--- a/C and D finder/commonality-working feb 21 20.R	Mon Feb 24 17:54:14 2020 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,302 +0,0 @@
-FirstSubstrateSet<- read.csv("input1.csv", stringsAsFactors=FALSE, header = FALSE)
-Firstsubbackfreq<- read.csv("input2.csv", header=FALSE, stringsAsFactors=FALSE)
-SubstrateHeader<-FirstSubstrateSet[1,]
-FirstSubstrateSet<- FirstSubstrateSet[2:nrow(FirstSubstrateSet),]
-if(nrow(Firstsubbackfreq[1,]>35)){
-  if(grepl(pattern = "Properties", x=Firstsubbackfreq[1,22])){
-    Firstsubbackfreq<-t(Firstsubbackfreq)
-  }
-}
-
-
-SecondSubstrateSet<- read.csv("input3.csv", stringsAsFactors=FALSE, header = FALSE)
-Secondsubbackfreq<- read.csv("input4.csv", header=FALSE, stringsAsFactors=FALSE)
-SecondSubstrateSet<- SecondSubstrateSet[2:nrow(SecondSubstrateSet),]
-if(nrow(Secondsubbackfreq[1,]>35)){
-  if(grepl(pattern = "Properties", x=Secondsubbackfreq[1,22])){
-    Secondsubbackfreq<-t(Secondsubbackfreq)
-  }
-}
-
-
-ThirdSubstrateSet<- read.csv("input5.csv", stringsAsFactors=FALSE, header = FALSE)
-Thirdsubbackfreq<- read.csv("input6.csv", header=FALSE, stringsAsFactors=FALSE)
-ThirdSubstrateSet<- ThirdSubstrateSet[2:nrow(ThirdSubstrateSet),]
-if(nrow(Thirdsubbackfreq[1,]>35)){
-  if(grepl(pattern = "Properties", x=Thirdsubbackfreq[1,22])){
-    Thirdsubbackfreq<-t(Thirdsubbackfreq)
-  }
-}
-
-
-
-
-#ff you want ONLY FULL MOTIFS, put "YES" here, please use all caps
-FullMotifsOnly_questionmark<-"NO"
-#If you want ONLY TRUNCATED MOTIFS, put "YES" here, please use all caps
-TruncatedMotifsOnly_questionmark<-"NO"
-#if you want to find the overlap, put a "YES" here (all caps), if you want to find the non-overlap, put "NO" (all caps)
-Are_You_Looking_For_Commonality<-"YES"
-
-
-#then put the names of your output files here
-Shared_motifs_table<-"sharedmotifs.csv"
-Shared_subbackfreq_table<-"sharedSBF.csv"
-
-# Shared_motifs_table<-"Shared motifs 7-27-17.csv"
-# Shared_subbackfreq_table<-"SubstrateBackgrounFrequency-for-shared-motifs 4 7-27-17.csv"
-
-First_unshared_motifs_table<-"R1 substrates.csv"
-First_unshared_subbackfreq<-"R1 SBF.csv"
-
-Second_unshared_motifs_table<-"R2 subs.csv"
-Second_unshared_subbackfreq<-"R2 SBf.csv"
-
-Third_unshared_motifs_table<-"R3 subs.csv"
-Third_unshared_subbackfreq<-"R3 SBF.csv"
-
-#final note, this code is going to be unworkable if you want to make a Venn diagram of more than 3 circles.  I think I'll poke around
-#other languages to see if any of them can do it.
-####################################################################################################################################
-
-
-
-
-
-FirstxY<-rep("xY",times=nrow(FirstSubstrateSet))
-FirstSubstrateSet[,11]<-FirstxY
-
-SecondxY<-rep("xY",times=nrow(SecondSubstrateSet))
-SecondSubstrateSet[,11]<-SecondxY
-
-ThirdxY<-rep("xY",times=nrow(ThirdSubstrateSet))
-ThirdSubstrateSet[,11]<-ThirdxY
-
-
-
-
-
-
-
-
-
-
-
-####################################################################################################################################
-####################################################################################################################################
-# better version of this code written in C: what happens when two kinases share a motif, but they found that motif in two 
-# separate proteins thus two separate accession numbers?
-# It should actually output the shared motif and BOTH accession numbers.  Right now it does not, it only maps out the second
-# accession number.  So that needs to be fixed BUT you need to keep the commonality between a motif and its accession number
-####################################################################################################################################
-####################################################################################################################################
-####################################################################################################################################
-####################################################################################################################################
-
-#Create the motif sets, deciding wether or not you're looking for truncated or full here
-#full only
- 
-FTLwtmotifs=matrix(,nrow = nrow(FirstSubstrateSet),ncol=1)
-FTLwtAccessionNumbers=matrix(data = Firstsubbackfreq[1,],ncol=1)
-
-for (i in 1:nrow(FirstSubstrateSet)){
-  FTLwtletters<-FirstSubstrateSet[i,4:18]
-  FTLwtletters<-FTLwtletters[FTLwtletters !="XXXXX"]
-  FTLwtletters<-paste(FTLwtletters, sep="", collapse="")
-  leftspaces<-c()
-  rightspaces<-c()
-  
-  YYYmotif <- unlist(strsplit(FTLwtletters, split = ""))
-  YYYposition <- match(x = "x", table = YYYmotif)
-  #position itself tells me how much is to the left of that X by what it's number is.  x at position 4 tells me that there are
-  #just 3 letters to the left of x
-  
-  YYYLettersToTheLeft <- YYYposition - 1
-  #how many letters to the right SHOULD just be length(motif)-position-1 if it's 5 long and x is at 3 then Y is at 4 and there is
-  #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1
-  YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1
-  #then sanity check, we're currently looking only at +/-4, but this spot allows for up to +/- 7 as well, just depends on what the
-  #variable the user puts in is
-  
-  
-  if (YYYLettersToTheLeft < 7 | YYYLettersToTheRight < 7) {
-    leftspaces<-rep(" ",times=(7-YYYLettersToTheLeft))
-    rightspaces<-rep(" ",times=7-(YYYLettersToTheRight))
-    #add blank spaces if the motif has less than 4 letters to the left/right
-    motif<-c(leftspaces,YYYmotif,rightspaces)
-    #save that motif, which is the Y and +/- 4 amino acids, including truncation
-    motif<-motif[!motif %in% "x"]
-    motif<-paste(motif, sep="", collapse="")
-    FTLwtletters<-motif
-    FTLwtmotifs[i,1]<-FTLwtletters
-    # FTLwtAccessionNumbers[i,1]<-FirstSubstrateSet[i,3]
-  }
-  
-  if(YYYLettersToTheLeft>6 && YYYLettersToTheRight>6){
-    motif<-YYYmotif
-    #add blank spaces if the motif has less than 4 letters to the left/right
-    motif<-c(leftspaces,YYYmotif,rightspaces)
-    #save that motif, which is the Y and +/- 4 amino acids, including truncation
-    motif<-motif[!motif %in% "x"]
-    motif<-paste(motif, sep="", collapse="")
-    FTLwtletters<-motif
-    FTLwtmotifs[i,1]<-FTLwtletters
-    # FTLwtAccessionNumbers[i,1]<-FirstSubstrateSet[i,3]
-    
-    
-  }
-  
-}
-
-D835Ymotifs=matrix(,nrow = nrow(SecondSubstrateSet),ncol=1)
-D835YAccessionNumbers<-matrix(data = Secondsubbackfreq[1,],ncol = 1)
-
-for (i in 1:nrow(SecondSubstrateSet)){
-  D835letters<-SecondSubstrateSet[i,4:18]
-  D835letters<-D835letters[D835letters !="XXXXX"]
-  D835letters<-paste(D835letters, sep="", collapse="")
-  leftspaces<-c()
-  rightspaces<-c()
-  
-  YYYmotif <- unlist(strsplit(D835letters, split = ""))
-  YYYposition <- match(x = "x", table = YYYmotif)
-  #position itself tells me how much is to the left of that X by what it's number is.  x at position 4 tells me that there are
-  #just 3 letters to the left of x
-  
-  YYYLettersToTheLeft <- YYYposition - 1
-  #how many letters to the right SHOULD just be length(motif)-position-1 if it's 5 long and x is at 3 then Y is at 4 and there is
-  #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1
-  YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1
-  #then sanity check, we're currently looking only at +/-4, but this spot allows for up to +/- 7 as well, just depends on what the
-  #variable the user puts in is
-  if (YYYLettersToTheLeft < 7 | YYYLettersToTheRight < 7) {
-    leftspaces<-rep(" ",times=(7-YYYLettersToTheLeft))
-    rightspaces<-rep(" ",times=7-(YYYLettersToTheRight))
-    #add blank spaces if the motif has less than 4 letters to the left/right
-    motif<-c(leftspaces,YYYmotif,rightspaces)
-    #save that motif, which is the Y and +/- 4 amino acids, including truncation
-    motif<-motif[!motif %in% "x"]
-    motif<-paste(motif, sep="", collapse="")
-    D835letters<-motif
-    D835Ymotifs[i,1]<-D835letters
-    # D835YAccessionNumbers[i,1]<-FirstSubstrateSet[i,3]
-  }
-  
-  if(YYYLettersToTheLeft>6 && YYYLettersToTheRight>6){
-    motif<-YYYmotif
-    #add blank spaces if the motif has less than 4 letters to the left/right
-    motif<-c(leftspaces,YYYmotif,rightspaces)
-    #save that motif, which is the Y and +/- 4 amino acids, including truncation
-    motif<-motif[!motif %in% "x"]
-    motif<-paste(motif, sep="", collapse="")
-    D835letters<-motif
-    D835Ymotifs[i,1]<-D835letters
-    # D835YAccessionNumbers[i,1]<-FirstSubstrateSet[i,3]
-  }
-}
-
-
-ITDmotifs=matrix(,nrow = nrow(ThirdSubstrateSet),ncol=1)
-ITDAccessionNumbers<-matrix(data = Thirdsubbackfreq[1,],ncol = 1)
-
-for (i in 1:nrow(ThirdSubstrateSet)){
-  ITDletters<-ThirdSubstrateSet[i,4:18]
-  ITDletters<-ITDletters[ITDletters !="XXXXX"]
-  ITDletters<-paste(ITDletters, sep="", collapse="")
-  YYYmotif <- unlist(strsplit(ITDletters, split = ""))
-  leftspaces<-c()
-  rightspaces<-c()
-  YYYposition <- match(x = "x", table = YYYmotif)
-  #position itself tells me how much is to the left of that X by what it's number is.  x at position 4 tells me that there are
-  #just 3 letters to the left of x
-  
-  YYYLettersToTheLeft <- YYYposition - 1
-  #how many letters to the right SHOULD just be length(motif)-position-1 if it's 5 long and x is at 3 then Y is at 4 and there is
-  #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1
-  YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1
-  #then sanity check, we're currently looking only at +/-4, but this spot allows for up to +/- 7 as well, just depends on what the
-  #variable the user puts in is
-  if (YYYLettersToTheLeft < 7 | YYYLettersToTheRight < 7) {
-    leftspaces<-rep(" ",times=(7-YYYLettersToTheLeft))
-    rightspaces<-rep(" ",times=7-(YYYLettersToTheRight))
-    #add blank spaces if the motif has less than 4 letters to the left/right
-    motif<-c(leftspaces,YYYmotif,rightspaces)
-    #save that motif, which is the Y and +/- 4 amino acids, including truncation
-    motif<-motif[!motif %in% "x"]
-    motif<-paste(motif, sep="", collapse="")
-    ITDletters<-motif
-    ITDmotifs[i,1]<-ITDletters
-    # ITDAccessionNumbers[i,1]<-FirstSubstrateSet[i,3]
-  }
-  
-  if(YYYLettersToTheLeft>6 && YYYLettersToTheRight>6){
-    motif<-YYYmotif
-    #add blank spaces if the motif has less than 4 letters to the left/right
-    motif<-c(leftspaces,YYYmotif,rightspaces)
-    #save that motif, which is the Y and +/- 4 amino acids, including truncation
-    motif<-motif[!motif %in% "x"]
-    motif<-paste(motif, sep="", collapse="")
-    ITDletters<-motif
-    ITDmotifs[i,1]<-ITDletters
-    # ITDAccessionNumbers[i,1]<-FirstSubstrateSet[i,3]
-  }
-}
-  
-#############################################################################################################################
-#############################################################################################################################
-#############################################################################################################################
-#############################################################################################################################
-#############################################################################################################################
-
-#now look for either commonality or difference.  Actually could you look for both...
-
-if (Are_You_Looking_For_Commonality=="YES"){
-  
-  columnalheader<-c(as.character(Thirdsubbackfreq[1:36,1]))
-  columnalheader<-matrix(columnalheader,nrow = 1)
-
-  SubstrateOverlap1<-intersect(D835Ymotifs,ITDmotifs)
-  SubstrateOverlap1<-as.matrix(SubstrateOverlap1)
-  
-  
-  columnalheader<-c(rep(NA,36))
-  FinalMatrix<-matrix(data =columnalheader,ncol = 1)
-
-  SubstrateOverlapFINAL<-intersect(FTLwtmotifs,SubstrateOverlap1)
-  AccessionOverlap1<-intersect(D835YAccessionNumbers,ITDAccessionNumbers)
-  AccessionOverlapFinal<-intersect(AccessionOverlap1,FTLwtAccessionNumbers)
-  AccessionOverlapFinal<-unlist(AccessionOverlapFinal)
-  
-  for (x in 1:length(AccessionOverlapFinal)) {
-    for (y in 1:ncol(Firstsubbackfreq)) {
-      Acc<-AccessionOverlapFinal[x]
-      SBF<-Firstsubbackfreq[1,y]
-      if(Acc==SBF){
-        FinalMatrix<-cbind(FinalMatrix,Firstsubbackfreq[,y])
-      }
-    }
-  }
-  FinalMatrix<-FinalMatrix[,2:ncol(FinalMatrix)]
-  
-  if(grepl(pattern = "Properties", x=FinalMatrix[22,1])==FALSE){
-    Outputmatrix<-cbind(Firstsubbackfreq[,1],FinalMatrix)
-    write.table(x=Outputmatrix,file = Shared_subbackfreq_table,quote = FALSE,sep = ",",row.names = FALSE,col.names = FALSE,na="")
-  } else {
-    write.table(x=FinalMatrix,file = Shared_subbackfreq_table,quote = FALSE,sep = ",",row.names = FALSE,col.names = FALSE,na="")
-  }
-  
-  SubstrateMatrix<-SubstrateHeader
-  if(ncol(SubstrateMatrix)>18){
-    SubstrateMatrix<-SubstrateMatrix[,1:18]
-  }
-  
-  for (z in 1:length(SubstrateOverlapFINAL)) {
-    motif<-SubstrateOverlapFINAL[z]
-    newmotif<-unlist(strsplit(motif,split = ""))
-    
-    Addition<-""
-    outputmotif<-c(Addition,Addition,Addition,newmotif)
-    SubstrateMatrix<-rbind(SubstrateMatrix,outputmotif)
-  }
-  write.table(x=SubstrateMatrix,file = Shared_motifs_table,quote = FALSE,sep = ",",row.names = FALSE,col.names = FALSE,na="")
-}