Mercurial > repos > jfb > difference_finder
view all stuff/Difference finderMADE 7 TO 7 fastversion 2-14-2019.R @ 8:4dd15c41d9e7 draft
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author | jfb |
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date | Fri, 19 Apr 2019 16:55:29 -0400 |
parents | 74ada21ceb70 |
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#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 #S2 is negatives #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("Substrates 1A TiO2 and FeNTA no duplicates.csv", stringsAsFactors=FALSE) Firstsubbackfreq<- read.csv("SBF 1A TiO2 and FeNTA no duplicates.csv", header=FALSE, stringsAsFactors=FALSE) SecondSubstrateSet<- read.csv("Substrates 1B TiO2 and FeNTA no duplicates.csv", stringsAsFactors=FALSE) Secondsubbackfreq<- read.csv("SBF 1B TiO2 and FeNTA no duplicates.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<-"pka_minus_wo-plus_wo_vector_subs.csv" First_unshared_subbackfreq<-"pka_minus_wo-plus_wo_vector_sbf.csv" Second_unshared_motifs_table<-"pka_plus_wo-minus_wo_vector_subs.csv" Second_unshared_subbackfreq<-"pka_plus_wo-minus_wo_vector_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) #so what this does is #find the central phospho position and add spaces to either side of it #create a pasted together motif which will be used for difference finding #keep motifs and accession numbers in the same index position of two vectors #so instead just take the FLTwt[i,4:18], and replace "" with "O" #then perform paste function #then FLTwt with "O" can be the motif that will get printed to the CSV (after re-removing the "O") and the pasted motif is in its own vector that follows the A #s FTLwtmotifs<-FirstSubstrateSet[,4:18] # FTLwtmotifs<-sapply(FTLwtmotifs, gsub, pattern=" ", replacement="O",ignore.case=TRUE) FTLwtmotifs<-replace(FTLwtmotifs, FTLwtmotifs=="", "O") FTLwtmotifs<-apply(FTLwtmotifs, 1, paste, sep="", collapse="") FTLwtAccessionNumbers<-FirstSubstrateSet[,3] # D835Ymotifs=matrix(,nrow = nrow(SecondSubstrateSet),ncol=1) # D835YAccessionNumbers<-matrix(,nrow = nrow(SecondSubstrateSet),ncol = 1) D835Ymotifs<-SecondSubstrateSet[,4:18] # D835Ymotifs<-sapply(D835Ymotifs, gsub, patter="", replacement="O",ignore.case=TRUE) D835Ymotifs<-replace(D835Ymotifs, D835Ymotifs=="", "O") D835Ymotifs<-replace(D835Ymotifs, D835Ymotifs=="", "O") D835Ymotifs<-apply(D835Ymotifs, 1, paste, sep="", collapse="") D835YAccessionNumbers<-SecondSubstrateSet[,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) # #how to make this an apply #actual first turn names(motifsFINAL) into a vector, then gsub to replace all "|" pipe characters with "*" star characters #first take the accession numbers as Firstsubbackfreq[1,], then gsub to replace all "|" pipe characters with "*" star characters #then use AccessionNumbers as a vector and use #matches <- unique (grep(paste(toMatch,collapse="|"), names(motifsFINAL), value=TRUE)) FLTwtNames<-names(FTLwtmotifsFINAL) FLTwtNames<-FLTwtNames[!duplicated(FLTwtNames)] #the problem is the names includes a lot of things that are multi names separated by ; #I need to do soem paper writing and poster writing FLTwtNames<-gsub(pattern = '\\|', replacement = "*", x=FLTwtNames) FLTwtNames<-paste(FLTwtNames,collapse = "|") AccNums<-as.character(Firstsubbackfreq[1,]) AccNums<-gsub(pattern = "\\|", replacement = "*", x=AccNums) firstthree123<-gsub(pattern = "\\|", replacement = "", x=FLTwtNames) lastthree123<-gsub(pattern = "\\|", replacement = "", x=AccNums) pasty<-paste(lastthree123,collapse = "|") my_matches<-unique(grep(pattern = FLTwtNames, x=AccNums, value = TRUE)) # matches <- unique (grep(paste(FLTwtNames,collapse="|"), AccNums, value=TRUE)) My_matches<- AccNums %in% FLTwtNames #use apply grep function My_matches<-grep(pattern = pasty, x=firstthree123, ignore.case = TRUE) sensation<-firstthree123[My_matches] what<-firstthree123[!firstthree123 %in% sensation] #my matches are which columns in the SBF file still have a motif with them FirstFINALSBF<-Firstsubbackfreq[My_matches] FTLFinalMatrix<-FirstFINALSBF duped<-FTLFinalMatrix[1,] duped<-duped[!duplicated(duped)] names(duped)<-NULL duped<-unlist(duped) unduped<-FTLFinalMatrix[,!duplicated(duped)] FTLFinalMatrix<-unduped # FTLFinalMatrix<-FTLFinalMatrix[2:nrow(FTLFinalMatrix),] # columnalheader<-c(rep(NA,36)) # D835YFinalMatrix<-matrix(data =columnalheader,nrow = 1) D835names<-names(D835YmotifsFINAL) D835names<-D835names[!duplicated(D835names)] AccNums<-as.character(Secondsubbackfreq[1,]) My_matches<-AccNums %in% D835names SecondFINALSBF<-Secondsubbackfreq[My_matches] D835YFinalMatrix<-SecondFINALSBF duped<-D835YFinalMatrix[1,] duped<-duped[!duplicated(duped)] names(duped)<-NULL duped<-unlist(duped) unduped<-D835YFinalMatrix[,!duplicated(duped)] D835YFinalMatrix<-unduped #there's a problem, accession numbers are duplicated # FTLoutputmatrix<-matrix(data=c(FTLwtmotifsFINAL,names(FTLwtmotifsFINAL)),ncol = 2) FTLwtmotifsFINAL<-gsub(pattern = "O", replacement = " ", x=FTLwtmotifsFINAL) FTLwtmotifsFINAL<-gsub(pattern = "x", replacement = "", x=FTLwtmotifsFINAL) FTLoutputmatrix<-matrix(data = c(FTLwtmotifsFINAL,names(FTLwtmotifsFINAL)), ncol=2) # FTLwtmotifsFINAL<-gsub(pattern = "O", replacement = " ", x=FTLwtmotifsFINAL) # FTLwtmotifsFINAL<-gsub(pattern = "x", replacement = "", x=FTLwtmotifsFINAL) # 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,ncol = 1) # write.table(x=columnalheader, # file=First_unshared_subbackfreq, # quote=FALSE, sep=",", # row.names=FALSE,col.names = FALSE, na="", append=TRUE) FTLFinalMatrix<-cbind(columnalheader,FTLFinalMatrix) write.table(x=FTLFinalMatrix, file=First_unshared_subbackfreq, quote=FALSE, sep=",", row.names=FALSE,col.names = FALSE, na="", append=TRUE) ############################################################################################################ D835YmotifsFINAL<-gsub(pattern = "O", replacement = " ", x=D835YmotifsFINAL) D835YmotifsFINAL<-gsub(pattern = "x", replacement = "", x=D835YmotifsFINAL) D835Youtputmatrix<-matrix(data = c(D835YmotifsFINAL,names(D835YmotifsFINAL)), ncol=2) # D835YmotifsFINAL<-gsub(pattern = "O", replacement = " ", x=D835YoutputmatrixL) # D835YmotifsFINAL<-gsub(pattern = "x", replacement = "", x=D835Youtputmatrix) # D835Youtputmatrix<-matrix(data = c(D835Youtputmatrix,names(D835Youtputmatrix)), ncol=2) # # 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) # FTLmeat<-sapply(FTLoutputmatrix[,1], strsplit, "") # FTLmeat<-sapply(FTLmeat, unlist) # colnames(FTLmeat)<-NULL # FTLmeat<-t(FTLmeat) 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,ncol = 1) # write.table(x=columnalheader, # file=Second_unshared_subbackfreq, # quote=FALSE, sep=",", # row.names=FALSE,col.names = FALSE, na="", append=TRUE) D835YFinalMatrix<-cbind(columnalheader,D835YFinalMatrix) write.table(x=D835YFinalMatrix, file=Second_unshared_subbackfreq, quote=FALSE, sep=",", row.names=FALSE,col.names = FALSE, na="", append=TRUE) } # 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] # # # } # # } # 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] # } # } # 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) # } # } # } # 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) # } # } # }