#I should make an SOP for this.  Problems we encountered: no x in the xY motif, and the kilodemon
#the output files have both Y and xY, they shouldn't why is that happening?  make it not happen
#make sure that accession numbers stay locked to each motif, somehow
#output should look just like the KALIP input
#S2 is negatives
#ff you want ONLY FULL MOTIFS, put "YES" here, please use all caps
FullMotifsOnly_questionmark<-"NO"
#If you want ONLY TRUNCATED MOTIFS, put "YES" here, please use all caps
TruncatedMotifsOnly_questionmark<-"NO"
#if you want to find the overlap, put a "YES" here (all caps), if you want to find the non-overlap, put "NO" (all caps)
Are_You_Looking_For_Commonality<-"NO"


#put the names of your input files here
FirstSubstrateSet<- read.csv("S1.csv", stringsAsFactors=FALSE)
Firstsubbackfreq<- read.csv("SBF1.csv", header=FALSE, stringsAsFactors=FALSE)

SecondSubstrateSet<- read.csv("S2.csv", stringsAsFactors=FALSE)
Secondsubbackfreq<- read.csv("SBF2.csv", header=FALSE, stringsAsFactors=FALSE)

# ThirdSubstrateSet<- read.csv("Galaxy69-BTK_PLUS_R3_Substrates.csv", stringsAsFactors=FALSE)
# Thirdsubbackfreq<- read.csv("Galaxy70-BTK_PLUS_R3_SubstrateBackgroundFrequency.csv", header=FALSE, stringsAsFactors=FALSE)

#then put the names of your output files here
# Shared_motifs_table<-"180719_GALAXY-BTK-plus-rep-OVLP-7to7-substrates.csv"
# Shared_subbackfreq_table<-"180719_GALAXY-BTK-plus-rep-OVLP-7to7-SubBackFreq.csv"

# Shared_motifs_table<-"Shared motifs 7-27-17.csv"
# Shared_subbackfreq_table<-"SubstrateBackgrounFrequency-for-shared-motifs 4 7-27-17.csv"

First_unshared_motifs_table<-"1RS.csv"
First_unshared_subbackfreq<-"1RSBF.csv"

Second_unshared_motifs_table<-"2RS.csv"
Second_unshared_subbackfreq<-"2RSBF.csv"

# Third_unshared_motifs_table<-"R3 subs.csv"
# Third_unshared_subbackfreq<-"R3 SBF.csv"

#final note, this code is going to be unworkable if you want to make a Venn diagram of more than 3 circles.  I think I'll poke around
#other languages to see if any of them can do it.
####################################################################################################################################





# grepl(pattern = "S", x=asdf, ignore.case = TRUE)

FirstCentralLetters<-FirstSubstrateSet[,11]
SecondCentralLetters<-SecondSubstrateSet[,11]

FirstEsses<-sapply(FirstCentralLetters, grepl, pattern="S", ignore.case=TRUE)
FirstTees<-sapply(FirstCentralLetters, grepl, pattern="T", ignore.case=TRUE)
FirstWys<-sapply(FirstCentralLetters, grepl, pattern="Y", ignore.case=TRUE)

SecondEsses<-sapply(SecondCentralLetters, grepl, pattern="S", ignore.case=TRUE)
SecondTees<-sapply(SecondCentralLetters, grepl, pattern="T", ignore.case=TRUE)
SecondWys<-sapply(SecondCentralLetters, grepl, pattern="Y", ignore.case=TRUE)

FirstCentralLetters<-replace(FirstCentralLetters,FirstEsses,"xS")
FirstCentralLetters<-replace(FirstCentralLetters,FirstTees,"xT")
FirstCentralLetters<-replace(FirstCentralLetters,FirstWys,"xY")

SecondCentralLetters<-replace(SecondCentralLetters,SecondEsses,"xS")
SecondCentralLetters<-replace(SecondCentralLetters,SecondTees,"xT")
SecondCentralLetters<-replace(SecondCentralLetters,SecondWys,"xY")

FirstCentralLetters->FirstSubstrateSet[,11]
SecondCentralLetters->SecondSubstrateSet[,11]

####################################################################################################################################
####################################################################################################################################
# better version of this code written in C: what happens when two kinases share a motif, but they found that motif in two 
# separate proteins thus two separate accession numbers?
# It should actually output the shared motif and BOTH accession numbers.  Right now it does not, it only maps out the second
# accession number.  So that needs to be fixed BUT you need to keep the commonality between a motif and its accession number
####################################################################################################################################
####################################################################################################################################
####################################################################################################################################
####################################################################################################################################

#Create the motif sets, deciding wether or not you're looking for truncated or full here
#full only


if (Are_You_Looking_For_Commonality=="NO"){
  
  ###############################################
  #ALL motifs, full and truncated
  
  if (FullMotifsOnly_questionmark!="YES"&&TruncatedMotifsOnly_questionmark!="YES"){
    # FTLwtmotifs=matrix(,nrow = nrow(FirstSubstrateSet),ncol=1)
    # FTLwtAccessionNumbers=matrix(,nrow = nrow(FirstSubstrateSet),ncol=1)
    
    #so what this does is
    #find the central phospho position and add spaces to either side of it
    #create a pasted together motif which will be used for difference finding
    #keep motifs and accession numbers in the same index position of two vectors
    
    #so instead just take the FLTwt[i,4:18], and replace "" with "O"
    #then perform paste function
    #then FLTwt with "O" can be the motif that will get printed to the CSV (after re-removing the "O") and the pasted motif is in its own vector that follows the A #s
    
    FTLwtmotifs<-FirstSubstrateSet[,4:18]
    # FTLwtmotifs<-sapply(FTLwtmotifs, gsub, pattern=" ", replacement="O",ignore.case=TRUE)
    FTLwtmotifs<-replace(FTLwtmotifs, FTLwtmotifs=="", "O")
    FTLwtmotifs<-apply(FTLwtmotifs, 1, paste, sep="", collapse="")
    FTLwtAccessionNumbers<-FirstSubstrateSet[,3]
    
    # D835Ymotifs=matrix(,nrow = nrow(SecondSubstrateSet),ncol=1)
    # D835YAccessionNumbers<-matrix(,nrow = nrow(SecondSubstrateSet),ncol = 1)
    
    D835Ymotifs<-SecondSubstrateSet[,4:18]
    # D835Ymotifs<-sapply(D835Ymotifs, gsub, patter="", replacement="O",ignore.case=TRUE)
    D835Ymotifs<-replace(D835Ymotifs, D835Ymotifs=="", "O")
    D835Ymotifs<-replace(D835Ymotifs, D835Ymotifs=="", "O")
    D835Ymotifs<-apply(D835Ymotifs, 1, paste, sep="", collapse="")
    D835YAccessionNumbers<-SecondSubstrateSet[,3]
    
    names(FTLwtmotifs)<-FTLwtAccessionNumbers
    names(D835Ymotifs)<-D835YAccessionNumbers
    
  }
  
  
  FTLwtmotifsFINAL<-FTLwtmotifs[!FTLwtmotifs %in% D835Ymotifs]
  FTLwtmotifsFINAL<-FTLwtmotifsFINAL[!duplicated(FTLwtmotifsFINAL)]
  
  D835YmotifsFINAL<-D835Ymotifs[!D835Ymotifs %in% FTLwtmotifs]
  D835YmotifsFINAL<-D835YmotifsFINAL[!duplicated(D835YmotifsFINAL)]
  
  
  
  # columnalheader<-c(rep(NA,36))
  # FTLFinalMatrix<-matrix(data =columnalheader,nrow = 1)
  # 
  #how to make this an apply
  #actual first turn names(motifsFINAL) into a vector, then gsub to replace all "|" pipe characters with "*" star characters
  #first take the accession numbers as Firstsubbackfreq[1,], then gsub to replace all "|" pipe characters with "*" star characters
  #then use AccessionNumbers as a vector and use 
  #matches <- unique (grep(paste(toMatch,collapse="|"), names(motifsFINAL), value=TRUE))
  
  FLTwtNames<-names(FTLwtmotifsFINAL)
  FLTwtNames<-FLTwtNames[!duplicated(FLTwtNames)]
  #the problem is the names includes a lot of things that are multi names separated by ;
  #I need to do soem paper writing and poster writing
  
  # FLTwtNames<-gsub(pattern = '\\|', replacement = "*", x=FLTwtNames)
  # FLTwtNames<-paste(FLTwtNames,collapse = "|")
  
  AccNums<-as.character(Firstsubbackfreq[1,])
  # AccNums<-gsub(pattern = "\\|", replacement = "*", x=AccNums)
  
  # my_matches<-unique(grep(pattern = FLTwtNames, x=AccNums, value = TRUE))
  # matches <- unique (grep(paste(FLTwtNames,collapse="|"), AccNums, value=TRUE))
  My_matches<- AccNums %in% FLTwtNames
  #my matches are which columns in the SBF file still have a motif with them
  FirstFINALSBF<-Firstsubbackfreq[My_matches]
  FTLFinalMatrix<-FirstFINALSBF
  duped<-FTLFinalMatrix[1,]
  duped<-duped[!duplicated(duped)]
  names(duped)<-NULL
  duped<-unlist(duped)
  unduped<-FTLFinalMatrix[,!duplicated(duped)]
  FTLFinalMatrix<-unduped
  # FTLFinalMatrix<-FTLFinalMatrix[2:nrow(FTLFinalMatrix),]
  
  # columnalheader<-c(rep(NA,36))
  # D835YFinalMatrix<-matrix(data =columnalheader,nrow = 1)
  
  D835names<-names(D835YmotifsFINAL)
  D835names<-D835names[!duplicated(D835names)]
  AccNums<-as.character(Secondsubbackfreq[1,])
  My_matches<-AccNums %in% D835names
  SecondFINALSBF<-Secondsubbackfreq[My_matches]
  D835YFinalMatrix<-SecondFINALSBF
  duped<-D835YFinalMatrix[1,]
  duped<-duped[!duplicated(duped)]
  names(duped)<-NULL
  duped<-unlist(duped)
  unduped<-D835YFinalMatrix[,!duplicated(duped)]
  D835YFinalMatrix<-unduped
  #there's a problem, accession numbers are duplicated
  
  # FTLoutputmatrix<-matrix(data=c(FTLwtmotifsFINAL,names(FTLwtmotifsFINAL)),ncol = 2)
  
  FTLwtmotifsFINAL<-gsub(pattern = "O", replacement = " ", x=FTLwtmotifsFINAL)
  FTLwtmotifsFINAL<-gsub(pattern = "x", replacement = "", x=FTLwtmotifsFINAL)
  FTLoutputmatrix<-matrix(data = c(FTLwtmotifsFINAL,names(FTLwtmotifsFINAL)), ncol=2)
  
  # FTLwtmotifsFINAL<-gsub(pattern = "O", replacement = " ", x=FTLwtmotifsFINAL)
  # FTLwtmotifsFINAL<-gsub(pattern = "x", replacement = "", x=FTLwtmotifsFINAL)
  # FTLoutputmatrix<-matrix(data = c(FTLwtmotifsFINAL,names(FTLwtmotifsFINAL)), ncol=2)
  
  FLTheader<-c("Substrate","Species","Reference","-7","-6","-5","-4","-3","-2","-1","0","1","2","3","4","5","6","7","Phosphite")
  # FLTheader<-unlist(FLTheader)
  lefthandFLT<-matrix(data = rep(NA,times=2*nrow(FTLoutputmatrix)),nrow=nrow(FTLoutputmatrix))
  righthandFLT<-matrix(data = rep(NA,times=1*nrow(FTLoutputmatrix)),nrow=nrow(FTLoutputmatrix))
  FLTaccessionset<-FTLoutputmatrix[,2]
  FTLmeat<-sapply(FTLoutputmatrix[,1], strsplit, "")
  FTLmeat<-sapply(FTLmeat, unlist)
  colnames(FTLmeat)<-NULL
  FTLmeat<-t(FTLmeat)
  
  FTLoutputmatrix2<-cbind(lefthandFLT,FLTaccessionset,FTLmeat,righthandFLT)
  colnames(FTLoutputmatrix2)<-NULL
  rownames(FTLoutputmatrix2)<-NULL
  colnames(FLTheader)<-NULL
  rownames(FLTheader)<-NULL
  
  
  FirstCentralLettersAGAIN<-FTLoutputmatrix2[,11]
  
  FirstEsses<-sapply(FirstCentralLettersAGAIN, grepl, pattern="S", ignore.case=TRUE)
  FirstTees<-sapply(FirstCentralLettersAGAIN, grepl, pattern="T", ignore.case=TRUE)
  FirstWys<-sapply(FirstCentralLettersAGAIN, grepl, pattern="Y", ignore.case=TRUE)
  
  FirstCentralLettersAGAIN<-replace(FirstCentralLettersAGAIN,FirstEsses,"xS")
  FirstCentralLettersAGAIN<-replace(FirstCentralLettersAGAIN,FirstTees,"xT")
  FirstCentralLettersAGAIN<-replace(FirstCentralLettersAGAIN,FirstWys,"xY")
  
  FirstCentralLettersAGAIN->FTLoutputmatrix2[,11]
  
  FTLoutputmatrix2<-rbind(FLTheader,FTLoutputmatrix2)
  
  write.table(x=FTLoutputmatrix2,
              file=First_unshared_motifs_table,
              quote=FALSE, sep=",",
              row.names=FALSE,col.names = FALSE, na="", append=TRUE)
  
  columnalheader<-c("Accession Numbers",as.character(Firstsubbackfreq[1:35,1]))
  columnalheader<-matrix(columnalheader,ncol = 1)
  # write.table(x=columnalheader,
  #             file=First_unshared_subbackfreq,
  #             quote=FALSE, sep=",",
  #             row.names=FALSE,col.names = FALSE, na="", append=TRUE)
  
  FTLFinalMatrix<-cbind(columnalheader,FTLFinalMatrix)
  
  write.table(x=FTLFinalMatrix,
              file=First_unshared_subbackfreq,
              quote=FALSE, sep=",",
              row.names=FALSE,col.names = FALSE, na="", append=TRUE)
  
  ############################################################################################################
  
  D835YmotifsFINAL<-gsub(pattern = "O", replacement = " ", x=D835YmotifsFINAL)
  D835YmotifsFINAL<-gsub(pattern = "x", replacement = "", x=D835YmotifsFINAL)
  D835Youtputmatrix<-matrix(data = c(D835YmotifsFINAL,names(D835YmotifsFINAL)), ncol=2)
  
  # D835YmotifsFINAL<-gsub(pattern = "O", replacement = " ", x=D835YoutputmatrixL)
  # D835YmotifsFINAL<-gsub(pattern = "x", replacement = "", x=D835Youtputmatrix)
  # D835Youtputmatrix<-matrix(data = c(D835Youtputmatrix,names(D835Youtputmatrix)), ncol=2)
  # 

  # D835Youtputmatrix<-matrix(data=c(D835YmotifsFINAL,names(D835YmotifsFINAL)),ncol = 2)
  
  D835Yheader<-c("Substrate","Species","Reference","-7","-6","-5","-4","-3","-2","-1","0","1","2","3","4","5","6","7","Phosphite")
  # D835Yheader<-unlist(D835Yheader)
  lefthandD835<-matrix(data = rep(NA,times=2*nrow(D835Youtputmatrix)),nrow=nrow(D835Youtputmatrix))
  righthandD835<-matrix(data = rep(NA,times=1*nrow(D835Youtputmatrix)),nrow=nrow(D835Youtputmatrix))
  D835Yaset<-D835Youtputmatrix[,2]
  D835meat<-sapply(D835Youtputmatrix[,1], strsplit, "")
  D835meat<-sapply(D835meat, unlist)
  colnames(D835meat)<-NULL
  D835meat<-t(D835meat)

  # FTLmeat<-sapply(FTLoutputmatrix[,1], strsplit, "")
  # FTLmeat<-sapply(FTLmeat, unlist)
  # colnames(FTLmeat)<-NULL
  # FTLmeat<-t(FTLmeat)


  D835Youtputmatrix2<-cbind(lefthandD835,D835Yaset,D835meat,righthandD835)
  colnames(D835Youtputmatrix2)<-NULL
  rownames(D835Youtputmatrix2)<-NULL
  colnames(D835Yheader)<-NULL
  rownames(D835Yheader)<-NULL


  SecondCentralLettersAGAIN<-D835Youtputmatrix2[,11]

  SecondEsses<-sapply(SecondCentralLettersAGAIN, grepl, pattern="S", ignore.case=TRUE)
  SecondTees<-sapply(SecondCentralLettersAGAIN, grepl, pattern="T", ignore.case=TRUE)
  SecondWys<-sapply(SecondCentralLettersAGAIN, grepl, pattern="Y", ignore.case=TRUE)

  SecondCentralLettersAGAIN<-replace(SecondCentralLettersAGAIN,SecondEsses,"xS")
  SecondCentralLettersAGAIN<-replace(SecondCentralLettersAGAIN,SecondTees,"xT")
  SecondCentralLettersAGAIN<-replace(SecondCentralLettersAGAIN,SecondWys,"xY")

  SecondCentralLettersAGAIN->D835Youtputmatrix2[,11]

  D835Youtputmatrix2<-rbind(D835Yheader,D835Youtputmatrix2)

  write.table(x=D835Youtputmatrix2,
              file=Second_unshared_motifs_table,
              quote=FALSE, sep=",",
              row.names=FALSE,col.names = FALSE, na="", append=TRUE)
  
  columnalheader<-c("Accession Numbers",as.character(Firstsubbackfreq[1:35,1]))
  columnalheader<-matrix(columnalheader,ncol = 1)
  # write.table(x=columnalheader,
  #             file=Second_unshared_subbackfreq,
  #             quote=FALSE, sep=",",
  #             row.names=FALSE,col.names = FALSE, na="", append=TRUE)
  
  D835YFinalMatrix<-cbind(columnalheader,D835YFinalMatrix)
  
  write.table(x=D835YFinalMatrix,
              file=Second_unshared_subbackfreq,
              quote=FALSE, sep=",",
              row.names=FALSE,col.names = FALSE, na="", append=TRUE)
}



#  for (i in 1:nrow(FirstSubstrateSet)){
#   FTLwtletters<-FirstSubstrateSet[i,4:18]
#   FTLwtletters<-FTLwtletters[FTLwtletters !="XXXXX"]
#   FTLwtletters<-paste(FTLwtletters, sep="", collapse="")
#   leftspaces<-c()
#   rightspaces<-c()
#   
#   YYYmotif <- unlist(strsplit(FTLwtletters, split = ""))
#   YYYposition <- match(x = "x", table = YYYmotif)
#   #position itself tells me how much is to the left of that X by what it's number is.  x at position 4 tells me that there are
#   #just 3 letters to the left of x
#   
#   YYYLettersToTheLeft <- YYYposition - 1
#   #how many letters to the right SHOULD just be length(motif)-position-1 if it's 5 long and x is at 3 then Y is at 4 and there is
#   #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1
#   YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1
#   #then sanity check, we're currently looking only at +/-4, but this spot allows for up to +/- 7 as well, just depends on what the
#   #variable the user puts in is
#   
#   
#   if (YYYLettersToTheLeft < 7 | YYYLettersToTheRight < 7) {
#     leftspaces<-rep(" ",times=(7-YYYLettersToTheLeft))
#     rightspaces<-rep(" ",times=7-(YYYLettersToTheRight))
#     #add blank spaces if the motif has less than 4 letters to the left/right
#     motif<-c(leftspaces,YYYmotif,rightspaces)
#     #save that motif, which is the Y and +/- 4 amino acids, including truncation
#     motif<-motif[!motif %in% "x"]
#     motif<-paste(motif, sep="", collapse="")
#     FTLwtletters<-motif
#     FTLwtmotifs[i,1]<-FTLwtletters
#     FTLwtAccessionNumbers[i,1]<-FirstSubstrateSet[i,3]
#   }
#   
#   if(YYYLettersToTheLeft>6 && YYYLettersToTheRight>6){
#     motif<-YYYmotif
#     #add blank spaces if the motif has less than 4 letters to the left/right
#     motif<-c(leftspaces,YYYmotif,rightspaces)
#     #save that motif, which is the Y and +/- 4 amino acids, including truncation
#     motif<-motif[!motif %in% "x"]
#     motif<-paste(motif, sep="", collapse="")
#     FTLwtletters<-motif
#     FTLwtmotifs[i,1]<-FTLwtletters
#     FTLwtAccessionNumbers[i,1]<-FirstSubstrateSet[i,3]
#     
#     
#   }
#   
# }



# for (i in 1:nrow(SecondSubstrateSet)){
#   D835letters<-SecondSubstrateSet[i,4:18]
#   D835letters<-D835letters[D835letters !="XXXXX"]
#   D835letters<-paste(D835letters, sep="", collapse="")
#   leftspaces<-c()
#   rightspaces<-c()
#   
#   YYYmotif <- unlist(strsplit(D835letters, split = ""))
#   YYYposition <- match(x = "x", table = YYYmotif)
#   #position itself tells me how much is to the left of that X by what it's number is.  x at position 4 tells me that there are
#   #just 3 letters to the left of x
#   
#   YYYLettersToTheLeft <- YYYposition - 1
#   #how many letters to the right SHOULD just be length(motif)-position-1 if it's 5 long and x is at 3 then Y is at 4 and there is
#   #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1
#   YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1
#   #then sanity check, we're currently looking only at +/-4, but this spot allows for up to +/- 7 as well, just depends on what the
#   #variable the user puts in is
#   if (YYYLettersToTheLeft < 7 | YYYLettersToTheRight < 7) {
#     leftspaces<-rep(" ",times=(7-YYYLettersToTheLeft))
#     rightspaces<-rep(" ",times=7-(YYYLettersToTheRight))
#     #add blank spaces if the motif has less than 4 letters to the left/right
#     motif<-c(leftspaces,YYYmotif,rightspaces)
#     #save that motif, which is the Y and +/- 4 amino acids, including truncation
#     motif<-motif[!motif %in% "x"]
#     motif<-paste(motif, sep="", collapse="")
#     D835letters<-motif
#     D835Ymotifs[i,1]<-D835letters
#     D835YAccessionNumbers[i,1]<-FirstSubstrateSet[i,3]
#   }
#   
#   if(YYYLettersToTheLeft>6 && YYYLettersToTheRight>6){
#     motif<-YYYmotif
#     #add blank spaces if the motif has less than 4 letters to the left/right
#     motif<-c(leftspaces,YYYmotif,rightspaces)
#     #save that motif, which is the Y and +/- 4 amino acids, including truncation
#     motif<-motif[!motif %in% "x"]
#     motif<-paste(motif, sep="", collapse="")
#     D835letters<-motif
#     D835Ymotifs[i,1]<-D835letters
#     D835YAccessionNumbers[i,1]<-FirstSubstrateSet[i,3]
#   }
# }

# for (k in 1:length(FTLwtmotifsFINAL)) {
#   AN<-00000
#   #I don't remember why, but I felt it necessary to destroy the accession number multiple times to ensure it is
#   #destroyed immediately after use
#   for (m in 1:ncol(Firstsubbackfreq)) {
#     AN <- as.character(Firstsubbackfreq[1, m])
#     if (grepl(pattern = AN,
#               x = names(FTLwtmotifsFINAL[k]),
#               fixed = TRUE) == TRUE) {
#       outputmatrix <- as.character(Firstsubbackfreq[, m])
#       outputmatrix <- matrix(outputmatrix, nrow = 1)
#       #with that accession number, find a match in the subbackfreq file and save it here
#       FTLFinalMatrix<-rbind(FTLFinalMatrix,outputmatrix)
#     }
#   }
# }
# for (k in 1:length(D835YmotifsFINAL)) {
#   #I don't remember why, but I felt it necessary to destroy the accession number multiple times to ensure it is
#   #destroyed immediately after use
#   for (m in 1:ncol(Secondsubbackfreq)) {
#     AN <- as.character(Secondsubbackfreq[1, m])
#     if (grepl(pattern = AN,
#               x = names(D835YmotifsFINAL[k]),
#               fixed = TRUE) == TRUE) {
#       outputmatrix <- as.character(Secondsubbackfreq[, m])
#       outputmatrix <- matrix(outputmatrix, nrow = 1)
#       #with that accession number, find a match in the subbackfreq file and save it here
#       D835YFinalMatrix<-rbind(D835YFinalMatrix,outputmatrix)
#     }
#   }
# }