# HG changeset patch # User jfb # Date 1594770814 14400 # Node ID 77e47268b6506446fe2c258f50b70cc7912c5a4c # Parent 78f16bc92ba699734ede04f96695860c22b052c5 Uploaded diff -r 78f16bc92ba6 -r 77e47268b650 all stuff/Difference finder for GalaxyP 2-21-20.R --- a/all stuff/Difference finder for GalaxyP 2-21-20.R Fri Feb 21 16:37:08 2020 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,358 +0,0 @@ -#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,colClasses = "character") -Firstsubbackfreq<- read.csv("SBF1.csv", header=FALSE, stringsAsFactors=FALSE) - -SecondSubstrateSet<- read.csv("S2.csv", stringsAsFactors=FALSE,colClasses = "character") -Secondsubbackfreq<- read.csv("SBF2.csv", header=FALSE, stringsAsFactors=FALSE) - - -First_unshared_motifs_table<-"1RS.csv" -First_unshared_subbackfreq<-"1RSBF.csv" - -Second_unshared_motifs_table<-"2RS.csv" -Second_unshared_subbackfreq<-"2RSBF.csv" - -EmptySubHeader<-colnames(FirstSubstrateSet) -EmptySubHeader<-matrix(EmptySubHeader, nrow=1) -EmptySBFHeader<-Firstsubbackfreq[,1] - -#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. -#################################################################################################################################### - - -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 - - -############################################### -#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) - -FLTheader<-c("Substrate","Species","Reference","-7","-6","-5","-4","-3","-2","-1","0","1","2","3","4","5","6","7","Phosphite") - -if (length(FTLwtmotifsFINAL)>0){ - 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),] - - - FTLoutputmatrix<-matrix(data=c(FTLwtmotifsFINAL,names(FTLwtmotifsFINAL)),ncol = 2) - # 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(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) - - write.table(x=FTLFinalMatrix, - file=First_unshared_subbackfreq, - quote=FALSE, sep=",", - row.names=FALSE,col.names = FALSE, na="", append=TRUE) -} else{ - FTLFinalMatrix<-columnalheader - write.table(x=EmptySubHeader, - 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) -} - - -columnalheader<-c(rep(NA,36)) -D835YFinalMatrix<-matrix(data =columnalheader,nrow = 1) - -if (length(D835YmotifsFINAL)>0){ - 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),] - - 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(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) - - write.table(x=D835YFinalMatrix, - file=Second_unshared_subbackfreq, - quote=FALSE, sep=",", - row.names=FALSE,col.names = FALSE, na="", append=TRUE) -} else { - D835YFinalMatrix<- columnalheader - write.table(x=EmptySubHeader, - 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) -} \ No newline at end of file diff -r 78f16bc92ba6 -r 77e47268b650 all stuff/Difference finder for GalaxyP july 2020.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/all stuff/Difference finder for GalaxyP july 2020.R Tue Jul 14 19:53:34 2020 -0400 @@ -0,0 +1,333 @@ +FirstSubstrateSet<- read.csv("S1.csv", stringsAsFactors=FALSE,colClasses = "character") +Firstsubbackfreq<- read.csv("SBF1.csv", header=FALSE, stringsAsFactors=FALSE) +SecondSubstrateSet<- read.csv("S2.csv", stringsAsFactors=FALSE,colClasses = "character") +Secondsubbackfreq<- read.csv("SBF2.csv", header=FALSE, stringsAsFactors=FALSE) +#this brings in the input files + + +First_unshared_motifs_table<-"1RS.csv" +First_unshared_subbackfreq<-"1RSBF.csv" +Second_unshared_motifs_table<-"2RS.csv" +Second_unshared_subbackfreq<-"2RSBF.csv" +#this names the output files + +EmptySubHeader<-colnames(FirstSubstrateSet) +EmptySubHeader<-matrix(EmptySubHeader, nrow=1) +EmptySBFHeader<-Firstsubbackfreq[,1] +#this creates the headers which comes from the input files, so that the output files can be given this header so that they will look identical to the input files + + +#the below code is used to ensure that all phospho-amino acids get marked with an "x" to denote their phosphoness +FirstCentralLetters<-FirstSubstrateSet[,11] +SecondCentralLetters<-SecondSubstrateSet[,11] +#the phospho AAs are always found in position 12, so take them from there + +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) +#use an 3 apply functions to create vectors, these vetors have true values where they find an S, T or Y. +#so FirstEsses has a True anywhere it sees an S, and FirstTees has a True anywhere it sees a Y + +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) +#do the same for the second substrate set's central letters + +FirstCentralLetters<-replace(FirstCentralLetters,FirstEsses,"xS") +FirstCentralLetters<-replace(FirstCentralLetters,FirstTees,"xT") +FirstCentralLetters<-replace(FirstCentralLetters,FirstWys,"xY") +#where there is a True value in FirstEsses, replace that value in the original substrate set with an xS. This is because there was originally an S in that +#position, and I want that S to be marked with an x, denoting phospho + +SecondCentralLetters<-replace(SecondCentralLetters,SecondEsses,"xS") +SecondCentralLetters<-replace(SecondCentralLetters,SecondTees,"xT") +SecondCentralLetters<-replace(SecondCentralLetters,SecondWys,"xY") + +FirstCentralLetters->FirstSubstrateSet[,11] +SecondCentralLetters->SecondSubstrateSet[,11] +#then I put these x-marked letters back where I found them, in position 11 of the substrate sets + +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) + +FLTheader<-c("Substrate","Species","Reference","-7","-6","-5","-4","-3","-2","-1","0","1","2","3","4","5","6","7","Phosphite") + +if (length(FTLwtmotifsFINAL)>0){ + for (k in 1:length(FTLwtmotifsFINAL)) { + AN<-00000 + #it is 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),] + + + FTLoutputmatrix<-matrix(data=c(FTLwtmotifsFINAL,names(FTLwtmotifsFINAL)),ncol = 2) + # 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(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) + + write.table(x=FTLFinalMatrix, + file=First_unshared_subbackfreq, + quote=FALSE, sep=",", + row.names=FALSE,col.names = FALSE, na="", append=TRUE) +} else{ + FTLFinalMatrix<-columnalheader + write.table(x=EmptySubHeader, + 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) +} + + +columnalheader<-c(rep(NA,36)) +D835YFinalMatrix<-matrix(data =columnalheader,nrow = 1) + +if (length(D835YmotifsFINAL)>0){ + for (k in 1:length(D835YmotifsFINAL)) { + #it is 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),] + + 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(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) + + write.table(x=D835YFinalMatrix, + file=Second_unshared_subbackfreq, + quote=FALSE, sep=",", + row.names=FALSE,col.names = FALSE, na="", append=TRUE) +} else { + D835YFinalMatrix<- columnalheader + write.table(x=EmptySubHeader, + 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) +} \ No newline at end of file diff -r 78f16bc92ba6 -r 77e47268b650 all stuff/Difference finder for GalaxyP working.R --- a/all stuff/Difference finder for GalaxyP working.R Fri Feb 21 16:37:08 2020 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,358 +0,0 @@ -#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,colClasses = "character") -Firstsubbackfreq<- read.csv("SBF1.csv", header=FALSE, stringsAsFactors=FALSE) - -SecondSubstrateSet<- read.csv("S2.csv", stringsAsFactors=FALSE,colClasses = "character") -Secondsubbackfreq<- read.csv("SBF2.csv", header=FALSE, stringsAsFactors=FALSE) - - -First_unshared_motifs_table<-"1RS.csv" -First_unshared_subbackfreq<-"1RSBF.csv" - -Second_unshared_motifs_table<-"2RS.csv" -Second_unshared_subbackfreq<-"2RSBF.csv" - -EmptySubHeader<-colnames(FirstSubstrateSet) -EmptySubHeader<-matrix(EmptySubHeader, nrow=1) -EmptySBFHeader<-Firstsubbackfreq[,1] - -#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. -#################################################################################################################################### - - -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 - - -############################################### -#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) - -FLTheader<-c("Substrate","Species","Reference","-7","-6","-5","-4","-3","-2","-1","0","1","2","3","4","5","6","7","Phosphite") - -if (length(FTLwtmotifsFINAL)>0){ - 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),] - - - FTLoutputmatrix<-matrix(data=c(FTLwtmotifsFINAL,names(FTLwtmotifsFINAL)),ncol = 2) - # 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) -} else{ - FTLFinalMatrix<-columnalheader - write.table(x=EmptySubHeader, - 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) -} - - -columnalheader<-c(rep(NA,36)) -D835YFinalMatrix<-matrix(data =columnalheader,nrow = 1) - -if (length(D835YmotifsFINAL)>0){ - 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),] - - 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) -} else { - D835YFinalMatrix<- columnalheader - write.table(x=EmptySubHeader, - 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) -} \ No newline at end of file diff -r 78f16bc92ba6 -r 77e47268b650 all stuff/differenceFinder.xml --- a/all stuff/differenceFinder.xml Fri Feb 21 16:37:08 2020 -0500 +++ b/all stuff/differenceFinder.xml Tue Jul 14 19:53:34 2020 -0400 @@ -9,7 +9,7 @@ ln -s '$input3' S2.csv && ln -s '$input4' SBF2.csv && - Rscript '$__tool_directory__/Difference finder for GalaxyP 2-21-20.R' + Rscript '$__tool_directory__/Difference finder for GalaxyP july 2020.R' ]]>