--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/all stuff/Difference finder for GalaxyP working.R	Fri Feb 21 13:07:45 2020 -0500
@@ -0,0 +1,358 @@
+#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,colClasses = "character")
+Firstsubbackfreq<- read.csv("SBF1.csv", header=FALSE, stringsAsFactors=FALSE)
+
+SecondSubstrateSet<- read.csv("S2.csv", stringsAsFactors=FALSE,colClasses = "character")
+Secondsubbackfreq<- read.csv("SBF2.csv", header=FALSE, stringsAsFactors=FALSE)
+
+
+First_unshared_motifs_table<-"1RS.csv"
+First_unshared_subbackfreq<-"1RSBF.csv"
+
+Second_unshared_motifs_table<-"2RS.csv"
+Second_unshared_subbackfreq<-"2RSBF.csv"
+
+EmptySubHeader<-colnames(FirstSubstrateSet)
+EmptySubHeader<-matrix(EmptySubHeader, nrow=1)
+EmptySBFHeader<-Firstsubbackfreq[,1]
+
+#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.
+####################################################################################################################################
+
+
+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
+
+
+###############################################
+#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)
+  
+  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]
+      
+      
+    }
+    
+  }
+  
+  D835Ymotifs=matrix(,nrow = nrow(SecondSubstrateSet),ncol=1)
+  D835YAccessionNumbers<-matrix(,nrow = nrow(SecondSubstrateSet),ncol = 1)
+  
+  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]<-SecondSubstrateSet[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]<-SecondSubstrateSet[i,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)
+
+FLTheader<-c("Substrate","Species","Reference","-7","-6","-5","-4","-3","-2","-1","0","1","2","3","4","5","6","7","Phosphite")
+
+if (length(FTLwtmotifsFINAL)>0){
+  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)
+      }
+    }
+  }
+  FTLFinalMatrix<-FTLFinalMatrix[!duplicated(FTLFinalMatrix),]
+  FTLFinalMatrix<-FTLFinalMatrix[2:nrow(FTLFinalMatrix),]
+  
+  
+  FTLoutputmatrix<-matrix(data=c(FTLwtmotifsFINAL,names(FTLwtmotifsFINAL)),ncol = 2)
+  # 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,nrow = 1)
+  write.table(x=columnalheader,
+              file=First_unshared_subbackfreq,
+              quote=FALSE, sep=",",
+              row.names=FALSE,col.names = FALSE, na="", append=TRUE)
+  
+  write.table(x=FTLFinalMatrix,
+              file=First_unshared_subbackfreq,
+              quote=FALSE, sep=",",
+              row.names=FALSE,col.names = FALSE, na="", append=TRUE)
+} else{
+  FTLFinalMatrix<-columnalheader
+  write.table(x=EmptySubHeader,
+              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,nrow = 1)
+  write.table(x=columnalheader,
+              file=First_unshared_subbackfreq,
+              quote=FALSE, sep=",",
+              row.names=FALSE,col.names = FALSE, na="", append=TRUE)
+}
+
+
+columnalheader<-c(rep(NA,36))
+D835YFinalMatrix<-matrix(data =columnalheader,nrow = 1)
+
+if (length(D835YmotifsFINAL)>0){
+  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)
+      }
+    }
+  }
+  D835YFinalMatrix<-D835YFinalMatrix[!duplicated(D835YFinalMatrix),]
+  D835YFinalMatrix<-D835YFinalMatrix[2:nrow(D835YFinalMatrix),]
+  
+  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)
+  
+  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,nrow = 1)
+  write.table(x=columnalheader,
+              file=Second_unshared_subbackfreq,
+              quote=FALSE, sep=",",
+              row.names=FALSE,col.names = FALSE, na="", append=TRUE)
+  
+  write.table(x=D835YFinalMatrix,
+              file=Second_unshared_subbackfreq,
+              quote=FALSE, sep=",",
+              row.names=FALSE,col.names = FALSE, na="", append=TRUE)
+} else {
+  D835YFinalMatrix<- columnalheader
+  write.table(x=EmptySubHeader,
+              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,nrow = 1)
+  write.table(x=columnalheader,
+              file=Second_unshared_subbackfreq,
+              quote=FALSE, sep=",",
+              row.names=FALSE,col.names = FALSE, na="", append=TRUE)
+}
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