--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/C and D finder/commonality-working feb 21 20.R	Fri Feb 21 16:38:55 2020 -0500
@@ -0,0 +1,302 @@
+FirstSubstrateSet<- read.csv("r1sub.csv", stringsAsFactors=FALSE, header = FALSE)
+Firstsubbackfreq<- read.csv("r1sbf.csv", header=FALSE, stringsAsFactors=FALSE)
+SubstrateHeader<-FirstSubstrateSet[1,]
+FirstSubstrateSet<- FirstSubstrateSet[2:nrow(FirstSubstrateSet),]
+if(nrow(Firstsubbackfreq[1,]>35)){
+  if(grepl(pattern = "Properties", x=Firstsubbackfreq[1,22])){
+    Firstsubbackfreq<-t(Firstsubbackfreq)
+  }
+}
+
+
+SecondSubstrateSet<- read.csv("r1sub.csv", stringsAsFactors=FALSE, header = FALSE)
+Secondsubbackfreq<- read.csv("r1sbf.csv", header=FALSE, stringsAsFactors=FALSE)
+SecondSubstrateSet<- SecondSubstrateSet[2:nrow(SecondSubstrateSet),]
+if(nrow(Secondsubbackfreq[1,]>35)){
+  if(grepl(pattern = "Properties", x=Secondsubbackfreq[1,22])){
+    Secondsubbackfreq<-t(Secondsubbackfreq)
+  }
+}
+
+
+ThirdSubstrateSet<- read.csv("r2sub.csv", stringsAsFactors=FALSE, header = FALSE)
+Thirdsubbackfreq<- read.csv("r2sbf.csv", header=FALSE, stringsAsFactors=FALSE)
+ThirdSubstrateSet<- ThirdSubstrateSet[2:nrow(ThirdSubstrateSet),]
+if(nrow(Thirdsubbackfreq[1,]>35)){
+  if(grepl(pattern = "Properties", x=Thirdsubbackfreq[1,22])){
+    Thirdsubbackfreq<-t(Thirdsubbackfreq)
+  }
+}
+
+
+
+
+#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<-"YES"
+
+
+#then put the names of your output files here
+Shared_motifs_table<-"sharedmotifs.csv"
+Shared_subbackfreq_table<-"sharedSBF.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<-"R1 substrates.csv"
+First_unshared_subbackfreq<-"R1 SBF.csv"
+
+Second_unshared_motifs_table<-"R2 subs.csv"
+Second_unshared_subbackfreq<-"R2 SBf.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.
+####################################################################################################################################
+
+
+
+
+
+FirstxY<-rep("xY",times=nrow(FirstSubstrateSet))
+FirstSubstrateSet[,11]<-FirstxY
+
+SecondxY<-rep("xY",times=nrow(SecondSubstrateSet))
+SecondSubstrateSet[,11]<-SecondxY
+
+ThirdxY<-rep("xY",times=nrow(ThirdSubstrateSet))
+ThirdSubstrateSet[,11]<-ThirdxY
+
+
+
+
+
+
+
+
+
+
+
+####################################################################################################################################
+####################################################################################################################################
+# 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
+ 
+FTLwtmotifs=matrix(,nrow = nrow(FirstSubstrateSet),ncol=1)
+FTLwtAccessionNumbers=matrix(data = Firstsubbackfreq[1,],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(data = Secondsubbackfreq[1,],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]<-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]
+  }
+}
+
+
+ITDmotifs=matrix(,nrow = nrow(ThirdSubstrateSet),ncol=1)
+ITDAccessionNumbers<-matrix(data = Thirdsubbackfreq[1,],ncol = 1)
+
+for (i in 1:nrow(ThirdSubstrateSet)){
+  ITDletters<-ThirdSubstrateSet[i,4:18]
+  ITDletters<-ITDletters[ITDletters !="XXXXX"]
+  ITDletters<-paste(ITDletters, sep="", collapse="")
+  YYYmotif <- unlist(strsplit(ITDletters, split = ""))
+  leftspaces<-c()
+  rightspaces<-c()
+  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="")
+    ITDletters<-motif
+    ITDmotifs[i,1]<-ITDletters
+    # ITDAccessionNumbers[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="")
+    ITDletters<-motif
+    ITDmotifs[i,1]<-ITDletters
+    # ITDAccessionNumbers[i,1]<-FirstSubstrateSet[i,3]
+  }
+}
+  
+#############################################################################################################################
+#############################################################################################################################
+#############################################################################################################################
+#############################################################################################################################
+#############################################################################################################################
+
+#now look for either commonality or difference.  Actually could you look for both...
+
+if (Are_You_Looking_For_Commonality=="YES"){
+  
+  columnalheader<-c(as.character(Thirdsubbackfreq[1:36,1]))
+  columnalheader<-matrix(columnalheader,nrow = 1)
+
+  SubstrateOverlap1<-intersect(D835Ymotifs,ITDmotifs)
+  SubstrateOverlap1<-as.matrix(SubstrateOverlap1)
+  
+  
+  columnalheader<-c(rep(NA,36))
+  FinalMatrix<-matrix(data =columnalheader,ncol = 1)
+
+  SubstrateOverlapFINAL<-intersect(FTLwtmotifs,SubstrateOverlap1)
+  AccessionOverlap1<-intersect(D835YAccessionNumbers,ITDAccessionNumbers)
+  AccessionOverlapFinal<-intersect(AccessionOverlap1,FTLwtAccessionNumbers)
+  AccessionOverlapFinal<-unlist(AccessionOverlapFinal)
+  
+  for (x in 1:length(AccessionOverlapFinal)) {
+    for (y in 1:ncol(Firstsubbackfreq)) {
+      Acc<-AccessionOverlapFinal[x]
+      SBF<-Firstsubbackfreq[1,y]
+      if(Acc==SBF){
+        FinalMatrix<-cbind(FinalMatrix,Firstsubbackfreq[,y])
+      }
+    }
+  }
+  FinalMatrix<-FinalMatrix[,2:ncol(FinalMatrix)]
+  
+  if(grepl(pattern = "Properties", x=FinalMatrix[22,1])==FALSE){
+    Outputmatrix<-cbind(Firstsubbackfreq[,1],FinalMatrix)
+    write.table(x=Outputmatrix,file = Shared_subbackfreq_table,quote = FALSE,sep = ",",row.names = FALSE,col.names = FALSE,na="")
+  } else {
+    write.table(x=FinalMatrix,file = Shared_subbackfreq_table,quote = FALSE,sep = ",",row.names = FALSE,col.names = FALSE,na="")
+  }
+  
+  SubstrateMatrix<-SubstrateHeader
+  if(ncol(SubstrateMatrix)>18){
+    SubstrateMatrix<-SubstrateMatrix[,1:18]
+  }
+  
+  for (z in 1:length(SubstrateOverlapFINAL)) {
+    motif<-SubstrateOverlapFINAL[z]
+    newmotif<-unlist(strsplit(motif,split = ""))
+    
+    Addition<-""
+    outputmotif<-c(Addition,Addition,Addition,newmotif)
+    SubstrateMatrix<-rbind(SubstrateMatrix,outputmotif)
+  }
+  write.table(x=SubstrateMatrix,file = Shared_motifs_table,quote = FALSE,sep = ",",row.names = FALSE,col.names = FALSE,na="")
+}