annotate kinatestid_r/Kinatest-R_part2.R @ 13:d71eb1d66a88 draft

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#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 = ",")