--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/all stuff/difference finder for 2 overlaps proper names 7-7_1-15-2019.R	Wed Jan 16 13:55:22 2019 -0500
@@ -0,0 +1,547 @@
+#Difference finder for only 2 
+
+#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"
+
+FirstSubstrateSet<- read.csv("170922-BTK-MINUS-COMBO FILES_Substrates.csv", stringsAsFactors=FALSE)
+Firstsubbackfreq<- read.csv("170922-BTK-MINUS-COMBO FILES_Substrates.csv", header=FALSE, stringsAsFactors=FALSE)
+
+SecondSubstrateSet<- read.csv("170922-btk-rep OVLP-plus_Substrates.csv", stringsAsFactors=FALSE)
+Secondsubbackfreq<- read.csv("170922-btk-rep OVLP-plus_SubBackFreq.csv", header=FALSE, stringsAsFactors=FALSE)
+
+First_unshared_motifs_table<-"170922-BTK-MINUS-COMBO FILES_Substrates-unique.csv"
+First_unshared_subbackfreq<-"170922-BTK-MINUS-COMBO FILES_SubBackFreq-unique.csv"
+
+Second_unshared_motifs_table<-"170922-btk-rep OVLP-plus_Substrates-unique.csv"
+Second_unshared_subbackfreq<-"170922-btk-rep OVLP-plus_SubBackFreq-unique.csv"
+
+
+LeftOfYLetters<-7
+RightOfYLetters<-7
+
+if (FullMotifsOnly_questionmark=="YES"){
+  FirstMotifs=rep(NA,times=nrow(FirstSubstrateSet))
+  FirstAccessionNumbers=rep(NA,times=nrow(FirstSubstrateSet))
+  leftspaces<-c()
+  rightspaces<-c()
+  for (i in 1:nrow(FirstSubstrateSet)){
+    FirstLetters<-FirstSubstrateSet[i,7:15]
+    FirstLetters<-FirstLetters[FirstLetters !="XXXXX"]
+    FirstLetters<-paste(FirstLetters, sep="", collapse="")
+    
+    
+    YYYmotif <- unlist(strsplit(FirstLetters, 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 > 3 && YYYLettersToTheRight > 3) {
+      motif<-YYYmotif
+      #save that motif, which is the Y and +/- 4 amino acids, including truncation
+      motif<-motif[!motif %in% "x"]
+      motif<-paste(motif, sep="", collapse="")
+      FirstLetters<-motif
+      FirstMotifs[i]<-FirstLetters
+      FirstAccessionNumbers[i]<-FirstSubstrateSet[i,3]
+    }
+    
+  }
+  # FirstMotifs <- FirstMotifs[!is.na(FirstMotifs)]
+  # FirstMotifs<-matrix(FirstMotifs,ncol = 1)
+  # 
+  
+  SecondMotifs=rep(NA,times=nrow(FirstSubstrateSet))
+  SecondAccessionNumbers=rep(NA,times=nrow(FirstSubstrateSet))
+  
+  for (i in 1:nrow(SecondSubstrateSet)){
+    SecondLetters<-SecondSubstrateSet[i,7:15]
+    SecondLetters<-SecondLetters[SecondLetters !="XXXXX"]
+    SecondLetters<-paste(SecondLetters, sep="", collapse="")
+    
+    
+    YYYmotif <- unlist(strsplit(SecondLetters, 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 > 3 && YYYLettersToTheRight > 3) {
+      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="")
+      SecondLetters<-motif
+      SecondMotifs[i]<-SecondLetters
+      SecondAccessionNumbers[i]<-SecondSubstrateSet[i,3]
+    }
+  }
+  names(FirstMotifs)<-FirstAccessionNumbers
+  names(SecondMotifs)<-SecondAccessionNumbers
+  
+  
+#  ITDmotifs=rep(NA,times=nrow(FirstSubstrateSet))
+#  ITDAccessionNumbers=rep(NA,times=nrow(FirstSubstrateSet))
+  if(1==0){
+    for (i in 1:nrow(ThirdSubstrateSet)){
+      ITDletters<-ThirdSubstrateSet[i,7:15]
+      ITDletters<-ITDletters[ITDletters !="XXXXX"]
+      ITDletters<-paste(ITDletters, sep="", collapse="")
+      YYYmotif <- unlist(strsplit(ITDletters, 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 > 3 && YYYLettersToTheRight > 3) {
+        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]<-ITDletters
+        ITDAccessionNumbers[i]<-ThirdSubstrateSet[i,3]
+        
+      }
+    }
+  }  
+  #names(ITDmotifs)<-ITDAccessionNumbers
+  names(SecondMotifs)<-SecondAccessionNumbers
+  names(FirstMotifs)<-FirstAccessionNumbers
+}
+
+
+##############################################3
+#Truncated only
+if (TruncatedMotifsOnly_questionmark=="YES"){
+  FirstMotifs=matrix(,nrow = nrow(FirstSubstrateSet),ncol=1)
+  FirstAccessionNumbers=matrix(,nrow = nrow(FirstSubstrateSet),ncol=1)
+  
+  for (i in 1:nrow(FirstSubstrateSet)){
+    FirstLetters<-FirstSubstrateSet[i,7:15]
+    FirstLetters<-FirstLetters[FirstLetters !="XXXXX"]
+    FirstLetters<-paste(FirstLetters, sep="", collapse="")
+    
+    
+    YYYmotif <- unlist(strsplit(FirstLetters, 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 < 4 | YYYLettersToTheRight < 4) {
+      leftspaces<-rep(" ",times=(4-YYYLettersToTheLeft))
+      rightspaces<-rep(" ",times=4-(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="")
+      FirstLetters<-motif
+      FirstMotifs[i,1]<-FirstLetters
+      FirstAccessionNumbers[i,1]<-FirstSubstrateSet[i,3]
+    }
+    
+  }
+  
+  SecondMotifs=matrix(,nrow = nrow(SecondSubstrateSet),ncol=1)
+  SecondAccessionNumbers<-matrix(,nrow = nrow(SecondSubstrateSet),ncol = 1)
+  i=2
+  for (i in 1:nrow(SecondSubstrateSet)){
+    SecondLetters<-SecondSubstrateSet[i,7:15]
+    SecondLetters<-SecondLetters[SecondLetters !="XXXXX"]
+    SecondLetters<-paste(SecondLetters, sep="", collapse="")
+    
+    
+    YYYmotif <- unlist(strsplit(SecondLetters, 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 < 4 | YYYLettersToTheRight < 4) {
+      leftspaces<-rep(" ",times=(4-YYYLettersToTheLeft))
+      rightspaces<-rep(" ",times=4-(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="")
+      SecondLetters<-motif
+      SecondAccessionNumbers[i,1]<-SecondSubstrateSet[i,3]
+      SecondMotifs[i,1]<-SecondLetters
+    }
+  }
+  
+#  ITDmotifs=matrix(,nrow = nrow(ThirdSubstrateSet),ncol=1)
+#  ITDAccessionNumbers<-matrix(,nrow = nrow(ThirdSubstrateSet))
+  if(1==0){
+    for (i in 1:nrow(ThirdSubstrateSet)){
+      ITDletters<-ThirdSubstrateSet[i,7:15]
+      ITDletters<-ITDletters[ITDletters !="XXXXX"]
+      ITDletters<-paste(ITDletters, sep="", collapse="")
+      YYYmotif <- unlist(strsplit(ITDletters, 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 < 4 | YYYLettersToTheRight < 4) {
+        leftspaces<-rep(" ",times=(4-YYYLettersToTheLeft))
+        rightspaces<-rep(" ",times=4-(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
+        ITDAccessionNumbers[i,1]<-ThirdSubstrateSet[i,3]
+        ITDmotifs[i,1]<-ITDletters
+      }
+    }
+  }
+  names(FirstMotifs)<-FirstAccessionNumbers
+  names(SecondMotifs)<-SecondAccessionNumbers
+  #names(ITDmotifs)<-ITDAccessionNumbers
+}
+
+###############################################
+#ALL motifs, full and truncated
+
+if (FullMotifsOnly_questionmark!="YES"&&TruncatedMotifsOnly_questionmark!="YES"){
+  #print("!")}
+  FirstMotifs=matrix(,nrow = nrow(FirstSubstrateSet),ncol=1)
+  FirstAccessionNumbers=matrix(,nrow = nrow(FirstSubstrateSet),ncol=1)
+  
+  for (i in 1:nrow(FirstSubstrateSet)){
+    FirstLetters<-FirstSubstrateSet[i,7:15]
+    FirstLetters<-FirstLetters[FirstLetters !="XXXXX"]
+    FirstLetters<-paste(FirstLetters, sep="", collapse="")
+    leftspaces<-c()
+    rightspaces<-c()
+    
+    YYYmotif <- unlist(strsplit(FirstLetters, 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 < 4 | YYYLettersToTheRight < 4) {
+      leftspaces<-rep(" ",times=(4-YYYLettersToTheLeft))
+      rightspaces<-rep(" ",times=4-(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="")
+      FirstLetters<-motif
+      FirstMotifs[i,1]<-FirstLetters
+      FirstAccessionNumbers[i,1]<-FirstSubstrateSet[i,3]
+    }
+    
+    if(YYYLettersToTheLeft>3 && YYYLettersToTheRight>3){
+      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="")
+      FirstLetters<-motif
+      FirstMotifs[i,1]<-FirstLetters
+      FirstAccessionNumbers[i,1]<-FirstSubstrateSet[i,3]
+      
+      
+    }
+    
+  }
+  
+  SecondMotifs=matrix(,nrow = nrow(SecondSubstrateSet),ncol=1)
+  SecondAccessionNumbers<-matrix(,nrow = nrow(SecondSubstrateSet),ncol = 1)
+  
+  for (i in 1:nrow(SecondSubstrateSet)){
+    SecondLetters<-SecondSubstrateSet[i,7:15]
+    SecondLetters<-SecondLetters[SecondLetters !="XXXXX"]
+    SecondLetters<-paste(SecondLetters, sep="", collapse="")
+    leftspaces<-c()
+    rightspaces<-c()
+    
+    YYYmotif <- unlist(strsplit(SecondLetters, 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 < 4 | YYYLettersToTheRight < 4) {
+      leftspaces<-rep(" ",times=(4-YYYLettersToTheLeft))
+      rightspaces<-rep(" ",times=4-(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="")
+      SecondLetters<-motif
+      SecondMotifs[i,1]<-SecondLetters
+      SecondAccessionNumbers[i,1]<-SecondSubstrateSet[i,3]
+    }
+    
+    if(YYYLettersToTheLeft>3 && YYYLettersToTheRight>3){
+      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="")
+      SecondLetters<-motif
+      SecondMotifs[i,1]<-SecondLetters
+      SecondAccessionNumbers[i,1]<-SecondSubstrateSet[i,3]
+    }
+  }
+  
+  
+  #ITDmotifs=matrix(,nrow = nrow(ThirdSubstrateSet),ncol=1)
+  #ITDAccessionNumbers<-matrix(,nrow = nrow(ThirdSubstrateSet))
+  if(1==0){
+  for (i in 1:nrow(ThirdSubstrateSet)){
+    ITDletters<-ThirdSubstrateSet[i,7:15]
+    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 < 4 | YYYLettersToTheRight < 4) {
+      leftspaces<-rep(" ",times=(4-YYYLettersToTheLeft))
+      rightspaces<-rep(" ",times=4-(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>3 && YYYLettersToTheRight>3){
+      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]
+    }
+  }
+  }
+  names(FirstMotifs)<-FirstAccessionNumbers
+  names(SecondMotifs)<-SecondAccessionNumbers
+  #names(ITDmotifs)<-ITDAccessionNumbers
+}
+
+
+FirstMotifsFINAL<-FirstMotifs[!FirstMotifs %in% SecondMotifs]
+#FirstMotifsFINAL<-FirstMotifsFINAL[!FirstMotifsFINAL %in% ITDmotifs]
+FirstMotifsFINAL<-FirstMotifsFINAL[!duplicated(FirstMotifsFINAL)]
+
+
+# ITDmotifsFINAL<-ITDmotifs[!ITDmotifs %in% SecondMotifs]
+# ITDmotifsFINAL<-ITDmotifsFINAL[!ITDmotifsFINAL %in% FirstMotifs]
+# ITDmotifsFINAL<-ITDmotifsFINAL[!duplicated(ITDmotifsFINAL)]
+
+
+SecondMotifsFINAL<-SecondMotifs[!SecondMotifs %in% FirstMotifs]
+#SecondMotifsFINAL<-SecondMotifsFINAL[!SecondMotifsFINAL %in% ITDmotifs]
+SecondMotifsFINAL<-SecondMotifsFINAL[!duplicated(SecondMotifsFINAL)]
+
+
+columnalheader<-c(rep(NA,36))
+FirstFinalMatrix<-matrix(data =columnalheader,nrow = 1)
+
+for (k in 1:length(FirstMotifsFINAL)) {
+  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 2:ncol(Firstsubbackfreq)) {
+    AN <- as.character(Firstsubbackfreq[2, m])
+    #print(AN)}
+    if (grepl(pattern = AN,
+              x = names(FirstMotifsFINAL[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
+      FirstFinalMatrix<-rbind(FirstFinalMatrix,outputmatrix)
+      #      print(AN,outputmatrix)}
+    }
+  }
+}
+FirstFinalMatrix<-FirstFinalMatrix[!duplicated(FirstFinalMatrix),]
+
+#columnalheader<-c(rep(NA,36))
+#ITDFinalMatrix<-matrix(data =columnalheader,nrow = 1)
+
+if(1==0){
+  for (k in 1:length(ITDmotifsFINAL)) {
+    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(Thirdsubbackfreq)) {
+      AN <- as.character(Thirdsubbackfreq[1, m])
+      if (grepl(pattern = AN,
+                x = names(ITDmotifsFINAL[k]),
+                fixed = TRUE) == TRUE) {
+        outputmatrix <- as.character(Thirdsubbackfreq[, m])
+        outputmatrix <- matrix(outputmatrix, nrow = 1)
+        #with that accession number, find a match in the subbackfreq file and save it here
+        ITDFinalMatrix<-rbind(ITDFinalMatrix,outputmatrix)
+      }
+    }
+  }
+  ITDFinalMatrix<-ITDFinalMatrix[!duplicated(ITDFinalMatrix),]
+}
+
+columnalheader<-c(rep(NA,36))
+SecondFinalMatrix<-matrix(data =columnalheader,nrow = 1)
+
+for (k in 1:length(SecondMotifsFINAL)) {
+  #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(SecondMotifsFINAL[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
+      SecondFinalMatrix<-rbind(SecondFinalMatrix,outputmatrix)
+    }
+  }
+}
+SecondFinalMatrix<-SecondFinalMatrix[!duplicated(SecondFinalMatrix),]
+FTLoutputmatrix<-matrix(data=c(FirstMotifsFINAL,names(FirstMotifsFINAL)),ncol = 2)
+
+
+write.table(x=FTLoutputmatrix,
+            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)
+FirstFinalMatrix<-FirstFinalMatrix[2:nrow(FirstFinalMatrix),]
+write.table(x=FirstFinalMatrix,
+            file=First_unshared_subbackfreq,
+            quote=FALSE, sep=",",
+            row.names=FALSE,col.names = FALSE, na="", append=TRUE)
+
+############################################################################################################
+
+D835Youtputmatrix<-matrix(data=c(SecondMotifsFINAL,names(SecondMotifsFINAL)),ncol = 2)
+
+write.table(x=D835Youtputmatrix,
+            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)
+SecondFinalMatrix<-SecondFinalMatrix[2:nrow(SecondFinalMatrix),]  
+write.table(x=SecondFinalMatrix,
+            file=Second_unshared_subbackfreq,
+            quote=FALSE, sep=",",
+            row.names=FALSE,col.names = FALSE, na="", append=TRUE)
+
+############################################################################################################
+
+# ITDoutputmatrix<-matrix(data = c(ITDmotifsFINAL,names(ITDmotifsFINAL)),ncol = 2)
+# 
+# write.table(x=ITDoutputmatrix,
+#             file=Third_unshared_motifs_table,
+#             quote=FALSE, sep=",",
+#             row.names=FALSE,col.names = FALSE, na="", append=TRUE)
+# 
+# columnalheader<-c(as.character(Thirdsubbackfreq[1:36,1]))
+# columnalheader<-matrix(columnalheader,nrow = 1)
+# write.table(x=columnalheader,
+#             file=Third_unshared_subbackfreq,
+#             quote=FALSE, sep=",",
+#             row.names=FALSE,col.names = FALSE, na="", append=TRUE)
+# ITDFinalMatrix<-ITDFinalMatrix[2:nrow(ITDFinalMatrix),]
+# write.table(x=ITDFinalMatrix,
+#             file=Third_unshared_subbackfreq,
+#             quote=FALSE, sep=",",
+#             row.names=FALSE,col.names = FALSE, na="", append=TRUE)
\ No newline at end of file