])
+JAK2Thresh<-as.numeric(JAK2[24,1])
+JAK2TrueThresh<-((JAK2Thresh*JAK2Norm)/(100-JAK2Thresh))
+JAk2Active<-unlist(JAK2GeneratedScores)>JAK2TrueThresh
+
+LckNorm<-1/as.numeric(Lck[22,1])
+LckThresh<-as.numeric(Lck[24,1])
+LckTrueThresh<-((LckThresh*LckNorm)/(100-LckThresh))
+LckActive<-unlist(LckGeneratedScores)>LckTrueThresh
+
+LynNorm<-1/as.numeric(Lyn[22,1])
+LynThresh<-as.numeric(Lyn[24,1])
+LynTrueThresh<-((LynThresh*LynNorm)/(100-LynThresh))
+LynActive<-unlist(LynGeneratedScores)>LynTrueThresh
+
+Pyk2Norm<-1/as.numeric(Pyk2[22,1])
+Pyk2Thresh<-as.numeric(Pyk2[24,1])
+Pyk2TrueThresh<-((Pyk2Thresh*Pyk2Norm)/(100-Pyk2Thresh))
+Pyk2Active<-unlist(Pyk2GeneratedScores)>Pyk2TrueThresh
+
+SrcNorm<-1/as.numeric(Src[22,1])
+SrcThresh<-as.numeric(Src[24,1])
+SrcTrueThresh<-((SrcThresh*SrcNorm)/(100-SrcThresh))
+SrcActive<-unlist(SrcGeneratedScores)>SrcTrueThresh
+
+SykNorm<-1/as.numeric(Syk[22,1])
+SykThresh<-as.numeric(Syk[24,1])
+SykTrueThresh<-((SykThresh*SykNorm)/(100-SykThresh))
+SykActive<-unlist(SykGeneratedScores)>SykTrueThresh
+
+YesNorm<-1/as.numeric(Yes[22,1])
+YesThresh<-as.numeric(Yes[24,1])
+YesTrueThresh<-((YesThresh*YesNorm)/(100-YesThresh))
+YesActive<-unlist(YesGeneratedScores)>YesTrueThresh
+
+AllActive<-AblActive+ArgActive+BtkActive+CskActive+FynActive+HckActive+JAk2Active+LckActive+LynActive+Pyk2Active+SrcActive+SykActive+YesActive
+#Btkactive+
+
+Scores<-ThisKinGeneratedScores
+ThresholdValues<-ThisKinGenWeirdScore
+
+FullMotifs<-rep("Z",times=nrow(GeneratedPeptides))
+for (i in 1:nrow(GeneratedPeptides)) {
+  motif<-GeneratedPeptides[i,1:15]
+  motif<-paste(motif,sep = "", collapse = "")
+  FullMotifs[i]<-motif
+}
+
+PeptidesWithRanks<-cbind.data.frame(FullMotifs,GeneratedPeptides,Scores,ThresholdValues)
+PeptidesWithRanks<-cbind.data.frame(PeptidesWithRanks,AllActive,AblActive,ArgActive,BtkActive,CskActive,FynActive,HckActive,JAk2Active,LckActive,LynActive,Pyk2Active,SrcActive,SykActive,YesActive)
+RanksPeptides<-PeptidesWithRanks[order(PeptidesWithRanks$AllActive,decreasing = FALSE),]
+# PepRankHead<-c(1:9,"Sequence","RPMS","PMS")
+# RanksPeptides<-rbind.data.frame(PepRankHead,PeptidesWithRanks)
+#head(RanksPeptides)
+
+
+#now I have to score the negative sequences... for some reason
+#write up how we transfect with lipofectamine
+#3,4,5 questions
+
+#PAUSED EHRE AT 4:50, HOPING THAT FIXING MINERVOTHING SO THAT LEFT SPACES WORKS FIXES A THING.  OTHERWISE
+#I FUCKED WITH THE MCC TABLE AND NEED TO FINISH IT 
+
+ThisKinBlanks<-rep(1,times=17)
+#indx <- sapply(breast, is.factor)
+#ThisKinTable[indx] <- lapply(ThisKinTable[indx], function(x) as.character(x))
+ThisKinTable$SetOfAAs<-as.character(ThisKinTable$SetOfAAs)
+
+#ThisKinTest<-rbind.data.frame(ThisKinTable,ThisKinBlanks)
+ThisKinTable<-rbind.data.frame(ThisKinTable,ThisKinBlanks)
+
+NegativeScores<-rep(NA,times=nrow(NegativeSubstrateList))
+NegativeWeirdScores<-rep(NA,times=nrow(NegativeSubstrateList))
+for (v in 1:nrow(NegativeSubstrateList)) {
+  motif<-NegativeSubstrateList[v,2]
+  motif<-unlist(strsplit(motif,""))
+  #if (length(motif)<9){print(v)}}
+  # motif[1] <- sapply(motif[1], function (x) aa_props[x])
+  # motif[2] <- sapply(motif[2], function (x) aa_props[x])
+  # motif[3] <- sapply(motif[3], function (x) aa_props[x])
+  # motif[4] <- sapply(motif[4], function (x) aa_props[x])
+  # motif[5] <- sapply(motif[5], function (x) aa_props[x])
+  # motif[6] <- sapply(motif[6], function (x) aa_props[x])
+  # motif[7] <- sapply(motif[7], function (x) aa_props[x])
+  # motif[8] <- sapply(motif[8], function (x) aa_props[x])
+  # motif[9] <- sapply(motif[9], function (x) aa_props[x])
+  motif<- gsub(" ","O",motif)  
+  motif <- sapply(motif, function (x) aa_props[x])
+  Scoringpeptide<-motif
+  Scoringpeptide<-Scoringpeptide+1
+  ThisKinTableScore<-as.numeric(ThisKinTable[Scoringpeptide[1],3])*ThisKinTable[as.numeric(Scoringpeptide[2]),4]*ThisKinTable[as.numeric(Scoringpeptide[3]),5]*
+    ThisKinTable[as.numeric(Scoringpeptide[4]),6]*ThisKinTable[as.numeric(Scoringpeptide[5]),7]*ThisKinTable[as.numeric(Scoringpeptide[6]),8]*ThisKinTable[as.numeric(Scoringpeptide[7]),9]*
+    #ThisKinTable[as.numeric(Scoringpeptide[8]),10]*
+    ThisKinTable[as.numeric(Scoringpeptide[9]),11]*ThisKinTable[as.numeric(Scoringpeptide[10]),12]*ThisKinTable[as.numeric(Scoringpeptide[11]),13]*
+    ThisKinTable[as.numeric(Scoringpeptide[12]),14]*ThisKinTable[as.numeric(Scoringpeptide[13]),15]*ThisKinTable[as.numeric(Scoringpeptide[14]),16]*ThisKinTable[as.numeric(Scoringpeptide[15]),17]
+  NegativeScores[v]<-ThisKinTableScore
+  ThisKinTableScore<-(ThisKinTableScore/(ThisKinTableScore+1/as.numeric(NormalizationScore[2])))
+  NegativeWeirdScores[v]<-ThisKinTableScore*100
+}
+
+negativesubstrates<-NegativeSubstrateList[,2]
+NegativeWithScores<-cbind(negativesubstrates,as.character(NegativeScores),as.character(NegativeWeirdScores))
+
+
+#NEED TO HAVE THE NEGATIVE SUBSTRATES BE OUTPUTTED
+
+PositiveScores<-rep(NA,times=nrow(ImportedSubstrateList))
+PositiveWeirdScores<-rep(NA,times=nrow(ImportedSubstrateList))
+
+for (v in 1:nrow(ImportedSubstrateList)) {
+  motif<-ImportedSubstrateList[v,4:18]
+  motif<-unlist(motif)
+  motif<- gsub("^$","O",motif)  
+  motif <- sapply(motif, function (x) aa_props[x])
+  Scoringpeptide<-motif
+  Scoringpeptide<-Scoringpeptide+1
+  ThisKinTableScore<-as.numeric(ThisKinTable[Scoringpeptide[1],3])*ThisKinTable[as.numeric(Scoringpeptide[2]),4]*ThisKinTable[as.numeric(Scoringpeptide[3]),5]*
+    ThisKinTable[as.numeric(Scoringpeptide[4]),6]*ThisKinTable[as.numeric(Scoringpeptide[5]),7]*ThisKinTable[as.numeric(Scoringpeptide[6]),8]*ThisKinTable[as.numeric(Scoringpeptide[7]),9]*
+    #ThisKinTable[as.numeric(Scoringpeptide[8]),10]*
+    ThisKinTable[as.numeric(Scoringpeptide[9]),11]*ThisKinTable[as.numeric(Scoringpeptide[10]),12]*ThisKinTable[as.numeric(Scoringpeptide[11]),13]*
+    ThisKinTable[as.numeric(Scoringpeptide[12]),14]*ThisKinTable[as.numeric(Scoringpeptide[13]),15]*ThisKinTable[as.numeric(Scoringpeptide[14]),16]*ThisKinTable[as.numeric(Scoringpeptide[15]),17]
+  
+  PositiveScores[v]<-ThisKinTableScore
+  ThisKinTableScore<-(ThisKinTableScore/(ThisKinTableScore+1/as.numeric(NormalizationScore[2])))
+  PositiveWeirdScores[v]<-ThisKinTableScore*100
+}
+
+positivesubstrates<-ImportedSubstrateList[,4:18]
+positivewithscores<-cbind.data.frame(positivesubstrates,PositiveScores,PositiveWeirdScores)
+
+
+#write down the transient transfection SOP and what we will be doing with them
+#write down the vector names I will be using
+#write down something about transforming bacteria and with what
+
+#90% whatevernness
+# TPninetyone<-length(PositiveWeirdScores[PositiveWeirdScores>=0.91])
+# Senseninetyone<-TPninetyone/nrow(positivesubstrates)
+# 
+# TNninetyone<-length(NegativeWeirdScores[NegativeWeirdScores<91])
+# Specninetyone<-TNninetyone/100
+
+#create the MCC table
+
+threshold<-c(1:100)
+threshold<-order(threshold,decreasing = TRUE)
+
+Truepositives<-c(1:100)
+Falsenegatives<-c(1:100)
+Sensitivity<-c(1:100)
+TrueNegatives<-c(1:100)
+FalsePositives<-c(1:100)
+Specificity<-c(1:100)
+Accuracy<-c(1:100)
+MCC<-c(1:100)
+EER<-c(1:100)
+
+#MAKE DAMN SURE THAT THE ACCESSION NUMBERS FOLLOW THE MOTIFS
+
+for (z in 1:100) {
+  thres<-101-z
+  Truepositives[z]<-length(PositiveWeirdScores[PositiveWeirdScores>=(thres)])
+  Falsenegatives[z]<-nrow(positivesubstrates)-Truepositives[z]
+  Sensitivity[z]<-Truepositives[z]/(Falsenegatives[z]+Truepositives[z])
+  TrueNegatives[z]<-length(NegativeWeirdScores[NegativeWeirdScores<(thres)])
+  # at thresh 100 this should be 0, because it is total minus true negatives
+  FalsePositives[z]<-nrow(NegativeSubstrateList)-TrueNegatives[z]
+  Specificity[z]<-1-(TrueNegatives[z]/(FalsePositives[z]+TrueNegatives[z]))
+  Accuracy[z]<-100*(Truepositives[z]+TrueNegatives[z])/(Falsenegatives[z]+FalsePositives[z]+TrueNegatives[z]+Truepositives[z])
+  MCC[z]<-((Truepositives[z]+TrueNegatives[z])-(Falsenegatives[z]+FalsePositives[z]))/sqrt(round(round(Truepositives[z]+Falsenegatives[z])*round(TrueNegatives[z]+FalsePositives[z])*round(Truepositives[z]+FalsePositives[z])*round(TrueNegatives[z]+Falsenegatives[z])))
+  EER[z]<-.01*(((1-(Sensitivity[z]))*(Truepositives[z]+Falsenegatives[z]))+(Specificity[z]*(1-(Truepositives[z]+Falsenegatives[z]))))
+}
+Characterization<-cbind.data.frame(threshold,Truepositives,Falsenegatives,Sensitivity,TrueNegatives,FalsePositives,Specificity,Accuracy,MCC,EER)
+
+positiveheader<-c(1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,"RPMS","PMS")
+positivewithscores<-rbind.data.frame(positiveheader,positivewithscores)
+
+negativeheader<-c("Substrate","RPMS","PMS")
+colnames(NegativeWithScores)<-negativeheader
+
+# write.xlsx(NegativeWithScores,file = FILENAME, sheetName = "Negative Sequences Scored",col.names = TRUE,row.names = FALSE,append = TRUE)
+# write.xlsx(Characterization,file = FILENAME,sheetName = "Characterization Table",col.names = TRUE,row.names = FALSE,append = TRUE)
+# write.xlsx(RanksPeptides,file = FILENAME,sheetName = "Ranked Generated Peptides",col.names = FALSE,row.names = FALSE,append = TRUE)
+# write.xlsx(positivewithscores,file = FILENAME, sheetName = "Positive Sequences Scored",col.names = FALSE,row.names = FALSE,append = TRUE)
+write.table(x=c("Characterzation Table"),file = FILENAME2, col.names = FALSE,row.names = FALSE, append = TRUE,sep = ",")
+header<-colnames(Characterization)
+Characterization<-rbind.data.frame(header,Characterization)
+write.table(Characterization,file = FILENAME2, col.names = FALSE,row.names = FALSE, append = TRUE,sep = ",")
+
+# header<-colnames(RanksPeptides)
+# RanksPeptides<-rbind.data.frame(header,RanksPeptides)
+write.table(RanksPeptides,file = FILENAME3,append = FALSE,row.names = FALSE,col.names = TRUE,sep = ",")