Mercurial > repos > jfb > commonality_finder
changeset 4:830e8dc3acac draft default tip
Uploaded
| author | jfb |
|---|---|
| date | Tue, 14 Jul 2020 19:51:12 -0400 |
| parents | 6eacb089b655 |
| children | |
| files | C and D finder/CandD.xml C and D finder/commonality-working feb 21 20.R C and D finder/commonality-working jan 13 2020.R C and D finder/commonality-working jul 13 2020.R |
| diffstat | 4 files changed, 258 insertions(+), 588 deletions(-) [+] |
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--- a/C and D finder/CandD.xml Mon Feb 24 17:54:14 2020 -0500 +++ b/C and D finder/CandD.xml Tue Jul 14 19:51:12 2020 -0400 @@ -11,7 +11,7 @@ ln -s '$input5' input5.csv && ln -s '$input6' input6.csv && - Rscript '$__tool_directory__/commonality-working feb 21 20.R' + Rscript '$__tool_directory__/commonality-working jul 13 2020.R' ]]></command> <inputs> <param format="csv" name="input1" type="data" label="First Substrate Set"/>
--- 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="") -}
--- a/C and D finder/commonality-working jan 13 2020.R Mon Feb 24 17:54:14 2020 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,285 +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),] - -SecondSubstrateSet<- read.csv("input3.csv", stringsAsFactors=FALSE, header = FALSE) -Secondsubbackfreq<- read.csv("input4.csv", header=FALSE, stringsAsFactors=FALSE) -SecondSubstrateSet<- SecondSubstrateSet[2:nrow(SecondSubstrateSet),] - - -ThirdSubstrateSet<- read.csv("input5.csv", stringsAsFactors=FALSE, header = FALSE) -Thirdsubbackfreq<- read.csv("input6.csv", header=FALSE, stringsAsFactors=FALSE) -ThirdSubstrateSet<- ThirdSubstrateSet[2:nrow(ThirdSubstrateSet),] - - -#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 -if (Are_You_Looking_For_Commonality=="YES"){ - - - ############################################### - #ALL motifs, full and truncated - - 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)] - Outputmatrix<-cbind(Firstsubbackfreq[,1],FinalMatrix) - write.table(x=Outputmatrix,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="") - } -} \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/C and D finder/commonality-working jul 13 2020.R Tue Jul 14 19:51:12 2020 -0400 @@ -0,0 +1,257 @@ +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) + } +} + +#the above three sections bring in the input files and ensure they are properly aligned. The if statements align them if they are misaligned + +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" + +#the above 4 sections create the names of the output files that this tool can create + + + + +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 + +#for each input file, mark the phospho-Tyrosine (which is always housed in column 11) +#with an xY to denote that is it a phospho and not regular tyrosine + + +#currently the substrates are a dataframe with many values, I want to collapse each substrate into a single variable, +#but if I simply use the paste() function then I lose any information about whether the substrate was truncated on the C or N terminal. +#so the for loops below then are constructed so as to retain that information on how any substrate is truncated. + +FTLwtmotifs=matrix(,nrow = nrow(FirstSubstrateSet),ncol=1) +FTLwtAccessionNumbers=matrix(data = Firstsubbackfreq[1,],ncol=1) +#create the vectors which will house the first set of substrates and the first set of accession numbers + + +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 + YYYLettersToTheRight <- length(YYYmotif) - 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 + + + + 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 + } + + 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 + } +} + +D835Ymotifs=matrix(,nrow = nrow(SecondSubstrateSet),ncol=1) +D835YAccessionNumbers<-matrix(data = Secondsubbackfreq[1,],ncol = 1) +#vectors to house the second set of substrates and accession numbers + +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 + } + + 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 + } +} + + +ITDmotifs=matrix(,nrow = nrow(ThirdSubstrateSet),ncol=1) +ITDAccessionNumbers<-matrix(data = Thirdsubbackfreq[1,],ncol = 1) +#third set of substrates and accession numbers + + +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] + } +} + + +SubstrateOverlap1<-intersect(D835Ymotifs,ITDmotifs) +SubstrateOverlap1<-as.matrix(SubstrateOverlap1) +SubstrateOverlapFINAL<-intersect(FTLwtmotifs,SubstrateOverlap1) +#this tool is essentially looking for the intersection of three sets, and to do so it performs 1 intersection at a time +#this find the intersection of the substrate sets + +AccessionOverlap1<-intersect(D835YAccessionNumbers,ITDAccessionNumbers) +AccessionOverlapFinal<-intersect(AccessionOverlap1,FTLwtAccessionNumbers) +AccessionOverlapFinal<-unlist(AccessionOverlapFinal) +#this tool is essentially looking for the intersection of three sets, and to do so it performs 1 intersection at a time +#this find the intersection of the accession number sets + + +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]) + } + } +} +#for every accession number, go back to the original substrate background frequency file and find the protein statistics associated with that number +#columnbind all those protein statistics together +FinalMatrix<-FinalMatrix[,2:ncol(FinalMatrix)] + + +#write all files, in the proper format so that the files coming out look like the files coming in + +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="")