# HG changeset patch
# User jfb
# Date 1555685848 14400
# Node ID dff99bed3f5687007b7f91bf89eb697abb731efe
# Parent  beba4066121ebd9d078cf60e8fa19a573b6ca9ec
Uploaded

diff -r beba4066121e -r dff99bed3f56 all stuff/Commonality and Difference finderMADE 7 TO 7 1-15-2019.R
--- a/all stuff/Commonality and Difference finderMADE 7 TO 7 1-15-2019.R	Wed Jan 16 14:33:39 2019 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1281 +0,0 @@
-#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
-
-#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("Galaxy63-BTK_PLUS-R1_Substrates.csv", stringsAsFactors=FALSE)
-Firstsubbackfreq<- read.csv("Galaxy64-BTK_PLUS-R1_SubstrateBackgroundFrequency.csv", header=FALSE, stringsAsFactors=FALSE)
-
-SecondSubstrateSet<- read.csv("Galaxy65-BTK_PLUS_R2_Substrates.csv", stringsAsFactors=FALSE)
-Secondsubbackfreq<- read.csv("Galaxy66-BTK_PLUS_R2_SubstrateBackgroundFrequency.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<-"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
-if (Are_You_Looking_For_Commonality=="YES"){
-  if (FullMotifsOnly_questionmark=="YES"){
-    FTLwtmotifs=matrix(,nrow = nrow(FirstSubstrateSet),ncol=1)
-    FTLwtAccessionNumbers=matrix(,nrow = nrow(FirstSubstrateSet),ncol=1)
-    leftspaces<-c()
-    rightspaces<-c()
-    for (i in 1:nrow(FirstSubstrateSet)){
-      FTLwtletters<-FirstSubstrateSet[i,4:18]
-      FTLwtletters<-FTLwtletters[FTLwtletters !="XXXXX"]
-      FTLwtletters<-paste(FTLwtletters, sep="", collapse="")
-      
-      
-      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 > 6 && YYYLettersToTheRight > 6) {
-        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="")
-        FTLwtletters<-motif
-        FTLwtmotifs[i,1]<-FTLwtletters
-        FTLwtAccessionNumbers[i,1]<-FirstSubstrateSet[i,3]
-        
-      }
-      
-    }
-    # FTLwtmotifs <- FTLwtmotifs[!is.na(FTLwtmotifs)]
-    # FTLwtmotifs<-matrix(FTLwtmotifs,ncol = 1)
-    # 
-    
-    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="")
-      
-      
-      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 > 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]
-        
-      }
-    }
-    
-    ITDmotifs=matrix(,nrow = nrow(ThirdSubstrateSet),ncol=1)
-    ITDAccessionNumbers<-matrix(,nrow = nrow(ThirdSubstrateSet))
-    
-    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 = ""))
-      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 > 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]<-ThirdSubstrateSet[i,3]
-        
-      }
-    }
-    
-  }
-  
-  ##############################################3
-  #Truncated only
-  if (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="")
-      
-      
-      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]
-      }
-      
-    }
-    
-    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="")
-      
-      
-      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
-        D835YAccessionNumbers[i,1]<-SecondSubstrateSet[i,3]
-        D835Ymotifs[i,1]<-D835letters
-      }
-    }
-    
-    ITDmotifs=matrix(,nrow = nrow(ThirdSubstrateSet),ncol=1)
-    ITDAccessionNumbers<-matrix(,nrow = nrow(ThirdSubstrateSet))
-    
-    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 = ""))
-      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
-        ITDAccessionNumbers[i,1]<-ThirdSubstrateSet[i,3]
-        ITDmotifs[i,1]<-ITDletters
-      }
-    }
-    
-  }
-  
-  ###############################################
-  #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]<-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(,nrow = nrow(ThirdSubstrateSet))
-    
-    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)
-    write.table(x=columnalheader,
-                file=Shared_subbackfreq_table,
-                quote=FALSE, sep=",",
-                row.names=FALSE,col.names = FALSE, na="", append=TRUE)
-    
-    FirstOverlapmotifs<-c()
-    for (i in 1:nrow(ITDmotifs)){
-      for (j in 1:nrow(D835Ymotifs)){
-        if (is.na(ITDmotifs[i,1])!=TRUE&&is.na(D835Ymotifs[j,1])!=TRUE){
-          if (ITDmotifs[i,1]==D835Ymotifs[j,1]){
-            FirstOverlapmotifs<-c(FirstOverlapmotifs,D835Ymotifs[j,1])
-          }
-        }
-      }
-    }
-    
-    AllAccessionNumbers<-c()
-    columnalheader<-c(rep(NA,36))
-    FinalMatrix<-matrix(data =columnalheader,nrow = 1)
-    
-    FinalMotifs<-c(rep(NA,20))
-    FinalMotifsMatrix<-matrix(data = FinalMotifs,nrow = 1)
-    
-    
-    for (l in 1:length(FirstOverlapmotifs)) {
-      AccessionNumber<-00000000000
-      for (k in 1:nrow(FTLwtmotifs)) {
-        AccessionNumber<-0000000000000
-        if(is.na(FTLwtmotifs[k])!=TRUE){
-          #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
-          if (FirstOverlapmotifs[l] == FTLwtmotifs[k]) {
-            substratematrix<-FirstSubstrateSet[k,1:20]
-            substratematrix<-as.matrix(substratematrix,nrow=1)
-            FinalMotifsMatrix<-rbind(FinalMotifsMatrix,substratematrix)
-            #when you find a match between the venn diagrams, save the substrate info you get into a matrix
-            
-            AccessionNumber <- as.character(FirstSubstrateSet[k, 3])
-            #then take the accession number 
-            
-            for (m in 1:ncol(Firstsubbackfreq)) {
-              AN <- as.character(Firstsubbackfreq[1, m])
-              if (grepl(pattern = AN,
-                        x = AccessionNumber,
-                        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
-                FinalMatrix<-rbind(FinalMatrix,outputmatrix)
-              }
-            }
-          }
-        }
-      }
-    }
-    
-    
-    TrueMatrix<-FinalMatrix[!duplicated(FinalMatrix),]
-    TrueFinalMotifsMatrix<-FinalMotifsMatrix[!duplicated(FinalMotifsMatrix),]
-    
-    TrueFinalMotifsMatrix<-TrueFinalMotifsMatrix[2:nrow(TrueFinalMotifsMatrix),]
-    TrueMatrix<-TrueMatrix[2:nrow(TrueMatrix),]
-    
-    write.table(
-      x = TrueFinalMotifsMatrix,
-      file = Shared_motifs_table,
-      quote = FALSE,
-      sep = ",",
-      row.names = FALSE,
-      col.names = TRUE,
-      na = "",
-      append = TRUE
-    )
-    
-    
-    write.table(
-      x = TrueMatrix,
-      file = Shared_subbackfreq_table,
-      quote = FALSE,
-      sep = ",",
-      row.names = FALSE,
-      col.names = FALSE,
-      na = "",
-      append = TRUE
-    )
-  }
-}
-
-if (Are_You_Looking_For_Commonality=="NO"){
-  if (FullMotifsOnly_questionmark=="YES"){
-    FTLwtmotifs=rep(NA,times=nrow(FirstSubstrateSet))
-    FTLwtAccessionNumbers=rep(NA,times=nrow(FirstSubstrateSet))
-    leftspaces<-c()
-    rightspaces<-c()
-    for (i in 1:nrow(FirstSubstrateSet)){
-      FTLwtletters<-FirstSubstrateSet[i,4:18]
-      FTLwtletters<-FTLwtletters[FTLwtletters !="XXXXX"]
-      FTLwtletters<-paste(FTLwtletters, sep="", collapse="")
-      
-      
-      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 > 6 && YYYLettersToTheRight > 6) {
-        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="")
-        FTLwtletters<-motif
-        FTLwtmotifs[i]<-FTLwtletters
-        FTLwtAccessionNumbers[i]<-FirstSubstrateSet[i,3]
-      }
-      
-    }
-    # FTLwtmotifs <- FTLwtmotifs[!is.na(FTLwtmotifs)]
-    # FTLwtmotifs<-matrix(FTLwtmotifs,ncol = 1)
-    # 
-    
-    D835Ymotifs=rep(NA,times=nrow(FirstSubstrateSet))
-    D835YAccessionNumbers=rep(NA,times=nrow(FirstSubstrateSet))
-    
-    for (i in 1:nrow(SecondSubstrateSet)){
-      D835letters<-SecondSubstrateSet[i,4:18]
-      D835letters<-D835letters[D835letters !="XXXXX"]
-      D835letters<-paste(D835letters, sep="", collapse="")
-      
-      
-      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 > 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]<-D835letters
-        D835YAccessionNumbers[i]<-SecondSubstrateSet[i,3]
-      }
-    }
-    
-    ITDmotifs=rep(NA,times=nrow(FirstSubstrateSet))
-    ITDAccessionNumbers=rep(NA,times=nrow(FirstSubstrateSet))
-    
-    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 = ""))
-      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 > 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]<-ITDletters
-        ITDAccessionNumbers[i]<-ThirdSubstrateSet[i,3]
-        
-      }
-    }
-    names(ITDmotifs)<-ITDAccessionNumbers
-    names(D835Ymotifs)<-D835YAccessionNumbers
-    names(FTLwtmotifs)<-FTLwtAccessionNumbers
-  }
-  
-  
-  ##############################################3
-  #Truncated only
-  if (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="")
-      
-      
-      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]
-      }
-      
-    }
-    
-    D835Ymotifs=matrix(,nrow = nrow(SecondSubstrateSet),ncol=1)
-    D835YAccessionNumbers<-matrix(,nrow = nrow(SecondSubstrateSet),ncol = 1)
-    i=2
-    for (i in 1:nrow(SecondSubstrateSet)){
-      D835letters<-SecondSubstrateSet[i,4:18]
-      D835letters<-D835letters[D835letters !="XXXXX"]
-      D835letters<-paste(D835letters, sep="", collapse="")
-      
-      
-      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
-        D835YAccessionNumbers[i,1]<-SecondSubstrateSet[i,3]
-        D835Ymotifs[i,1]<-D835letters
-      }
-    }
-    
-    ITDmotifs=matrix(,nrow = nrow(ThirdSubstrateSet),ncol=1)
-    ITDAccessionNumbers<-matrix(,nrow = nrow(ThirdSubstrateSet))
-    
-    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 = ""))
-      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
-        ITDAccessionNumbers[i,1]<-ThirdSubstrateSet[i,3]
-        ITDmotifs[i,1]<-ITDletters
-      }
-    }
-    names(FTLwtmotifs)<-FTLwtAccessionNumbers
-    names(D835Ymotifs)<-D835YAccessionNumbers
-    names(ITDmotifs)<-ITDAccessionNumbers
-  }
-  
-  ###############################################
-  #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]<-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(,nrow = nrow(ThirdSubstrateSet))
-    
-    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]
-      }
-    }
-    names(FTLwtmotifs)<-FTLwtAccessionNumbers
-    names(D835Ymotifs)<-D835YAccessionNumbers
-    names(ITDmotifs)<-ITDAccessionNumbers
-  }
-  
-  
-  FTLwtmotifsFINAL<-FTLwtmotifs[!FTLwtmotifs %in% D835Ymotifs]
-  FTLwtmotifsFINAL<-FTLwtmotifsFINAL[!FTLwtmotifsFINAL %in% ITDmotifs]
-  FTLwtmotifsFINAL<-FTLwtmotifsFINAL[!duplicated(FTLwtmotifsFINAL)]
-  
-  
-  ITDmotifsFINAL<-ITDmotifs[!ITDmotifs %in% D835Ymotifs]
-  ITDmotifsFINAL<-ITDmotifsFINAL[!ITDmotifsFINAL %in% FTLwtmotifs]
-  ITDmotifsFINAL<-ITDmotifsFINAL[!duplicated(ITDmotifsFINAL)]
-  
-  
-  D835YmotifsFINAL<-D835Ymotifs[!D835Ymotifs %in% FTLwtmotifs]
-  D835YmotifsFINAL<-D835YmotifsFINAL[!D835YmotifsFINAL %in% ITDmotifs]
-  D835YmotifsFINAL<-D835YmotifsFINAL[!duplicated(D835YmotifsFINAL)]
-  
-  
-  columnalheader<-c(rep(NA,35))
-  FTLFinalMatrix<-matrix(data =columnalheader,nrow = 1)
-  
-  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),]
-  
-  columnalheader<-c(rep(NA,35))
-  ITDFinalMatrix<-matrix(data =columnalheader,nrow = 1)
-  
-  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,35))
-  D835YFinalMatrix<-matrix(data =columnalheader,nrow = 1)
-  
-  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),]
-  
-  FTLoutputmatrix<-matrix(data=c(FTLwtmotifsFINAL,names(FTLwtmotifsFINAL)),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("Accession Numbers",as.character(Thirdsubbackfreq[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)
-  
-  ############################################################################################################
-  
-  D835Youtputmatrix<-matrix(data=c(D835YmotifsFINAL,names(D835YmotifsFINAL)),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("Accession Numbers",as.character(Thirdsubbackfreq[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)
-  
-  ############################################################################################################
-  
-  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("Accession Numbers",as.character(Thirdsubbackfreq[1:35,1]))
-  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)
-  
-  write.table(x=ITDFinalMatrix,
-              file=Third_unshared_subbackfreq,
-              quote=FALSE, sep=",",
-              row.names=FALSE,col.names = FALSE, na="", append=TRUE)
-  
-}
-
-# if (Are_You_Looking_For_Commonality=="NO"){
-#   
-#   
-#   FTLwtmotifsFULLMATRIX<-cbind(FTLwtmotifs,FTLwtAccessionNumbers)
-#   ITDmotifsFULLMATRIX<-cbind(ITDmotifs,ITDAccessionNumbers)
-#   D835YmotifsFULLMATRIX<-cbind(D835Ymotifs,D835YAccessionNumbers)
-#   # ?duplicated
-# 
-#   FTLwtmotifsFINAL<-FTLwtmotifs[!FTLwtmotifs %in% D835Ymotifs]
-#   FTLwtmotifsFINAL<-FTLwtmotifsFINAL[!FTLwtmotifsFINAL %in% ITDmotifs]
-#   FTLwtmotifsFINAL<-matrix(data=FTLwtmotifsFINAL, ncol = 1)
-# 
-#   ITDmotifsFINAL<-ITDmotifs[!ITDmotifs %in% D835Ymotifs]
-#   ITDmotifsFINAL<-ITDmotifsFINAL[!ITDmotifsFINAL %in% FTLwtmotifs]
-#   ITDmotifsFINAL<-matrix(data=ITDmotifsFINAL, ncol = 1)
-# 
-#   D835YmotifsFINAL<-D835Ymotifs[!D835Ymotifs %in% FTLwtmotifs]
-#   D835YmotifsFINAL<-D835YmotifsFINAL[!D835YmotifsFINAL %in% ITDmotifs]
-#   D835YmotifsFINAL<-matrix(data=D835YmotifsFINAL, ncol = 1)
-#   
-#   FTLnondupeAccessionNumbers<-c()
-#   
-#   for (z in 1:nrow(FTLwtmotifsFINAL)) {
-#     for (w in 1:nrow(FTLwtmotifsFULLMATRIX)) {
-#       if (is.na(FTLwtmotifsFULLMATRIX[w,1])!=TRUE)
-#         if (FTLwtmotifsFINAL[z]==FTLwtmotifsFULLMATRIX[w,1]){
-#           FTLnondupeAccessionNumbers<-c(FTLnondupeAccessionNumbers,FTLwtmotifsFULLMATRIX[w,2])
-#         }
-#     }  
-#   }
-# 
-#   
-#   #find accession numbers here, put a matrix of those things, amino acid %, but only after I've unduped them
-#   FTLnondupeAccessionNumbers<-FTLnondupeAccessionNumbers[!duplicated(FTLnondupeAccessionNumbers)]
-#   
-#   columnalheader<-c(rep(NA,35))
-#   FTLFinalMatrix<-matrix(data =columnalheader,nrow = 1)
-#   
-#   for (k in 1:length(FTLnondupeAccessionNumbers)) {
-#     #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 = FTLnondupeAccessionNumbers[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)
-#       }
-#     }
-#   }
-#   ITDnondupeAccessionNumbers<-c()
-#   
-#   for (z in 1:nrow(ITDmotifsFINAL)) {
-#     for (w in 1:nrow(ITDmotifsFULLMATRIX)) {
-#       if (is.na(ITDmotifsFULLMATRIX[w,1])!=TRUE)
-#         if (ITDmotifsFINAL[z]==ITDmotifsFULLMATRIX[w,1]){
-#           ITDnondupeAccessionNumbers<-c(ITDnondupeAccessionNumbers,ITDmotifsFULLMATRIX[w,2])
-#         }
-#     }  
-#   }
-#   
-#   
-#   #find accession numbers here, put a matrix of those things, amino acid %, but only after I've unduped them
-#   ITDnondupeAccessionNumbers<-ITDnondupeAccessionNumbers[!duplicated(ITDnondupeAccessionNumbers)]
-#   
-#   columnalheader<-c(rep(NA,35))
-#   ITDFinalMatrix<-matrix(data =columnalheader,nrow = 1)
-#   
-#   for (k in 1:length(ITDnondupeAccessionNumbers)) {
-#     #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 = ITDnondupeAccessionNumbers[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)
-#       }
-#     }
-#   }
-#   
-#   
-#   D835YnondupeAccessionNumbers<-c()
-#   
-#   for (z in 1:nrow(D835YmotifsFINAL)) {
-#     for (w in 1:nrow(D835YmotifsFULLMATRIX)) {
-#       if (is.na(D835YmotifsFULLMATRIX[w,1])!=TRUE)
-#         if (D835YmotifsFINAL[z]==D835YmotifsFULLMATRIX[w,1]){
-#           D835YnondupeAccessionNumbers<-c(D835YnondupeAccessionNumbers,D835YmotifsFULLMATRIX[w,2])
-#         }
-#     }  
-#   }
-#   
-#   
-#   #find accession numbers here, put a matrix of those things, amino acid %, but only after I've unduped them
-#   D835YnondupeAccessionNumbers<-D835YnondupeAccessionNumbers[!duplicated(D835YnondupeAccessionNumbers)]
-#   
-#   columnalheader<-c(rep(NA,35))
-#   D835YFinalMatrix<-matrix(data =columnalheader,nrow = 1)
-#   
-#   for (k in 1:length(D835YnondupeAccessionNumbers)) {
-#     #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 = D835YnondupeAccessionNumbers[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)
-#       }
-#     }
-#   }
-#   
-#   
-# 
-#   # FinalFTLmotifs<-FTLwtmotifsFINAL[!duplicated(FTLwtmotifsFINAL)]
-#   # FinalFTLAccessionNumbers<-FTLnondupeAccessionNumbers[!duplicated(FTLnondupeAccessionNumbers)]
-#   # necessaryNAs<-rep(NA,times=(length(FinalFTLmotifs)-length(FinalFTLAccessionNumbers)))
-#   # FinalFTLAccessionNumbers<-c(FinalFTLAccessionNumbers,necessaryNAs)
-#   # TRUEFTLoutputmatrix<-cbind(FinalFTLmotifs,FinalFTLAccessionNumbers)
-#   # TRUEFTLoutputmatrix
-# 
-#   write.table(x=FTLwtmotifsFINAL,
-#               file=First_unshared_motifs_table,
-#               quote=FALSE, sep=",",
-#               row.names=FALSE,col.names = FALSE, na="", append=TRUE)
-#   
-#   columnalheader<-c("Accession Numbers",as.character(Thirdsubbackfreq[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)
-#   
-# 
-#   
-#   
-#   
-#   
-#   
-#   
-#   
-#   
-#   
-#   
-#   write.table(x=D835YmotifsFINAL,
-#               file=Second_unshared_motifs_table,
-#               quote=FALSE, sep=",",
-#               row.names=FALSE,col.names = FALSE, na="", append=TRUE)
-#   
-#   columnalheader<-c("Accession Numbers",as.character(Thirdsubbackfreq[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)
-#   
-#   
-#   
-#   
-#   
-#   
-#   
-#   
-#   
-#   
-#   
-#   
-#   
-#   
-#   
-#   
-#   write.table(x=ITDmotifsFINAL,
-#               file=Third_unshared_motifs_table,
-#               quote=FALSE, sep=",",
-#               row.names=FALSE,col.names = FALSE, na="", append=TRUE)
-#   
-#   columnalheader<-c("Accession Numbers",as.character(Thirdsubbackfreq[1:35,1]))
-#   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)
-#   
-#   write.table(x=ITDFinalMatrix,
-#               file=Third_unshared_subbackfreq,
-#               quote=FALSE, sep=",",
-#               row.names=FALSE,col.names = FALSE, na="", append=TRUE)
-#   
-#   
-#   
-#   
-#   
-#   
-# }
diff -r beba4066121e -r dff99bed3f56 all stuff/Commonality and Difference finderMADE 7 TO 7.R
--- a/all stuff/Commonality and Difference finderMADE 7 TO 7.R	Wed Jan 16 14:33:39 2019 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1281 +0,0 @@
-#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
-
-#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"
-
-
-#put the names of your input files here
-FirstSubstrateSet<- read.csv("Galaxy63-BTK_PLUS-R1_Substrates.csv", stringsAsFactors=FALSE)
-Firstsubbackfreq<- read.csv("Galaxy64-BTK_PLUS-R1_SubstrateBackgroundFrequency.csv", header=FALSE, stringsAsFactors=FALSE)
-
-SecondSubstrateSet<- read.csv("Galaxy65-BTK_PLUS_R2_Substrates.csv", stringsAsFactors=FALSE)
-Secondsubbackfreq<- read.csv("Galaxy66-BTK_PLUS_R2_SubstrateBackgroundFrequency.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<-"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
-if (Are_You_Looking_For_Commonality=="YES"){
-  if (FullMotifsOnly_questionmark=="YES"){
-    FTLwtmotifs=matrix(,nrow = nrow(FirstSubstrateSet),ncol=1)
-    FTLwtAccessionNumbers=matrix(,nrow = nrow(FirstSubstrateSet),ncol=1)
-    leftspaces<-c()
-    rightspaces<-c()
-    for (i in 1:nrow(FirstSubstrateSet)){
-      FTLwtletters<-FirstSubstrateSet[i,4:18]
-      FTLwtletters<-FTLwtletters[FTLwtletters !="XXXXX"]
-      FTLwtletters<-paste(FTLwtletters, sep="", collapse="")
-      
-      
-      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 > 6 && YYYLettersToTheRight > 6) {
-        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="")
-        FTLwtletters<-motif
-        FTLwtmotifs[i,1]<-FTLwtletters
-        FTLwtAccessionNumbers[i,1]<-FirstSubstrateSet[i,3]
-        
-      }
-      
-    }
-    # FTLwtmotifs <- FTLwtmotifs[!is.na(FTLwtmotifs)]
-    # FTLwtmotifs<-matrix(FTLwtmotifs,ncol = 1)
-    # 
-    
-    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="")
-      
-      
-      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 > 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]
-        
-      }
-    }
-    
-    ITDmotifs=matrix(,nrow = nrow(ThirdSubstrateSet),ncol=1)
-    ITDAccessionNumbers<-matrix(,nrow = nrow(ThirdSubstrateSet))
-    
-    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 = ""))
-      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 > 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]<-ThirdSubstrateSet[i,3]
-        
-      }
-    }
-    
-  }
-  
-  ##############################################3
-  #Truncated only
-  if (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="")
-      
-      
-      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]
-      }
-      
-    }
-    
-    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="")
-      
-      
-      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
-        D835YAccessionNumbers[i,1]<-SecondSubstrateSet[i,3]
-        D835Ymotifs[i,1]<-D835letters
-      }
-    }
-    
-    ITDmotifs=matrix(,nrow = nrow(ThirdSubstrateSet),ncol=1)
-    ITDAccessionNumbers<-matrix(,nrow = nrow(ThirdSubstrateSet))
-    
-    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 = ""))
-      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
-        ITDAccessionNumbers[i,1]<-ThirdSubstrateSet[i,3]
-        ITDmotifs[i,1]<-ITDletters
-      }
-    }
-    
-  }
-  
-  ###############################################
-  #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]<-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(,nrow = nrow(ThirdSubstrateSet))
-    
-    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)
-    write.table(x=columnalheader,
-                file=Shared_subbackfreq_table,
-                quote=FALSE, sep=",",
-                row.names=FALSE,col.names = FALSE, na="", append=TRUE)
-    
-    FirstOverlapmotifs<-c()
-    for (i in 1:nrow(ITDmotifs)){
-      for (j in 1:nrow(D835Ymotifs)){
-        if (is.na(ITDmotifs[i,1])!=TRUE&&is.na(D835Ymotifs[j,1])!=TRUE){
-          if (ITDmotifs[i,1]==D835Ymotifs[j,1]){
-            FirstOverlapmotifs<-c(FirstOverlapmotifs,D835Ymotifs[j,1])
-          }
-        }
-      }
-    }
-    
-    AllAccessionNumbers<-c()
-    columnalheader<-c(rep(NA,36))
-    FinalMatrix<-matrix(data =columnalheader,nrow = 1)
-    
-    FinalMotifs<-c(rep(NA,20))
-    FinalMotifsMatrix<-matrix(data = FinalMotifs,nrow = 1)
-    
-    
-    for (l in 1:length(FirstOverlapmotifs)) {
-      AccessionNumber<-00000000000
-      for (k in 1:nrow(FTLwtmotifs)) {
-        AccessionNumber<-0000000000000
-        if(is.na(FTLwtmotifs[k])!=TRUE){
-          #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
-          if (FirstOverlapmotifs[l] == FTLwtmotifs[k]) {
-            substratematrix<-FirstSubstrateSet[k,1:20]
-            substratematrix<-as.matrix(substratematrix,nrow=1)
-            FinalMotifsMatrix<-rbind(FinalMotifsMatrix,substratematrix)
-            #when you find a match between the venn diagrams, save the substrate info you get into a matrix
-            
-            AccessionNumber <- as.character(FirstSubstrateSet[k, 3])
-            #then take the accession number 
-            
-            for (m in 1:ncol(Firstsubbackfreq)) {
-              AN <- as.character(Firstsubbackfreq[1, m])
-              if (grepl(pattern = AN,
-                        x = AccessionNumber,
-                        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
-                FinalMatrix<-rbind(FinalMatrix,outputmatrix)
-              }
-            }
-          }
-        }
-      }
-    }
-    
-    
-    TrueMatrix<-FinalMatrix[!duplicated(FinalMatrix),]
-    TrueFinalMotifsMatrix<-FinalMotifsMatrix[!duplicated(FinalMotifsMatrix),]
-    
-    TrueFinalMotifsMatrix<-TrueFinalMotifsMatrix[2:nrow(TrueFinalMotifsMatrix),]
-    TrueMatrix<-TrueMatrix[2:nrow(TrueMatrix),]
-    
-    write.table(
-      x = TrueFinalMotifsMatrix,
-      file = Shared_motifs_table,
-      quote = FALSE,
-      sep = ",",
-      row.names = FALSE,
-      col.names = TRUE,
-      na = "",
-      append = TRUE
-    )
-    
-    
-    write.table(
-      x = TrueMatrix,
-      file = Shared_subbackfreq_table,
-      quote = FALSE,
-      sep = ",",
-      row.names = FALSE,
-      col.names = FALSE,
-      na = "",
-      append = TRUE
-    )
-  }
-}
-
-if (Are_You_Looking_For_Commonality=="NO"){
-  if (FullMotifsOnly_questionmark=="YES"){
-    FTLwtmotifs=rep(NA,times=nrow(FirstSubstrateSet))
-    FTLwtAccessionNumbers=rep(NA,times=nrow(FirstSubstrateSet))
-    leftspaces<-c()
-    rightspaces<-c()
-    for (i in 1:nrow(FirstSubstrateSet)){
-      FTLwtletters<-FirstSubstrateSet[i,4:18]
-      FTLwtletters<-FTLwtletters[FTLwtletters !="XXXXX"]
-      FTLwtletters<-paste(FTLwtletters, sep="", collapse="")
-      
-      
-      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 > 6 && YYYLettersToTheRight > 6) {
-        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="")
-        FTLwtletters<-motif
-        FTLwtmotifs[i]<-FTLwtletters
-        FTLwtAccessionNumbers[i]<-FirstSubstrateSet[i,3]
-      }
-      
-    }
-    # FTLwtmotifs <- FTLwtmotifs[!is.na(FTLwtmotifs)]
-    # FTLwtmotifs<-matrix(FTLwtmotifs,ncol = 1)
-    # 
-    
-    D835Ymotifs=rep(NA,times=nrow(FirstSubstrateSet))
-    D835YAccessionNumbers=rep(NA,times=nrow(FirstSubstrateSet))
-    
-    for (i in 1:nrow(SecondSubstrateSet)){
-      D835letters<-SecondSubstrateSet[i,4:18]
-      D835letters<-D835letters[D835letters !="XXXXX"]
-      D835letters<-paste(D835letters, sep="", collapse="")
-      
-      
-      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 > 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]<-D835letters
-        D835YAccessionNumbers[i]<-SecondSubstrateSet[i,3]
-      }
-    }
-    
-    ITDmotifs=rep(NA,times=nrow(FirstSubstrateSet))
-    ITDAccessionNumbers=rep(NA,times=nrow(FirstSubstrateSet))
-    
-    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 = ""))
-      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 > 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]<-ITDletters
-        ITDAccessionNumbers[i]<-ThirdSubstrateSet[i,3]
-        
-      }
-    }
-    names(ITDmotifs)<-ITDAccessionNumbers
-    names(D835Ymotifs)<-D835YAccessionNumbers
-    names(FTLwtmotifs)<-FTLwtAccessionNumbers
-  }
-  
-  
-  ##############################################3
-  #Truncated only
-  if (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="")
-      
-      
-      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]
-      }
-      
-    }
-    
-    D835Ymotifs=matrix(,nrow = nrow(SecondSubstrateSet),ncol=1)
-    D835YAccessionNumbers<-matrix(,nrow = nrow(SecondSubstrateSet),ncol = 1)
-    i=2
-    for (i in 1:nrow(SecondSubstrateSet)){
-      D835letters<-SecondSubstrateSet[i,4:18]
-      D835letters<-D835letters[D835letters !="XXXXX"]
-      D835letters<-paste(D835letters, sep="", collapse="")
-      
-      
-      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
-        D835YAccessionNumbers[i,1]<-SecondSubstrateSet[i,3]
-        D835Ymotifs[i,1]<-D835letters
-      }
-    }
-    
-    ITDmotifs=matrix(,nrow = nrow(ThirdSubstrateSet),ncol=1)
-    ITDAccessionNumbers<-matrix(,nrow = nrow(ThirdSubstrateSet))
-    
-    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 = ""))
-      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
-        ITDAccessionNumbers[i,1]<-ThirdSubstrateSet[i,3]
-        ITDmotifs[i,1]<-ITDletters
-      }
-    }
-    names(FTLwtmotifs)<-FTLwtAccessionNumbers
-    names(D835Ymotifs)<-D835YAccessionNumbers
-    names(ITDmotifs)<-ITDAccessionNumbers
-  }
-  
-  ###############################################
-  #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]<-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(,nrow = nrow(ThirdSubstrateSet))
-    
-    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]
-      }
-    }
-    names(FTLwtmotifs)<-FTLwtAccessionNumbers
-    names(D835Ymotifs)<-D835YAccessionNumbers
-    names(ITDmotifs)<-ITDAccessionNumbers
-  }
-  
-  
-  FTLwtmotifsFINAL<-FTLwtmotifs[!FTLwtmotifs %in% D835Ymotifs]
-  FTLwtmotifsFINAL<-FTLwtmotifsFINAL[!FTLwtmotifsFINAL %in% ITDmotifs]
-  FTLwtmotifsFINAL<-FTLwtmotifsFINAL[!duplicated(FTLwtmotifsFINAL)]
-  
-  
-  ITDmotifsFINAL<-ITDmotifs[!ITDmotifs %in% D835Ymotifs]
-  ITDmotifsFINAL<-ITDmotifsFINAL[!ITDmotifsFINAL %in% FTLwtmotifs]
-  ITDmotifsFINAL<-ITDmotifsFINAL[!duplicated(ITDmotifsFINAL)]
-  
-  
-  D835YmotifsFINAL<-D835Ymotifs[!D835Ymotifs %in% FTLwtmotifs]
-  D835YmotifsFINAL<-D835YmotifsFINAL[!D835YmotifsFINAL %in% ITDmotifs]
-  D835YmotifsFINAL<-D835YmotifsFINAL[!duplicated(D835YmotifsFINAL)]
-  
-  
-  columnalheader<-c(rep(NA,35))
-  FTLFinalMatrix<-matrix(data =columnalheader,nrow = 1)
-  
-  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),]
-  
-  columnalheader<-c(rep(NA,35))
-  ITDFinalMatrix<-matrix(data =columnalheader,nrow = 1)
-  
-  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,35))
-  D835YFinalMatrix<-matrix(data =columnalheader,nrow = 1)
-  
-  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),]
-  
-  FTLoutputmatrix<-matrix(data=c(FTLwtmotifsFINAL,names(FTLwtmotifsFINAL)),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("Accession Numbers",as.character(Thirdsubbackfreq[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)
-  
-  ############################################################################################################
-  
-  D835Youtputmatrix<-matrix(data=c(D835YmotifsFINAL,names(D835YmotifsFINAL)),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("Accession Numbers",as.character(Thirdsubbackfreq[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)
-  
-  ############################################################################################################
-  
-  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("Accession Numbers",as.character(Thirdsubbackfreq[1:35,1]))
-  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)
-  
-  write.table(x=ITDFinalMatrix,
-              file=Third_unshared_subbackfreq,
-              quote=FALSE, sep=",",
-              row.names=FALSE,col.names = FALSE, na="", append=TRUE)
-  
-}
-
-# if (Are_You_Looking_For_Commonality=="NO"){
-#   
-#   
-#   FTLwtmotifsFULLMATRIX<-cbind(FTLwtmotifs,FTLwtAccessionNumbers)
-#   ITDmotifsFULLMATRIX<-cbind(ITDmotifs,ITDAccessionNumbers)
-#   D835YmotifsFULLMATRIX<-cbind(D835Ymotifs,D835YAccessionNumbers)
-#   # ?duplicated
-# 
-#   FTLwtmotifsFINAL<-FTLwtmotifs[!FTLwtmotifs %in% D835Ymotifs]
-#   FTLwtmotifsFINAL<-FTLwtmotifsFINAL[!FTLwtmotifsFINAL %in% ITDmotifs]
-#   FTLwtmotifsFINAL<-matrix(data=FTLwtmotifsFINAL, ncol = 1)
-# 
-#   ITDmotifsFINAL<-ITDmotifs[!ITDmotifs %in% D835Ymotifs]
-#   ITDmotifsFINAL<-ITDmotifsFINAL[!ITDmotifsFINAL %in% FTLwtmotifs]
-#   ITDmotifsFINAL<-matrix(data=ITDmotifsFINAL, ncol = 1)
-# 
-#   D835YmotifsFINAL<-D835Ymotifs[!D835Ymotifs %in% FTLwtmotifs]
-#   D835YmotifsFINAL<-D835YmotifsFINAL[!D835YmotifsFINAL %in% ITDmotifs]
-#   D835YmotifsFINAL<-matrix(data=D835YmotifsFINAL, ncol = 1)
-#   
-#   FTLnondupeAccessionNumbers<-c()
-#   
-#   for (z in 1:nrow(FTLwtmotifsFINAL)) {
-#     for (w in 1:nrow(FTLwtmotifsFULLMATRIX)) {
-#       if (is.na(FTLwtmotifsFULLMATRIX[w,1])!=TRUE)
-#         if (FTLwtmotifsFINAL[z]==FTLwtmotifsFULLMATRIX[w,1]){
-#           FTLnondupeAccessionNumbers<-c(FTLnondupeAccessionNumbers,FTLwtmotifsFULLMATRIX[w,2])
-#         }
-#     }  
-#   }
-# 
-#   
-#   #find accession numbers here, put a matrix of those things, amino acid %, but only after I've unduped them
-#   FTLnondupeAccessionNumbers<-FTLnondupeAccessionNumbers[!duplicated(FTLnondupeAccessionNumbers)]
-#   
-#   columnalheader<-c(rep(NA,35))
-#   FTLFinalMatrix<-matrix(data =columnalheader,nrow = 1)
-#   
-#   for (k in 1:length(FTLnondupeAccessionNumbers)) {
-#     #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 = FTLnondupeAccessionNumbers[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)
-#       }
-#     }
-#   }
-#   ITDnondupeAccessionNumbers<-c()
-#   
-#   for (z in 1:nrow(ITDmotifsFINAL)) {
-#     for (w in 1:nrow(ITDmotifsFULLMATRIX)) {
-#       if (is.na(ITDmotifsFULLMATRIX[w,1])!=TRUE)
-#         if (ITDmotifsFINAL[z]==ITDmotifsFULLMATRIX[w,1]){
-#           ITDnondupeAccessionNumbers<-c(ITDnondupeAccessionNumbers,ITDmotifsFULLMATRIX[w,2])
-#         }
-#     }  
-#   }
-#   
-#   
-#   #find accession numbers here, put a matrix of those things, amino acid %, but only after I've unduped them
-#   ITDnondupeAccessionNumbers<-ITDnondupeAccessionNumbers[!duplicated(ITDnondupeAccessionNumbers)]
-#   
-#   columnalheader<-c(rep(NA,35))
-#   ITDFinalMatrix<-matrix(data =columnalheader,nrow = 1)
-#   
-#   for (k in 1:length(ITDnondupeAccessionNumbers)) {
-#     #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 = ITDnondupeAccessionNumbers[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)
-#       }
-#     }
-#   }
-#   
-#   
-#   D835YnondupeAccessionNumbers<-c()
-#   
-#   for (z in 1:nrow(D835YmotifsFINAL)) {
-#     for (w in 1:nrow(D835YmotifsFULLMATRIX)) {
-#       if (is.na(D835YmotifsFULLMATRIX[w,1])!=TRUE)
-#         if (D835YmotifsFINAL[z]==D835YmotifsFULLMATRIX[w,1]){
-#           D835YnondupeAccessionNumbers<-c(D835YnondupeAccessionNumbers,D835YmotifsFULLMATRIX[w,2])
-#         }
-#     }  
-#   }
-#   
-#   
-#   #find accession numbers here, put a matrix of those things, amino acid %, but only after I've unduped them
-#   D835YnondupeAccessionNumbers<-D835YnondupeAccessionNumbers[!duplicated(D835YnondupeAccessionNumbers)]
-#   
-#   columnalheader<-c(rep(NA,35))
-#   D835YFinalMatrix<-matrix(data =columnalheader,nrow = 1)
-#   
-#   for (k in 1:length(D835YnondupeAccessionNumbers)) {
-#     #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 = D835YnondupeAccessionNumbers[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)
-#       }
-#     }
-#   }
-#   
-#   
-# 
-#   # FinalFTLmotifs<-FTLwtmotifsFINAL[!duplicated(FTLwtmotifsFINAL)]
-#   # FinalFTLAccessionNumbers<-FTLnondupeAccessionNumbers[!duplicated(FTLnondupeAccessionNumbers)]
-#   # necessaryNAs<-rep(NA,times=(length(FinalFTLmotifs)-length(FinalFTLAccessionNumbers)))
-#   # FinalFTLAccessionNumbers<-c(FinalFTLAccessionNumbers,necessaryNAs)
-#   # TRUEFTLoutputmatrix<-cbind(FinalFTLmotifs,FinalFTLAccessionNumbers)
-#   # TRUEFTLoutputmatrix
-# 
-#   write.table(x=FTLwtmotifsFINAL,
-#               file=First_unshared_motifs_table,
-#               quote=FALSE, sep=",",
-#               row.names=FALSE,col.names = FALSE, na="", append=TRUE)
-#   
-#   columnalheader<-c("Accession Numbers",as.character(Thirdsubbackfreq[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)
-#   
-# 
-#   
-#   
-#   
-#   
-#   
-#   
-#   
-#   
-#   
-#   
-#   write.table(x=D835YmotifsFINAL,
-#               file=Second_unshared_motifs_table,
-#               quote=FALSE, sep=",",
-#               row.names=FALSE,col.names = FALSE, na="", append=TRUE)
-#   
-#   columnalheader<-c("Accession Numbers",as.character(Thirdsubbackfreq[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)
-#   
-#   
-#   
-#   
-#   
-#   
-#   
-#   
-#   
-#   
-#   
-#   
-#   
-#   
-#   
-#   
-#   write.table(x=ITDmotifsFINAL,
-#               file=Third_unshared_motifs_table,
-#               quote=FALSE, sep=",",
-#               row.names=FALSE,col.names = FALSE, na="", append=TRUE)
-#   
-#   columnalheader<-c("Accession Numbers",as.character(Thirdsubbackfreq[1:35,1]))
-#   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)
-#   
-#   write.table(x=ITDFinalMatrix,
-#               file=Third_unshared_subbackfreq,
-#               quote=FALSE, sep=",",
-#               row.names=FALSE,col.names = FALSE, na="", append=TRUE)
-#   
-#   
-#   
-#   
-#   
-#   
-# }
diff -r beba4066121e -r dff99bed3f56 all stuff/Difference finder MADE 7 TO 7 4-18-2019.R
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/all stuff/Difference finder MADE 7 TO 7 4-18-2019.R	Fri Apr 19 10:57:28 2019 -0400
@@ -0,0 +1,351 @@
+#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
+
+#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("Galaxy1071-(17A_TiO2_Substrates.csv).csv", stringsAsFactors=FALSE)
+Firstsubbackfreq<- read.csv("Galaxy1072-(17A_TiO2_SubstrateBackgroundFrequency.csv).csv", header=FALSE, stringsAsFactors=FALSE)
+
+SecondSubstrateSet<- read.csv("Galaxy1073-(17A_FeNTA_Substrates.csv) (1).csv", stringsAsFactors=FALSE)
+Secondsubbackfreq<- read.csv("Galaxy1074-(17A_FeNTA_SubstrateBackgroundFrequency.csv).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<-"17A TIo2 without FeNTA.csv"
+First_unshared_subbackfreq<-"17A TIo2 without FeNTA sbf.csv"
+
+Second_unshared_motifs_table<-"17A FeNTA without TIo2.csv"
+Second_unshared_subbackfreq<-"17A FeNTA without TIo2 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.
+####################################################################################################################################
+
+
+
+
+
+# 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)
+    
+    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)
+  
+  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),]
+  
+  columnalheader<-c(rep(NA,36))
+  D835YFinalMatrix<-matrix(data =columnalheader,nrow = 1)
+  
+  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),]
+  
+  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,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)
+  
+  ############################################################################################################
+  
+  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)
+}
+
diff -r beba4066121e -r dff99bed3f56 all stuff/Difference finderMADE 7 TO 7 1-15-2019.R
--- a/all stuff/Difference finderMADE 7 TO 7 1-15-2019.R	Wed Jan 16 14:33:39 2019 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,351 +0,0 @@
-#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
-
-#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)
-    
-    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]<-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]
-      }
-    }
-    
-    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)
-  
-  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),]
-  
-  columnalheader<-c(rep(NA,36))
-  D835YFinalMatrix<-matrix(data =columnalheader,nrow = 1)
-  
-  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),]
-  
-  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,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)
-  
-  ############################################################################################################
-  
-  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)
-}
-
diff -r beba4066121e -r dff99bed3f56 all stuff/difference finder for 2 overlaps proper names 7-7_1-15-2019.R
--- a/all stuff/difference finder for 2 overlaps proper names 7-7_1-15-2019.R	Wed Jan 16 14:33:39 2019 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,547 +0,0 @@
-#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
diff -r beba4066121e -r dff99bed3f56 all stuff/differenceFinder.xml
--- a/all stuff/differenceFinder.xml	Wed Jan 16 14:33:39 2019 -0500
+++ b/all stuff/differenceFinder.xml	Fri Apr 19 10:57:28 2019 -0400
@@ -9,7 +9,7 @@
 		ln -s '$input3' S2.csv &&
 		ln -s '$input4' SBF2.csv &&
 		
-		Rscript '$__tool_directory__/Difference finderMADE 7 TO 7 1-15-2019.R'
+		Rscript '$__tool_directory__/Difference finder MADE 7 TO 7 4-18-2019.R'
     ]]></command>
     <inputs>
 		<param format="csv" name="input1" type="data" label="First Substrate Set"/>