diff all stuff/Difference finder for GalaxyP july 2020.R @ 11:77e47268b650 draft default tip

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/all stuff/Difference finder for GalaxyP july 2020.R	Tue Jul 14 19:53:34 2020 -0400
@@ -0,0 +1,333 @@
+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)
+#this brings in the input files
+
+
+First_unshared_motifs_table<-"1RS.csv"
+First_unshared_subbackfreq<-"1RSBF.csv"
+Second_unshared_motifs_table<-"2RS.csv"
+Second_unshared_subbackfreq<-"2RSBF.csv"
+#this names the output files
+
+EmptySubHeader<-colnames(FirstSubstrateSet)
+EmptySubHeader<-matrix(EmptySubHeader, nrow=1)
+EmptySBFHeader<-Firstsubbackfreq[,1]
+#this creates the headers which comes from the input files, so that the output files can be given this header so that they will look identical to the input files
+
+
+#the below code is used to ensure that all phospho-amino acids get marked with an "x" to denote their phosphoness
+FirstCentralLetters<-FirstSubstrateSet[,11]
+SecondCentralLetters<-SecondSubstrateSet[,11]
+#the phospho AAs are always found in position 12, so take them from there
+
+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)
+#use an 3 apply functions to create vectors, these vetors have true values where they find an S, T or Y.  
+#so FirstEsses has a True anywhere it sees an S, and FirstTees has a True anywhere it sees a Y
+
+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)
+#do the same for the second substrate set's central letters
+
+FirstCentralLetters<-replace(FirstCentralLetters,FirstEsses,"xS")
+FirstCentralLetters<-replace(FirstCentralLetters,FirstTees,"xT")
+FirstCentralLetters<-replace(FirstCentralLetters,FirstWys,"xY")
+#where there is a True value in FirstEsses, replace that value in the original substrate set with an xS.  This is because there was originally an S in that
+#position, and I want that S to be marked with an x, denoting phospho
+
+SecondCentralLetters<-replace(SecondCentralLetters,SecondEsses,"xS")
+SecondCentralLetters<-replace(SecondCentralLetters,SecondTees,"xT")
+SecondCentralLetters<-replace(SecondCentralLetters,SecondWys,"xY")
+
+FirstCentralLetters->FirstSubstrateSet[,11]
+SecondCentralLetters->SecondSubstrateSet[,11]
+#then I put these x-marked letters back where I found them, in position 11 of the substrate sets
+
+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
+    #it is 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(as.character(Firstsubbackfreq[1:36,1]))
+  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(as.character(Firstsubbackfreq[1:36,1]))
+  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)) {
+    #it is 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(as.character(Firstsubbackfreq[1:36,1]))
+  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(as.character(Firstsubbackfreq[1:36,1]))
+  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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