Mercurial > repos > jfb > difference_finder
changeset 9:033dd86d3e0c draft
Uploaded
| author | jfb |
|---|---|
| date | Fri, 21 Feb 2020 13:07:45 -0500 |
| parents | 4dd15c41d9e7 |
| children | 78f16bc92ba6 |
| files | all stuff/.RData all stuff/.Rhistory all stuff/1RS.csv all stuff/1RSBF.csv all stuff/2RS.csv all stuff/2RSBF.csv all stuff/Commonality and Difference finderMADE 7 TO 7 1-15-2019.R all stuff/Commonality and Difference finderMADE 7 TO 7.R all stuff/Difference finder MADE 7 TO 7 4-18-2019.R all stuff/Difference finder for GalaxyP 2-21-20.R all stuff/Difference finder for GalaxyP 4-18-2019.R all stuff/Difference finder for GalaxyP working.R all stuff/Difference finderMADE 7 TO 7 1-15-2019.R all stuff/Difference finderMADE 7 TO 7 fastversion 2-14-2019.R all stuff/Difference finderMADE 7 TO 7 fastversion.R all stuff/difference finder for 2 overlaps proper names 7-7_1-15-2019.R all stuff/differenceFinder.xml |
| diffstat | 17 files changed, 2956 insertions(+), 5067 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/all stuff/.Rhistory Fri Feb 21 13:07:45 2020 -0500 @@ -0,0 +1,288 @@ +?rnorm +?rnorm +?rnorm +pwr +?pwr +??pwr +power.t.test(n=6, power = .7, type = "two.sample", alternative = "two.sided") +power.t.test(n=6, power = .9, type = "two.sample", alternative = "two.sided") +?power.t.test +power.t.test(n=5, sd=1000, power = .7, type = "paired", alternative = "one.sided") +10^4 +power.t.test(n=5, sd=10000, power = .7, type = "paired", alternative = "one.sided") +power.t.test(n=10, delta = 7, sd=10, type = "paired", alternative = "one.sided") +setwd("C:/Users/John Blankenhor/Downloads/difference_finder-4dd15c41d9e7/difference_finder-4dd15c41d9e7/all stuff") +#put the names of your input files here +FirstSubstrateSet<- read.csv("S1.csv", stringsAsFactors=FALSE) +Firstsubbackfreq<- read.csv("SBF1.csv", header=FALSE, stringsAsFactors=FALSE) +FirstSubstrateSet +EmptySubHeader<-First_unshared_motifs_table[1,] +First_unshared_motifs_table<-"1RS.csv" +First_unshared_subbackfreq<-"1RSBF.csv" +#put the names of your input files here +FirstSubstrateSet<- read.csv("S1.csv", stringsAsFactors=FALSE) +Firstsubbackfreq<- read.csv("SBF1.csv", header=FALSE, stringsAsFactors=FALSE) +EmptySubHeader<-FirstSubstrateSet[1,] +head(Firstsubbackfreq) +EmptySBFHeader<-Firstsubbackfreq[,1] +#ff you want ONLY FULL MOTIFS, put "YES" here, please use all caps +FullMotifsOnly_questionmark<-"NO" +#If you want ONLY TRUNCATED MOTIFS, put "YES" here, please use all caps +TruncatedMotifsOnly_questionmark<-"NO" +#if you want to find the overlap, put a "YES" here (all caps), if you want to find the non-overlap, put "NO" (all caps) +Are_You_Looking_For_Commonality<-"NO" +#put the names of your input files here +FirstSubstrateSet<- read.csv("S1.csv", stringsAsFactors=FALSE) +Firstsubbackfreq<- read.csv("SBF1.csv", header=FALSE, stringsAsFactors=FALSE) +SecondSubstrateSet<- read.csv("S2.csv", stringsAsFactors=FALSE) +Secondsubbackfreq<- read.csv("SBF2.csv", header=FALSE, stringsAsFactors=FALSE) +First_unshared_motifs_table<-"1RS.csv" +First_unshared_subbackfreq<-"1RSBF.csv" +Second_unshared_motifs_table<-"2RS.csv" +Second_unshared_subbackfreq<-"2RSBF.csv" +EmptySubHeader<-FirstSubstrateSet[1,] +EmptySBFHeader<-Firstsubbackfreq[,1] +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] +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)] +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 +} +#ff you want ONLY FULL MOTIFS, put "YES" here, please use all caps +FullMotifsOnly_questionmark<-"NO" +#If you want ONLY TRUNCATED MOTIFS, put "YES" here, please use all caps +TruncatedMotifsOnly_questionmark<-"NO" +#if you want to find the overlap, put a "YES" here (all caps), if you want to find the non-overlap, put "NO" (all caps) +Are_You_Looking_For_Commonality<-"NO" +#put the names of your input files here +FirstSubstrateSet<- read.csv("S1.csv", stringsAsFactors=FALSE) +Firstsubbackfreq<- read.csv("SBF1.csv", header=FALSE, stringsAsFactors=FALSE) +SecondSubstrateSet<- read.csv("S2.csv", stringsAsFactors=FALSE) +Secondsubbackfreq<- read.csv("SBF2.csv", header=FALSE, stringsAsFactors=FALSE) +First_unshared_motifs_table<-"1RS.csv" +First_unshared_subbackfreq<-"1RSBF.csv" +Second_unshared_motifs_table<-"2RS.csv" +Second_unshared_subbackfreq<-"2RSBF.csv" +EmptySubHeader<-FirstSubstrateSet[1,] +EmptySBFHeader<-Firstsubbackfreq[,1] +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] +FirstSubstrateSet +#put the names of your input files here +FirstSubstrateSet<- read.csv("S1.csv", stringsAsFactors=FALSE) +FirstSubstrateSet +head(SecondSubstrateSet) +#put the names of your input files here +FirstSubstrateSet<- read.csv("S1.csv", stringsAsFactors=FALSE) +head(SecondSubstrateSet) +FirstSubstrateSet +#put the names of your input files here +FirstSubstrateSet<- read.csv("S1.csv", stringsAsFactors=FALSE) +FirstSubstrateSet +#put the names of your input files here +FirstSubstrateSet<- read.csv("S1.csv", stringsAsFactors=FALSE) +SecondSubstrateSet<- read.csv("S2.csv", stringsAsFactors=FALSE)
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/all stuff/1RS.csv Fri Feb 21 13:07:45 2020 -0500 @@ -0,0 +1,521 @@ +Substrate,Species,Reference,-7,-6,-5,-4,-3,-2,-1,0,1,2,3,4,5,6,7,Phosphite +,,sp|P48735|IDHP_HUMAN,E,A,E,A,A,H,G,xT,V,T,R, , , , , +,,sp|P29401|TKT_HUMAN, , , , , , ,S,xT,F,A,A,F,F,T,R, +,,sp|P30050|RL12_HUMAN, , , , , , ,L,xT,I,Q,N,R, , , , +,,sp|P56556|NDUA6_HUMAN, , , ,Q,A,T,S,xT,A,S,T,F,V,K,P, +,,sp|Q14554|PDIA5_HUMAN, , , , ,G,F,P,xT,I,C,Y,F,E,K, , +,,sp|P29401|TKT_HUMAN, , , , ,H,Q,P,xT,A,I,I,A,K, , , +,,sp|P29401|TKT_HUMAN, , , , , ,N,S,xT,F,S,E,I,F,K, , +,,sp|Q00839|HNRPU_HUMAN, , , , , , ,S,xS,G,P,T,S,L,F,A, +,,sp|Q8IXT5|RB12B_HUMAN, , , , , , , ,xS,P,T,E,D,F,R, , +,,sp|P52566|GDIR2_HUMAN, , , , , , ,A,xT,F,M,V,G,S,Y,G, +,,sp|Q9H9T3|ELP3_HUMAN, , , , ,L,Y,P,xT,L,V,I,R, , , , +,,sp|Q9UBT2|SAE2_HUMAN, , ,G,T,I,L,I,xS,S,E,E,G,E,T,E, +,,sp|Q9Y490|TLN1_HUMAN, , , ,E,G,T,E,xT,F,A,D,H,R, , , +,,sp|Q9NY61|AATF_HUMAN,G,M,D,D,L,G,S,xS,E,E,E,E,D,E,E, +,,sp|P29218|IMPA1_HUMAN, , , ,Y,P,S,H,xS,F,I,G,E,E,S,V, +,,sp|P29401|TKT_HUMAN, , , , , , , ,xS,T,F,A,A,F,F,T, +,,sp|P07900|HS90A_HUMAN, , , , , , ,E,xS,E,D,K,P,E,I,E, +,,sp|P28070|PSB4_HUMAN,N,S,T,M,L,G,A,xS,G,D,Y,A,D,F,Q, +,,sp|Q13564|ULA1_HUMAN, , , , , , ,Q,xT,P,S,F,W,I,L,A, +,,sp|P09429|HMGB1_HUMAN; sp|P26583|HMGB2_HUMAN, , , , ,R,P,P,xS,A,F,F,L,F, , , +,,sp|Q71UM5|RS27L_HUMAN; sp|P42677|RS27_HUMAN, , ,L,T,E,G,C,xS,F,R, , , , , , +,,sp|P00505|AATM_HUMAN, , , ,V,G,A,F,xT,M,V,C,K, , , , +,,sp|O43175|SERA_HUMAN, , , , , ,A,G,xT,G,V,D,N,V,D,L, +,,sp|P07437|TBB5_HUMAN,V,T,F,I,G,N,S,xT,A,I,Q,E,L,F,K, +,,sp|P10599|THIO_HUMAN, , , , ,C,M,P,xT,F,Q,F,F,K, , , +,,sp|Q9UQ35|SRRM2_HUMAN, , , , , ,S,P,xS,V,S,S,P,E,P,A, +,,sp|P40926|MDHM_HUMAN, , , ,A,G,A,G,xS,A,T,L,S,M,A,Y, +,,sp|Q96FS4|SIPA1_HUMAN,A,G,E,A,R,P,P,xT,P,A,S,P,R, , , +,,sp|Q9H0D6|XRN2_HUMAN, ,K,A,E,D,S,D,xS,E,P,E,P,E,D,N, +,,sp|P07814|SYEP_HUMAN, ,A,I,Q,G,G,T,xS,H,H,L,G,Q,N,F, +,,sp|P16403|H12_HUMAN; sp|P16401|H15_HUMAN, , , , , , ,G,xT,L,V,Q,T,K, , , +,,sp|Q92733|PRCC_HUMAN,P,E,L,H,K,G,D,xS,D,S,E,E,D,E,P, +,,sp|Q9UHB9|SRP68_HUMAN, , , , , ,F,E,xT,F,C,L,D,P,S,L, +,,sp|P46781|RS9_HUMAN, , , , ,R,L,Q,xT,Q,V,F,K, , , , +,,sp|Q93084|AT2A3_HUMAN; sp|P16615|AT2A2_HUMAN, , , , , ,T,G,xT,L,T,T,N,Q,M,S, +,,sp|P07237|PDIA1_HUMAN, , , , , ,V,H,xS,F,P,T,L,K, , , +,,sp|Q9Y3T9|NOC2L_HUMAN, , , , , , , ,xS,P,D,K,P,G,G,S, +,,sp|O00264|PGRC1_HUMAN; sp|O15173|PGRC2_HUMAN, , , , ,G,L,A,xT,F,C,L,D,K, , , +,,sp|Q9NVI7|ATD3A_HUMAN; sp|Q5T9A4|ATD3B_HUMAN, , , , , ,A,G,xT,L,F,G,E,G,F,R, +,,sp|O94903|PLPHP_HUMAN, , , , , , ,G,xS,T,I,F,G,E,R, , +,,sp|O15530|PDPK1_HUMAN, ,A,N,S,F,V,G,xT,A,Q,Y,V,S,P,E, +,,sp|Q96RP9|EFGM_HUMAN, , , , ,K,G,D,xT,I,Y,N,T,R, , , +,,sp|Q9UBS9|SUCO_HUMAN, , , , , ,L,G,xT,F,H,G,R, , , , +,,sp|Q14697|GANAB_HUMAN, , , , , ,G,G,xT,I,V,P,R, , , , +,,sp|Q13057|COASY_HUMAN, , ,G,A,V,G,G,xT,F,D,R, , , , , +,,sp|P25205|MCM3_HUMAN, ,G,G,Y,T,S,G,xT,F,R, , , , , , +,,sp|P08559|ODPA_HUMAN, , , , , ,G,G,xS,M,H,M,Y,A,K, , +,,sp|Q69YN4|VIR_HUMAN, , , ,K,Q,N,T,xS,R,P,P,S,M,H,V, +,,sp|Q9UQ35|SRRM2_HUMAN, , , , , , , ,xS,P,G,M,L,E,P,L, +,,sp|P60866|RS20_HUMAN, , , , , , ,I,xT,L,T,S,R, , , , +,,sp|P07900|HS90A_HUMAN, ,E,R,D,K,E,V,xS,D,D,E,A,E,E,K, +,,sp|O75449|KTNA1_HUMAN; sp|Q9BW62|KATL1_HUMAN, , , , , , ,T,xT,F,F,N,V,S,S,S, +,,sp|P06744|G6PI_HUMAN, , , , , ,T,F,xT,T,Q,E,T,I,T,N, +,,sp|P42166|LAP2A_HUMAN, , , , , ,S,S,xT,P,L,P,T,I,S,S, +,,sp|P39656|OST48_HUMAN, , , , , , ,S,xS,L,N,P,I,L,F,R, +,,sp|Q9H583|HEAT1_HUMAN, , , , , ,L,L,xT,F,Y,N,L,A,D,C, +,,sp|O60942|MCE1_HUMAN, ,G,H,G,E,C,P,xT,T,E,N,T,E,T,F, +,,sp|Q01469|FABP5_HUMAN, , , , , , ,K,xT,Q,T,V,C,N,F,T, +,,sp|Q9NYF8|BCLF1_HUMAN, , , , , ,Q,K,xS,P,E,I,H,R, , , +,,sp|P17844|DDX5_HUMAN, , , , , ,T,G,xT,A,Y,T,F,F,T,P, +,,sp|Q69YN4|VIR_HUMAN,Q,N,T,S,R,P,P,xS,M,H,V,D,D,F,V, +,,sp|P28070|PSB4_HUMAN, , , ,V,N,N,S,xT,M,L,G,A,S,G,D, +,,sp|P11940|PABP1_HUMAN, , , ,A,L,Y,D,xT,F,S,A,F,G,N,I, +,,sp|Q12905|ILF2_HUMAN,P,Q,G,E,E,E,E,xS,M,E,T,Q,E, , , +,,sp|Q7Z5L9|I2BP2_HUMAN, , , , , , , ,xS,P,P,G,A,A,A,S, +,,sp|Q69YN4|VIR_HUMAN, , , , ,K,Q,N,xT,S,R,P,P,S,M,H, +,,sp|P04181|OAT_HUMAN; sp|Q5UIP0|RIF1_HUMAN; sp|Q9H3T2|SEM6C_HUMAN; RRRRRsp|P48546|GIPR_HUMAN, , , , , , ,L,xT,L,T,S,R, , , , +,,sp|P35249|RFC4_HUMAN, , , , , ,G,T,xS,I,S,T,K,P,P,L, +,,sp|O00541|PESC_HUMAN, , , , , ,Y,P,xT,F,I,D,A,L,R, , +,,sp|Q9BVA1|TBB2B_HUMAN; sp|Q13885|TBB2A_HUMAN; sp|P68371|TBB4B_HUMAN, , , , ,M,S,A,xT,F,I,G,N,S,T,A, +,,sp|Q96I25|SPF45_HUMAN,S,P,T,G,P,S,N,xS,F,L,A,N,M,G,G, +,,sp|P26599|PTBP1_HUMAN, , , ,D,Y,G,N,xS,P,L,H,R, , , , +,,sp|P11142|HSP7C_HUMAN, , , , , , ,G,xT,L,D,P,V,E,K, , +,,sp|P61769|B2MG_HUMAN, , , ,V,N,H,V,xT,L,S,Q,P,K, , , +,,sp|P54687|BCAT1_HUMAN, , , , , , ,P,xT,F,I,G,T,E,P,S, +,,sp|P49327|FAS_HUMAN, , , , ,V,Y,A,xT,I,L,N,A,G,T,N, +,,sp|P62750|RL23A_HUMAN, , , , , ,V,N,xT,L,I,R,P,D,G,E, +,,sp|P11940|PABP1_HUMAN, , , , ,A,L,D,xT,M,N,F,D,V,I,K, +,,sp|Q00839|HNRPU_HUMAN, , , , , , , ,xS,S,G,P,T,S,L,F, +,,sp|Q8N6L1|KTAP2_HUMAN, , , , , ,I,S,xS,T,L,Y,Q,A,A,A, +,,sp|Q13442|HAP28_HUMAN, ,S,L,D,S,D,E,xS,E,D,E,E,D,D,Y, +,,sp|P40227|TCPZ_HUMAN, , , , , , ,H,xT,L,T,Q,I,K, , , +,,sp|Q13442|HAP28_HUMAN, , , , ,S,L,D,xS,D,E,S,E,D,E,E, +,,sp|Q9H1E3|NUCKS_HUMAN, , , , ,D,S,G,xS,D,E,D,F,L,M,E, +,,sp|Q96KR1|ZFR_HUMAN,T,A,A,W,T,G,T,xT,F,T,K, , , , , +,,sp|Q9C0C9|UBE2O_HUMAN,I,H,G,E,D,S,D,xS,E,G,E,E,E,G,R, +,,sp|Q9NY61|AATF_HUMAN,E,E,E,E,D,E,E,xS,G,M,E,E,G,D,D, +,,sp|P62888|RL30_HUMAN, , , , , ,V,C,xT,L,A,I,I,D,P,G, +,,sp|O43414|ERI3_HUMAN, , , , , ,A,Y,xS,F,A,M,G,C,W,P, +,,sp|O75449|KTNA1_HUMAN; sp|Q9BW62|KATL1_HUMAN, , , , , , , ,xT,T,F,F,N,V,S,S, +,,sp|O60942|MCE1_HUMAN,E,C,P,T,T,E,N,xT,E,T,F,I,R, , , +,,sp|Q9UBT2|SAE2_HUMAN, , , , , , ,G,xT,I,L,I,S,S,E,E, +,,sp|Q8IVH4|MMAA_HUMAN, , , , , , ,S,xT,F,I,E,Y,F,G,K, +,,sp|A0FGR8|ESYT2_HUMAN, ,G,A,N,T,H,L,xS,T,F,S,F,T,K, , +,,sp|P57764|GSDMD_HUMAN,T,V,T,I,P,S,G,xS,T,L,A,F,R, , , +,,sp|P21399|ACOC_HUMAN, , , , , , ,G,xT,F,A,N,I,R, , , +,,sp|P19338|NUCL_HUMAN, , , ,V,A,V,A,xT,P,A,K, , , , , +,,sp|Q9BSJ8|ESYT1_HUMAN, , , ,L,G,T,Q,xT,F,C,S,R, , , , +,,sp|O75964|ATP5L_HUMAN, , , , , ,L,A,xT,F,W,Y,Y,A,K, , +,,sp|O43175|SERA_HUMAN, , , , , , ,G,xT,I,Q,V,I,T,Q,G, +,,sp|Q9BSL1|UBAC1_HUMAN, , , , ,R,A,P,xS,P,L,P,K, , , , +,,sp|P27824|CALX_HUMAN, , , , ,G,T,L,xS,G,W,I,L,S,K, , +,,sp|Q86SU0|ILDR1_HUMAN, , , , , , ,I,xT,I,Q,N,R, , , , +,,sp|P25705|ATPA_HUMAN, , , , , ,T,G,xT,A,E,M,S,S,I,L, +,,sp|Q12979|ABR_HUMAN, ,D,M,S,L,K,R,xT,P,S,K, , , , , +,,sp|P00558|PGK1_HUMAN,T,G,Q,A,T,V,A,xS,G,I,P,A,G,W,M, +,,sp|P13639|EF2_HUMAN, , , , , , , ,xT,F,C,Q,L,I,L,D, +,,sp|P12236|ADT3_HUMAN; sp|Q9H0C2|ADT4_HUMAN; sp|P12235|ADT1_HUMAN; sp|P05141|ADT2_HUMAN, , , , ,Y,F,P,xT,Q,A,L,N,F,A,F, +,,sp|P60709|ACTB_HUMAN,I,T,A,L,A,P,S,xT,M,K, , , , , , +,,sp|Q02878|RL6_HUMAN, , , , ,A,S,I,xT,P,G,T,I,L,I,I, +,,sp|P39656|OST48_HUMAN, , , , , ,A,P,xT,I,V,G,K, , , , +,,sp|Q9Y5B9|SP16H_HUMAN,I,F,P,N,P,E,A,xT,F,V,K, , , , , +,,sp|P11171|41_HUMAN, ,V,V,V,H,Q,E,xT,E,I,A,D,E, , , +,,sp|P55265|DSRAD_HUMAN, , , , , ,A,M,xT,I,L,L,E,E,A,K, +,,sp|Q99832|TCPH_HUMAN, , , , , ,T,F,xS,Y,A,G,F,E,M,Q, +,,sp|P17844|DDX5_HUMAN; sp|Q92841|DDX17_HUMAN, , , , , , ,Q,xT,L,M,W,S,A,T,W, +,,sp|Q9UBT2|SAE2_HUMAN, ,G,T,I,L,I,S,xS,E,E,G,E,T,E,A, +,,sp|P06744|G6PI_HUMAN, , , , , , , ,xT,F,T,T,Q,E,T,I, +,,sp|P37802|TAGL2_HUMAN, , , , ,I,Q,A,xS,T,M,A,F,K, , , +,,sp|Q9BVA1|TBB2B_HUMAN; sp|Q13885|TBB2A_HUMAN; sp|P68371|TBB4B_HUMAN,S,A,T,F,I,G,N,xS,T,A,I,Q,E,L,F, +,,sp|O60927|PP1RB_HUMAN, , ,A,F,G,E,S,xS,T,E,S,D,E,E,E, +,,sp|Q8IZL8|PELP1_HUMAN, , , , , , ,G,xS,P,D,G,S,L,Q,T, +,,sp|P15531|NDKA_HUMAN, , ,N,I,I,H,G,xS,D,S,V,E,S,A,E, +,,sp|Q6PJG2|EMSA1_HUMAN, , , , , ,A,G,xT,F,I,A,P,P,V,Y, +,,sp|Q9BWW4|SSBP3_HUMAN; sp|Q9BWG4|SSBP4_HUMAN; sp|P81877|SSBP2_HUMAN, , , , ,S,A,Q,xT,F,L,S,E,I,R, , +,,sp|P14625|ENPL_HUMAN, , , , , ,G,T,xT,I,T,L,V,L,K, , +,,sp|Q9NY33|DPP3_HUMAN, , , , , ,F,S,xT,I,A,S,S,Y,E,E, +,,sp|P28070|PSB4_HUMAN, , , , ,V,N,N,xS,T,M,L,G,A,S,G, +,,sp|P56556|NDUA6_HUMAN,Q,A,T,S,T,A,S,xT,F,V,K,P,I,F,S, +,,sp|Q01130|SRSF2_HUMAN, , , , , , , ,xS,R,S,P,P,P,V,S, +,,sp|P00558|PGK1_HUMAN,C,A,N,P,A,A,G,xS,V,I,L,L,E,N,L, +,,sp|Q9BZF1|OSBL8_HUMAN, , , ,V,V,L,P,xT,F,I,L,E,P,R, , +,,sp|P29350|PTN6_HUMAN, , , ,A,G,P,G,xS,P,L,R, , , , , +,,sp|P52209|6PGD_HUMAN, , ,V,V,G,A,Q,xS,L,K, , , , , , +,,sp|O43491|E41L2_HUMAN, ,V,C,V,E,H,H,xT,F,Y,R, , , , , +,,sp|P00558|PGK1_HUMAN, , , ,T,G,Q,A,xT,V,A,S,G,I,P,A, +,,sp|Q96KR1|ZFR_HUMAN,A,A,A,T,A,A,W,xT,G,T,T,F,T,K, , +,,sp|O15120|PLCB_HUMAN, , , , , , ,T,xT,F,L,H,I,S,K, , +,,sp|Q5JTH9|RRP12_HUMAN, , , , ,R,V,P,xS,P,V,L,I,K, , , +,,sp|P78417|GSTO1_HUMAN, ,V,P,S,L,V,G,xS,F,I,R, , , , , +,,sp|O00154|BACH_HUMAN, , , , , , ,A,xT,L,W,Y,V,P,L,S, +,,sp|P78347|GTF2I_HUMAN, , , , , ,S,P,xT,W,F,G,I,P,R, , +,,sp|P08758|ANXA5_HUMAN, , , , , , ,G,xT,V,T,D,F,P,G,F, +,,sp|P51991|ROA3_HUMAN, , , , , ,Y,H,xT,I,N,G,H,N,C,E, +,,sp|P35659|DEK_HUMAN,L,L,Y,N,R,P,G,xT,V,S,S,L,K, , , +,,sp|Q00839|HNRPU_HUMAN, , ,S,S,G,P,T,xS,L,F,A,V,T,V,A, +,,sp|O60927|PP1RB_HUMAN, , , ,A,F,G,E,xS,S,T,E,S,D,E,E, +,,sp|P07900|HS90A_HUMAN; sp|P08238|HS90B_HUMAN, ,I,R,Y,E,S,L,xT,D,P,S,K, , , , +,,sp|Q96KR1|ZFR_HUMAN,A,T,A,A,W,T,G,xT,T,F,T,K, , , , +,,sp|Q8N6L1|KTAP2_HUMAN, , , , ,I,S,S,xT,L,Y,Q,A,A,A,P, +,,sp|P10809|CH60_HUMAN, , , ,V,G,G,T,xS,D,V,E,V,N,E,K, +,,RRRRRsp|O14529|CUX2_HUMAN, , , , , , , ,xS,A,L,A,A,E,L,R, +,,sp|P50991|TCPD_HUMAN, , , , , ,T,V,xT,I,V,V,R, , , , +,,RRRRRsp|Q9P2D7|DYH1_HUMAN, , , , ,L,T,R,xS,I,R, , , , , , +,,sp|P25205|MCM3_HUMAN, ,S,E,D,E,S,E,xT,E,D,E,E,E,K, , +,,sp|O75436|VP26A_HUMAN,A,G,Y,D,P,T,P,xT,M,R, , , , , , +,,sp|Q9BV79|MECR_HUMAN, , , , , ,G,G,xT,M,V,T,Y,G,G,M, +,,sp|Q9H299|SH3L3_HUMAN, , , , , ,V,Y,xS,T,S,V,T,G,S,R, +,,sp|P39656|OST48_HUMAN, , , , , , , ,xS,S,L,N,P,I,L,F, +,,sp|P62195|PRS8_HUMAN, , ,A,V,A,H,H,xT,D,C,T,F,I,R, , +,,sp|P06733|ENOA_HUMAN, , , , ,G,N,P,xT,V,E,V,D,L,F,T, +,,sp|P30041|PRDX6_HUMAN, , , , ,R,V,A,xT,P,V,D,W,K, , , +,,sp|P15531|NDKA_HUMAN,N,I,I,H,G,S,D,xS,V,E,S,A,E,K, , +,,sp|Q9BVG9|PTSS2_HUMAN,A,G,G,P,R,P,E,xS,P,V,P,A,G,R, , +,,sp|O60942|MCE1_HUMAN,P,T,T,E,N,T,E,xT,F,I,R, , , , , +,,sp|Q7L2R6|ZN765_HUMAN, , , , , , , ,xS,K,L,Q,I,H,R, , +,,sp|P29218|IMPA1_HUMAN, , , , , ,Y,P,xS,H,S,F,I,G,E,E, +,,sp|Q8NBS9|TXND5_HUMAN, , , , ,G,Y,P,xT,L,L,W,F,R, , , +,,RRRRRsp|O14529|CUX2_HUMAN,L,R,P,G,S,C,L,xT,F,N,V,K, , , , +,,sp|Q9NY33|DPP3_HUMAN, , , , , , ,F,xS,T,I,A,S,S,Y,E, +,,sp|P06744|G6PI_HUMAN, , , , ,T,F,T,xT,Q,E,T,I,T,N,A, +,,sp|O43684|BUB3_HUMAN, ,T,P,C,N,A,G,xT,F,S,Q,P,E,K, , +,,sp|O15417|TNC18_HUMAN,G,A,V,E,R,P,L,xT,P,A,P,R, , , , +,,sp|Q9H1E3|NUCKS_HUMAN,M,L,M,E,D,V,G,xS,E,E,E,Q,E,E,E, +,,sp|O15347|HMGB3_HUMAN, , , , ,R,P,P,xS,G,F,F,L,F, , , +,,sp|P51610|HCFC1_HUMAN,G,A,P,G,Q,P,G,xT,I,L,R, , , , , +,,sp|P0DP25|CALM3_HUMAN; sp|P0DP24|CALM2_HUMAN; sp|P0DP23|CALM1_HUMAN, , , , , , ,D,xT,D,S,E,E,E,I,R, +,,sp|Q15029|U5S1_HUMAN, , , , , ,T,A,xT,I,T,E,P,R, , , +,,sp|Q9Y4P3|TBL2_HUMAN,E,D,G,G,Y,T,F,xT,A,T,P,E,D,F,P, +,,sp|P19338|NUCL_HUMAN, , , , ,V,V,V,xS,P,T,K,K, , , , +,,sp|P37108|SRP14_HUMAN, , , , , , ,I,xS,T,V,V,S,S,K, , +,,sp|O60927|PP1RB_HUMAN,F,G,E,S,S,T,E,xS,D,E,E,E,E,E,G, +,,sp|P56556|NDUA6_HUMAN, , , , ,Q,A,T,xS,T,A,S,T,F,V,K, +,,sp|P49585|PCY1A_HUMAN, , , ,E,R,S,P,xS,P,S,F,R, , , , +,,sp|Q96I25|SPF45_HUMAN, , ,S,P,T,G,P,xS,N,S,F,L,A,N,M, +,,sp|Q7KZI7|MARK2_HUMAN, , , , , , , ,xS,T,F,H,A,G,Q,L, +,,sp|Q2KHR2|RFX7_HUMAN, , , , , , , ,xS,P,T,T,V,L,F,T, +,,sp|P10809|CH60_HUMAN, , , , ,V,G,G,xT,S,D,V,E,V,N,E, +,,sp|P08865|RSSA_HUMAN, , , , , , ,F,xT,P,G,T,F,T,N,Q, +,,sp|P62913|RL11_HUMAN, , ,I,A,V,H,C,xT,V,R, , , , , , +,,sp|P15880|RS2_HUMAN, , , , , , ,A,xT,F,D,A,I,S,K, , +,,sp|O75436|VP26A_HUMAN,F,L,A,G,Y,D,P,xT,P,T,M,R, , , , +,,sp|Q7KZI7|MARK2_HUMAN, , , , , , ,S,xT,F,H,A,G,Q,L,R, +,,sp|Q9UJF2|NGAP_HUMAN, , , ,T,G,G,P,xS,I,R,I,K, , , , +,,sp|B0I1T2|MYO1G_HUMAN, , , , , , ,G,xS,F,T,L,L,W,P,S, +,,sp|P25787|PSA2_HUMAN, , , , , ,G,Y,xS,F,S,L,T,T,F,S, +,,sp|Q96ST2|IWS1_HUMAN, , , ,A,A,V,L,xS,D,S,E,D,E,E,K, +,,sp|Q9UI08|EVL_HUMAN, ,Y,N,Q,A,T,P,xT,F,H,Q,W,R, , , +,,sp|Q96KR1|ZFR_HUMAN,A,A,A,A,A,A,A,xT,A,A,W,T,G,T,T, +,,sp|O60942|MCE1_HUMAN,G,H,G,E,C,P,T,xT,E,N,T,E,T,F,I, +,,sp|P53396|ACLY_HUMAN, , , , , ,S,T,xT,L,F,S,R, , , , +,,sp|Q9UPP1|PHF8_HUMAN, , , ,T,G,S,P,xT,F,V,R, , , , , +,,sp|Q96KR1|ZFR_HUMAN,A,W,T,G,T,T,F,xT,K, , , , , , , +,,sp|P62195|PRS8_HUMAN,V,A,H,H,T,D,C,xT,F,I,R, , , , , +,,sp|O60927|PP1RB_HUMAN, ,A,F,G,E,S,S,xT,E,S,D,E,E,E,E, +,,sp|Q9Y4P3|TBL2_HUMAN, ,R,E,D,G,G,Y,xT,F,T,A,T,P,E,D, +,,sp|Q9NVV0|TM38B_HUMAN, , , ,G,A,G,G,xT,I,I,T,N,F,E,R, +,,sp|Q5SSJ5|HP1B3_HUMAN, , , ,T,R,P,S,xS,T,V,I,K, , , , +,,tr|K7EKS7|K7EKS7_HUMAN; sp|P35268|RL22_HUMAN, , , , , , ,I,xT,V,T,S,E,V,P,F, +,,sp|Q8IYB3|SRRM1_HUMAN, , , , , ,K,E,xT,E,S,E,A,E,D,N, +,,sp|Q9P258|RCC2_HUMAN, , , , , , ,E,xS,T,M,Y,P,K, , , +,,sp|Q8IYU2|HACE1_HUMAN; sp|Q96R06|SPAG5_HUMAN; sp|A9Z1Z3|FR1L4_HUMAN; RRRRRsp|Q6ZRV2|FA83H_HUMAN; RRRRRsp|Q12788|TBL3_HUMAN; RRRRRsp|O14492|SH2B2_HUMAN, , , , ,L,T,R,xS,L,R, , , , , , +,,sp|Q93084|AT2A3_HUMAN; sp|P16615|AT2A2_HUMAN, , , , , , , ,xT,G,T,L,T,T,N,Q, +,,sp|Q86Y56|DAAF5_HUMAN, ,S,A,E,L,V,G,xT,F,V,S,P,E,V,F, +,,sp|P52756|RBM5_HUMAN, ,S,E,D,G,Y,H,xS,D,G,D,Y,G,E,H, +,,sp|Q8IYB3|SRRM1_HUMAN, , , , , ,R,E,xS,P,S,P,A,P,K,P, +,,sp|P07900|HS90A_HUMAN; sp|P08238|HS90B_HUMAN, , , , , , , ,xS,L,T,N,D,W,E,D, +,,sp|P35249|RFC4_HUMAN, , , , , , ,G,xT,S,I,S,T,K,P,P, +,,sp|Q8IZL8|PELP1_HUMAN, , ,G,S,P,D,G,xS,L,Q,T,G,K,P,S, +,,sp|Q01130|SRSF2_HUMAN, , , , , ,S,R,xS,P,P,P,V,S,K, , +,,sp|Q14137|BOP1_HUMAN,D,E,Y,A,E,D,S,xS,D,E,E,D,I,R, , +,,sp|P21439|MDR3_HUMAN; sp|P08183|MDR1_HUMAN, , , , , ,F,D,xT,L,V,G,E,R, , , +,,sp|P07686|HEXB_HUMAN, , , ,L,A,P,G,xT,I,V,E,V,W,K, , +,,sp|P07814|SYEP_HUMAN, , ,A,I,Q,G,G,xT,S,H,H,L,G,Q,N, +,,sp|Q9Y277|VDAC3_HUMAN, ,V,C,N,Y,G,L,xT,F,T,Q,K, , , , +,,sp|Q00839|HNRPU_HUMAN, , , ,S,S,G,P,xT,S,L,F,A,V,T,V, +,,sp|P62753|RS6_HUMAN; RRRRRsp|Q9Y5G2|PCDGE_HUMAN; sp|Q5H9U9|DDX6L_HUMAN; sp|Q8TCT7|SPP2B_HUMAN; RRRRRsp|Q9Y471|CMAH_HUMAN; RRRRRsp|Q9HAU5|RENT2_HUMAN, , , , , , , ,xT,F,Y,E,K, , , , +,,sp|P62805|H4_HUMAN, , , , ,D,A,V,xT,Y,T,E,H,A,K, , +,,sp|Q9Y678|COPG1_HUMAN; sp|Q9UBF2|COPG2_HUMAN, ,E,L,A,P,A,V,xS,V,L,Q,L,F,C,S, +,,sp|O75534|CSDE1_HUMAN, , , , , ,E,A,xT,F,S,N,P,K, , , +,,sp|P62263|RS14_HUMAN, , ,A,S,F,N,D,xT,F,V,H,V,T,D,L, +,,sp|P49406|RM19_HUMAN, , , ,G,L,G,A,xT,F,I,L,R, , , , +,,sp|P51692|STA5B_HUMAN; sp|P42229|STA5A_HUMAN, , , , , , ,A,xT,I,I,S,E,Q,Q,A, +,,sp|Q9C0C9|UBE2O_HUMAN, ,L,I,H,G,E,D,xS,D,S,E,G,E,E,E, +,,sp|Q9NY61|AATF_HUMAN, ,G,M,D,D,L,G,xS,S,E,E,E,E,D,E, +,,sp|P06733|ENOA_HUMAN, , , ,A,A,V,P,xS,G,A,S,T,G,I,Y, +,,sp|Q7Z4V5|HDGR2_HUMAN,S,S,S,S,D,S,D,xS,D,E,V,D,R, , , +,,sp|Q00839|HNRPU_HUMAN, , , , , , , ,xT,T,W,V,T,K, , , +,,sp|Q7Z4V5|HDGR2_HUMAN,P,E,R,P,P,S,S,xS,S,S,D,S,D,S,D, +,,sp|P40926|MDHM_HUMAN, ,E,G,V,V,E,C,xS,F,V,K, , , , , +,,sp|Q9BXY0|MAK16_HUMAN,Q,Q,E,A,E,S,D,xS,S,D,T,E,E,K,D, +,,sp|O75044|SRGP2_HUMAN; sp|P0DMP2|SRG2B_HUMAN; sp|P0DJJ0|SRG2C_HUMAN, , , , , , , ,xS,P,D,S,T,A,N,V, +,,sp|P51531|SMCA2_HUMAN, , , , , , , ,xS,D,S,E,E,S,D,S, +,,sp|P51532|SMCA4_HUMAN,P,V,V,S,D,D,D,xS,E,E,E,Q,E,E,D, +,,sp|Q15185|TEBP_HUMAN, , , , , , , ,xS,I,L,C,C,L,R, , +,,sp|Q07020|RL18_HUMAN, , , , , ,T,N,xS,T,F,N,Q,V,V,L, +,,sp|Q9BWS9|CHID1_HUMAN, , , ,N,V,L,D,xS,E,D,E,I,E,E,L, +,,sp|P54105|ICLN_HUMAN,A,D,E,E,E,E,D,xS,D,D,D,V,E,P,I, +,,sp|Q13111|CAF1A_HUMAN,P,S,T,T,Y,L,H,xT,P,T,P,S,E,D,A, +,,sp|Q9Y2M5|KLH20_HUMAN, , , ,L,P,L,L,xS,P,K, , , , , , +,,sp|Q9HCN4|GPN1_HUMAN,E,E,D,E,E,A,D,xS,D,T,D,D,I,D,H, +,,sp|Q7Z4V5|HDGR2_HUMAN,R,P,P,S,S,S,S,xS,D,S,D,S,D,E,V, +,,sp|Q9H4L5|OSBL3_HUMAN, ,A,L,V,H,Q,L,xS,N,E,S,R, , , , +,,sp|Q9Y2W1|TR150_HUMAN, , , , , , , ,xS,P,L,Q,S,V,V,V, +,,sp|P11021|BIP_HUMAN, , , , , , ,I,xT,I,T,N,D,Q,N,R, +,,sp|Q9Y2K6|UBP20_HUMAN,A,V,A,D,E,G,E,xS,E,S,E,D,D,D,L, +,,sp|P53396|ACLY_HUMAN, , , , , ,T,A,xS,F,S,E,S,R, , , +,,sp|P14866|HNRPL_HUMAN; tr|M0QYT0|M0QYT0_HUMAN, , , , , , ,S,xS,S,G,L,L,E,W,E, +,,sp|P61956|SUMO2_HUMAN; sp|Q6EEV6|SUMO4_HUMAN; sp|P55854|SUMO3_HUMAN, ,V,A,G,Q,D,G,xS,V,V,Q,F,K, , , +,,sp|P51784|UBP11_HUMAN, , ,D,G,H,Y,T,xT,F,A,C,N,K, , , +,,sp|P19338|NUCL_HUMAN, , , , , , , ,xS,G,E,E,V,V,I,P, +,,sp|Q9Y2W1|TR150_HUMAN, , , , , ,M,D,xS,F,D,E,D,L,A,R, +,,sp|Q92572|AP3S1_HUMAN, , , , , , ,E,xT,F,H,L,V,S,K, , +,,sp|O95671|ASML_HUMAN,A,D,T,F,E,D,L,xS,D,V,E,G,G,G,S, +,,sp|Q15047|SETB1_HUMAN, , , , , , ,G,xS,F,V,C,I,Y,A,G, +,,sp|P49959|MRE11_HUMAN, , , , ,G,N,D,xT,F,V,T,L,D,E,I, +,,sp|O00767|ACOD_HUMAN, , , , , ,G,S,xT,L,D,L,S,D,L,E, +,,sp|O15530|PDPK1_HUMAN, , , , , ,Q,V,xS,S,S,S,S,S,H,S, +,,sp|P35659|DEK_HUMAN, , ,N,K,E,E,S,xS,D,D,E,D,K,E,S, +,,sp|P07910|HNRPC_HUMAN,S,E,G,G,A,D,D,xS,A,E,E,G,D,L,L, +,,sp|Q9NXG2|THUM1_HUMAN, , , , , , ,G,xT,F,Q,I,V,Y,K, , +,,sp|O95218|ZRAB2_HUMAN, , , , , , ,E,xS,E,G,E,E,E,D,E, +,,sp|P17844|DDX5_HUMAN, , , , , , , ,xT,I,V,F,V,E,T,K, +,,sp|Q5VT52|RPRD2_HUMAN,D,V,E,D,M,E,L,xS,D,V,E,D,D,G,S, +,,sp|P47712|PA24A_HUMAN,H,I,V,S,N,D,S,xS,D,S,D,D,E,S,H, +,,sp|Q02790|FKBP4_HUMAN, , , , , ,E,G,xT,G,T,E,M,P,M,I, +,,sp|Q13769|THOC5_HUMAN,E,D,S,Q,D,D,E,xS,D,S,D,A,E,E,E, +,,sp|Q8N7H5|PAF1_HUMAN,D,S,E,D,D,A,D,xS,D,D,E,D,R, , , +,,sp|Q16539|MK14_HUMAN, , , , , , , ,xT,I,W,E,V,P,E,R, +,,sp|O94903|PLPHP_HUMAN, , , , , ,G,S,xT,I,F,G,E,R, , , +,,sp|P51531|SMCA2_HUMAN,P,V,V,S,D,F,D,xS,D,E,E,Q,D,E,R, +,,sp|Q9BXY0|MAK16_HUMAN,L,E,Q,Q,E,A,E,xS,D,S,S,D,T,E,E, +,,sp|Q9UNZ2|NSF1C_HUMAN, , , , , , , ,xS,P,N,E,L,V,D,D, +,,sp|P06748|NPM_HUMAN, , , , ,D,A,E,xS,E,D,E,E,E,E,D, +,,sp|Q06830|PRDX1_HUMAN, , , , , ,D,I,xS,L,S,D,Y,K, , , +,,sp|Q9UQ80|PA2G4_HUMAN,E,D,E,Q,Q,E,Q,xT,I,A,E,D,L,V,V, +,,sp|P60484|PTEN_HUMAN, ,Y,S,D,T,T,D,xS,D,P,E,N,E,P,F, +,,sp|P60484|PTEN_HUMAN, , , ,Y,S,D,T,xT,D,S,D,P,E,N,E, +,,sp|P0DP25|CALM3_HUMAN; sp|P0DP24|CALM2_HUMAN; sp|P0DP23|CALM1_HUMAN, ,D,G,N,G,Y,I,xS,A,A,E,L,R, , , +,,sp|O96018|APBA3_HUMAN, , , , , , , ,xS,P,S,G,P,P,A,M, +,,sp|O95714|HERC2_HUMAN,P,S,A,E,D,S,D,xT,E,D,D,S,E,A,E, +,,sp|Q01081|U2AF1_HUMAN; sp|P0DN76|U2AF5_HUMAN; tr|M0R2N4|M0R2N4_HUMAN; sp|Q8WU68|U2AF4_HUMAN, , , , ,V,N,C,xS,F,Y,F,K, , , , +,,sp|O15530|PDPK1_HUMAN, , , , , , , ,xS,L,S,A,S,D,T,G, +,,sp|Q96D46|NMD3_HUMAN,D,S,A,I,P,V,E,xS,D,T,D,D,E,G,A, +,,sp|Q9ULH1|ASAP1_HUMAN, ,Q,E,E,I,D,E,xS,D,D,D,L,D,D,K, +,,sp|Q8IYB3|SRRM1_HUMAN, , , , , , , ,xS,P,S,P,P,P,T,R, +,,sp|Q96T23|RSF1_HUMAN, , , , , ,I,E,xS,D,E,E,E,D,F,E, +,,sp|P19338|NUCL_HUMAN, , , , , , , ,xS,I,S,L,Y,Y,T,G, +,,sp|O00629|IMA3_HUMAN,H,E,D,I,C,E,D,xS,D,I,D,G,D,Y,R, +,,sp|Q6ZUV0|BACHL_HUMAN; sp|O00154|BACH_HUMAN, , , , , , ,M,xT,F,T,S,N,K, , , +,,sp|P42224|STAT1_HUMAN, , ,D,Q,Q,P,G,xT,F,L,L,R, , , , +,,sp|Q15459|SF3A1_HUMAN,E,V,E,M,E,V,E,xS,D,E,E,D,D,K,Q, +,,sp|Q15185|TEBP_HUMAN, , ,D,W,E,D,D,xS,D,E,D,M,S,N,F, +,,sp|P11142|HSP7C_HUMAN, , ,S,T,A,G,D,xT,H,L,G,G,E,D,F, +,,sp|O00170|AIP_HUMAN, , , , , , , ,xT,L,H,S,D,D,E,G, +,,sp|Q96N64|PWP2A_HUMAN, , , , , , , ,xS,P,E,A,V,G,P,E, +,,sp|Q9NWQ4|GPT2L_HUMAN, , , , , , , ,xS,P,S,S,E,W,L,V, +,,sp|P60709|ACTB_HUMAN; sp|P63261|ACTG_HUMAN, , , , , , , ,xS,Y,E,L,P,D,G,Q, +,,sp|O15164|TIF1A_HUMAN, , , , , , , ,xS,P,L,H,V,G,E,T, +,,sp|Q9UN86|G3BP2_HUMAN,E,P,E,L,D,E,E,xS,E,D,E,V,E,E,E, +,,sp|O43719|HTSF1_HUMAN, ,E,L,E,E,N,D,xS,E,N,S,E,F,E,D, +,,sp|P18858|DNLI1_HUMAN,Q,E,V,L,E,E,Q,xS,E,D,E,D,R, , , +,,sp|P08238|HS90B_HUMAN, , , , , ,D,N,xS,T,M,G,Y,M,M,A, +,,sp|Q86SQ4|AGRG6_HUMAN, , , , , , , ,xS,L,E,D,E,P,R, , +,,sp|Q7Z4V5|HDGR2_HUMAN,E,R,P,P,S,S,S,xS,S,D,S,D,S,D,E, +,,sp|Q8WVT3|TPC12_HUMAN, , , , , , , ,xS,P,S,F,G,G,A,S, +,,sp|Q9H6Z4|RANB3_HUMAN, , , , , , , ,xS,P,S,E,A,A,D,E, +,,sp|Q9BW71|HIRP3_HUMAN, , , ,L,L,G,D,xS,D,S,E,E,E,Q,K, +,,sp|Q13442|HAP28_HUMAN,K,S,L,D,S,D,E,xS,E,D,E,E,D,D,Y, +,,sp|Q16666|IF16_HUMAN, , , , , , ,G,xS,F,V,N,G,V,F,E, +,,sp|P11388|TOP2A_HUMAN, , , , , , , ,xS,F,G,S,T,C,Q,L, +,,sp|O15530|PDPK1_HUMAN,S,S,S,S,H,S,L,xS,A,S,D,T,G,L,P, +,,sp|Q6KC79|NIPBL_HUMAN, , , ,V,D,S,D,xS,D,S,D,S,E,D,D, +,,sp|Q7Z4V5|HDGR2_HUMAN,P,K,P,E,R,P,P,xS,S,S,S,S,D,S,D, +,,sp|Q8IYB3|SRRM1_HUMAN, , , ,S,R,S,P,xS,P,A,P,E,K, , , +,,RRRRRsp|Q9H7J1|PPR3E_HUMAN,G,G,G,G,A,P,A,xS,R, , , , , , , +,,sp|Q7Z4V5|HDGR2_HUMAN,K,P,E,R,P,P,S,xS,S,S,S,D,S,D,S, +,,sp|Q9P2I0|CPSF2_HUMAN, , ,E,A,D,I,D,xS,S,D,E,S,D,I,E, +,,sp|P19338|NUCL_HUMAN, , , , , , ,E,xS,F,D,G,S,V,R, , +,,sp|Q16778|H2B2E_HUMAN; sp|P33778|H2B1B_HUMAN; sp|P23527|H2B1O_HUMAN; sp|P06899|H2B1J_HUMAN; sp|Q8N257|H2B3B_HUMAN; sp|Q6DRA6|H2B2D_HUMAN; sp|Q6DN03|H2B2C_HUMAN, , , , , , ,E,xS,Y,S,I,Y,V,Y,K, +,,sp|Q9BWU0|NADAP_HUMAN, , , , , , ,G,xT,S,Y,C,L,F,G,R, +,,sp|O00571|DDX3X_HUMAN, , , , , , ,S,xS,F,F,S,D,R, , , +,,sp|P55010|IF5_HUMAN, ,E,A,E,E,E,S,xS,G,G,E,E,E,D,E, +,,sp|P23193|TCEA1_HUMAN, , , , , , ,D,xT,Y,V,S,S,F,P,R, +,,sp|P51531|SMCA2_HUMAN, , , , , ,S,D,xS,E,E,S,D,S,D,Y, +,,sp|P51531|SMCA2_HUMAN,E,E,E,S,E,D,E,xS,N,E,E,E,E,E,E, +,,sp|P62805|H4_HUMAN,S,G,L,I,Y,E,E,xT,R, , , , , , , +,,sp|Q8NFC6|BD1L1_HUMAN, , , ,Y,Y,S,D,xS,D,D,E,L,T,V,E, +,,sp|P06454|PTMA_HUMAN,D,A,A,V,D,T,S,xS,E,I,T,T,K, , , +,,sp|Q9H307|PININ_HUMAN, , , , , ,Q,E,xS,D,P,E,D,D,D,V, +,,sp|Q9Y3X0|CCDC9_HUMAN, , , , , , , ,xS,P,G,T,P,R,P,P, +,,sp|Q15653|IKBB_HUMAN,S,G,P,C,S,S,S,xS,D,S,D,S,G,D,E, +,,sp|O94826|TOM70_HUMAN, , , ,N,V,D,L,xS,T,F,Y,Q,N,R, , +,,sp|Q99733|NP1L4_HUMAN,V,E,P,T,D,A,E,xS,E,W,H,S,E,N,E, +,,sp|Q7L1Q6|BZW1_HUMAN, , ,N,A,E,E,E,xS,E,S,E,A,E,E,G, +,,sp|Q71U36|TBA1A_HUMAN; sp|P68363|TBA1B_HUMAN; sp|Q9BQE3|TBA1C_HUMAN, , , , , , , ,xT,I,G,G,G,D,D,S, +,,sp|O60841|IF2P_HUMAN, ,I,N,S,S,G,E,xS,G,D,E,S,D,E,F, +,,sp|Q5T0Z8|CF132_HUMAN, , , , , , ,S,xS,A,A,F,P,P,K, , +,,sp|Q9UK45|LSM7_HUMAN, , , , , , ,E,xS,I,L,D,L,S,K, , +,,sp|Q9Y6I3|EPN1_HUMAN, , , , , , , ,xS,P,G,A,F,D,M,S, +,,sp|Q14978|NOLC1_HUMAN,S,S,D,S,E,D,S,xS,E,E,E,E,E,V,Q, +,,sp|Q14444|CAPR1_HUMAN, , , , , , , ,xS,F,M,A,L,S,Q,D, +,,sp|Q7Z4V5|HDGR2_HUMAN,P,S,S,S,S,S,D,xS,D,S,D,E,V,D,R, +,,sp|O15530|PDPK1_HUMAN,S,S,S,S,S,S,H,xS,L,S,A,S,D,T,G, +,,sp|P04075|ALDOA_HUMAN, , , ,A,L,A,N,xS,L,A,C,Q,G,K, , +,,sp|O43310|CTIF_HUMAN, , , , , , , ,xS,P,D,T,L,A,P,V, +,,sp|Q13769|THOC5_HUMAN,L,F,K,P,P,E,D,xS,Q,D,D,E,S,D,S, +,,sp|P51858|HDGF_HUMAN, , ,G,N,A,E,G,xS,S,D,E,E,G,K,L, +,,sp|Q9Y5J1|UTP18_HUMAN, , , , , , , ,xT,S,S,D,D,E,S,E, +,,sp|Q96HE9|PRR11_HUMAN; tr|J3QRE1|J3QRE1_HUMAN, , , , , , , ,xS,P,G,G,T,P,L,T, +,,sp|Q8TBC4|UBA3_HUMAN, ,I,Q,D,F,N,D,xT,F,Y,R, , , , , +,,sp|O60841|IF2P_HUMAN, , , , , ,I,N,xS,S,G,E,S,G,D,E, +,,sp|Q8NFC6|BD1L1_HUMAN, , , , , ,Y,Y,xS,D,S,D,D,E,L,T, +,,sp|P52756|RBM5_HUMAN, ,G,L,V,A,A,Y,xS,G,D,S,D,N,E,E, +,,sp|Q92797|SYMPK_HUMAN, , , , ,S,P,Q,xT,L,A,P,V,G,E,D, +,,sp|P40227|TCPZ_HUMAN, , , , , , ,E,xT,L,I,D,V,A,R, , +,,sp|Q9Y5B6|PAXB1_HUMAN, ,E,D,E,N,D,A,xS,D,D,E,D,D,D,E, +,,sp|Q6KC79|NIPBL_HUMAN, ,V,D,S,D,S,D,xS,D,S,E,D,D,I,N, +,,sp|Q9P2I0|CPSF2_HUMAN,D,I,D,S,S,D,E,xS,D,I,E,E,D,I,D, +,,sp|P49915|GUAA_HUMAN, , , ,I,I,G,D,xT,F,V,K, , , , , +,,sp|P14866|HNRPL_HUMAN; tr|M0QYT0|M0QYT0_HUMAN, , , , , ,S,S,xS,G,L,L,E,W,E,S, +,,sp|P51531|SMCA2_HUMAN,S,D,S,E,E,S,D,xS,D,Y,E,E,E,D,E, +,,sp|Q15653|IKBB_HUMAN,S,S,S,S,D,S,D,xS,G,D,E,G,D,E,Y, +,,sp|Q5VUA4|ZN318_HUMAN, , , , , , , ,xS,P,T,V,L,C,Q,K, +,,sp|O43719|HTSF1_HUMAN,E,E,N,D,S,E,N,xS,E,F,E,D,D,G,S, +,,sp|P25205|MCM3_HUMAN, , , , , ,A,G,xT,V,V,L,D,D,V,E, +,,sp|Q7L1Q6|BZW1_HUMAN,N,A,E,E,E,S,E,xS,E,A,E,E,G,D, , +,,sp|P49736|MCM2_HUMAN, , ,G,L,L,Y,D,xS,D,E,E,D,E,E,R, +,,sp|O60341|KDM1A_HUMAN, , , , , ,S,T,xS,Q,T,F,I,Y,K, , +,,sp|O00170|AIP_HUMAN, , , , ,T,L,H,xS,D,D,E,G,T,V,L, +,,sp|Q15653|IKBB_HUMAN, ,S,G,P,C,S,S,xS,S,D,S,D,S,G,D, +,,sp|Q9Y5J1|UTP18_HUMAN, , , , , , ,T,xS,S,D,D,E,S,E,E, +,,sp|P25205|MCM3_HUMAN,D,P,Y,D,F,S,D,xT,E,E,E,M,P,Q,V, +,,sp|Q9Y5B6|PAXB1_HUMAN,R,E,D,E,N,D,A,xS,D,D,E,D,D,D,E, +,,sp|Q15785|TOM34_HUMAN, ,V,L,Q,A,Q,G,xS,S,D,P,E,E,E,S, +,,sp|Q9BW71|HIRP3_HUMAN,G,S,T,S,G,E,E,xS,D,L,E,R, , , , +,,sp|P19338|NUCL_HUMAN, , , ,V,E,E,D,xS,E,D,E,E,M,S,E, +,,sp|Q14978|NOLC1_HUMAN,S,S,S,D,S,E,D,xS,S,E,E,E,E,E,V, +,,sp|P41250|GARS_HUMAN,A,A,A,Q,I,G,N,xS,F,R, , , , , , +,,sp|P06748|NPM_HUMAN, , , , , , , ,xS,E,D,E,E,E,E,D, +,,sp|Q6UN15|FIP1_HUMAN; tr|A0A0B4J203|A0A0B4J203_HUMAN,E,T,E,D,D,S,D,xS,D,S,D,D,D,E,D, +,,sp|P25205|MCM3_HUMAN,S,Y,D,P,Y,D,F,xS,D,T,E,E,E,M,P, +,,sp|Q9HC44|GPBL1_HUMAN, , , , , ,S,P,xT,A,T,F,E,K, , , +,,sp|P19338|NUCL_HUMAN, , , , , , , ,xT,G,I,S,D,V,F,A, +,,sp|Q9P2I0|CPSF2_HUMAN, ,E,A,D,I,D,S,xS,D,E,S,D,I,E,E, +,,sp|P07900|HS90A_HUMAN,P,E,I,E,D,V,G,xS,D,E,E,E,E,K, , +,,sp|P55010|IF5_HUMAN, , ,E,A,E,E,E,xS,S,G,G,E,E,E,D, +,,sp|P52788|SPSY_HUMAN, , , , , ,N,G,xS,F,A,N,L,R, , , +,,sp|Q99618|CDCA3_HUMAN, , , , , , , ,xS,P,T,L,G,I,A,R, +,,sp|O00499|BIN1_HUMAN, , , , , , , ,xS,P,P,D,G,S,P,A, +,,RRRRRsp|Q9P2D6|F135A_HUMAN, , , , , , , ,xS,Q,L,V,P,R, , , +,,sp|Q8IYB3|SRRM1_HUMAN, , , , , ,S,P,xS,A,S,P,P,R, , , +,,sp|P11388|TOP2A_HUMAN, , , , ,S,F,G,xS,T,C,Q,L,S,E,K, +,,sp|P55197|AF10_HUMAN, , , , , , , ,xS,P,V,S,S,L,Q,I, +,,sp|Q53T59|H1BP3_HUMAN, , , , , , , ,xS,P,G,A,A,G,L,T, +,,sp|Q6UN15|FIP1_HUMAN; tr|A0A0B4J203|A0A0B4J203_HUMAN,V,T,E,T,E,D,D,xS,D,S,D,S,D,D,D, +,,sp|Q9NWQ4|GPT2L_HUMAN, , , , , ,S,P,xS,S,E,W,L,V,R, , +,,sp|Q8IUR0|TPPC5_HUMAN, , , , , , , ,xT,F,Y,I,I,E,R, , +,,tr|A0A2R8Y422|A0A2R8Y422_HUMAN; sp|P62987|RL40_HUMAN; sp|P62979|RS27A_HUMAN; sp|P0CG48|UBC_HUMAN; sp|P0CG48|UBC_HUMAN; sp|P0CG48|UBC_HUMAN; sp|P0CG48|UBC_HUMAN; sp|P0CG48|UBC_HUMAN; sp|P0CG48|UBC_HUMAN; sp|P0CG48|UBC_HUMAN; sp|P0CG48|UBC_HUMAN; sp|P0CG48|UBC_HUMAN; sp|P0CG47|UBB_HUMAN; sp|P0CG47|UBB_HUMAN; sp|P0CG47|UBB_HUMAN, , , , , , , ,xT,L,S,D,Y,N,I,Q, +,,sp|Q9BXY0|MAK16_HUMAN,Q,E,A,E,S,D,S,xS,D,T,E,E,K,D,D, +,,sp|P25054|APC_HUMAN, , , , , , , ,xS,P,T,G,N,T,P,P, +,,sp|Q9BPX3|CND3_HUMAN,C,E,G,T,E,I,N,xS,D,D,E,Q,E,S,K, +,,sp|P51531|SMCA2_HUMAN, , ,S,D,S,E,E,xS,D,S,D,Y,E,E,E, +,,sp|P14625|ENPL_HUMAN, , , , , , , ,xT,F,E,I,N,P,R, , +,,sp|Q9NWQ8|PHAG1_HUMAN,A,E,F,A,E,Y,A,xS,V,D,R, , , , , +,,sp|Q99618|CDCA3_HUMAN, , , , , , , ,xS,P,S,A,G,I,L,R, +,,sp|Q9BXY0|MAK16_HUMAN,A,E,S,D,S,S,D,xT,E,E,K,D,D,D,D, +,,sp|Q13523|PRP4B_HUMAN, , , , , , , ,xS,P,V,D,L,R, , , +,,sp|Q15785|TOM34_HUMAN,V,L,Q,A,Q,G,S,xS,D,P,E,E,E,S,V, +,,tr|A0A1W2PNV4|A0A1W2PNV4_HUMAN, , , , ,G,C,L,xT,F,V,S,K, , , , +,,sp|Q8IX90|SKA3_HUMAN, ,A,L,D,G,E,E,xS,D,F,E,D,Y,P,M, +,,sp|Q9NSD9|SYFB_HUMAN, , , ,D,R,Y,D,xS,F,I,E,L,Q,E,K, +,,RRRRRsp|Q9NQ90|ANO2_HUMAN, , , , , , , ,xT,R,V,A,D,P,R, , +,,sp|Q15459|SF3A1_HUMAN, , , , , ,T,A,xS,F,V,A,R, , , , +,,sp|Q15653|IKBB_HUMAN, , , , , , , ,xS,G,P,C,S,S,S,S, +,,sp|P14866|HNRPL_HUMAN; tr|M0QYT0|M0QYT0_HUMAN, , , , , , , ,xS,S,S,G,L,L,E,W, +,,sp|O00767|ACOD_HUMAN, , , , , , ,G,xS,T,L,D,L,S,D,L, +,,sp|Q99733|NP1L4_HUMAN,I,T,G,D,V,E,P,xT,D,A,E,S,E,W,H, +,,sp|Q12904|AIMP1_HUMAN, , , , , ,A,Q,xT,M,S,N,S,G,I,K, +,,sp|P41212|ETV6_HUMAN, , , , , , , ,xS,P,L,D,N,M,I,R, +,,sp|Q09028|RBBP4_HUMAN; sp|Q16576|RBBP7_HUMAN, , , , , , , ,xT,V,A,L,W,D,L,R, +,,sp|P53999|TCP4_HUMAN, , , , ,E,Q,I,xS,D,I,D,D,A,V,R, +,,sp|Q15723|ELF2_HUMAN, , , , , , , ,xS,P,T,T,T,A,S,V, +,,sp|Q13435|SF3B2_HUMAN,K,D,S,D,D,D,S,xS,D,D,E,Q,E,K, , +,,tr|A0A2R8Y422|A0A2R8Y422_HUMAN; sp|P62987|RL40_HUMAN; sp|P62979|RS27A_HUMAN; sp|P0CG48|UBC_HUMAN; sp|P0CG48|UBC_HUMAN; sp|P0CG48|UBC_HUMAN; sp|P0CG48|UBC_HUMAN; sp|P0CG48|UBC_HUMAN; sp|P0CG48|UBC_HUMAN; sp|P0CG48|UBC_HUMAN; sp|P0CG48|UBC_HUMAN; sp|P0CG48|UBC_HUMAN; sp|P0CG47|UBB_HUMAN; sp|P0CG47|UBB_HUMAN; sp|P0CG47|UBB_HUMAN, , , , , ,T,L,xS,D,Y,N,I,Q,K, , +,,sp|O15530|PDPK1_HUMAN, , , , ,Q,V,S,xS,S,S,S,S,H,S,L, +,,sp|Q9BVC4|LST8_HUMAN, , , , , , , ,xT,V,Q,H,Q,D,S,Q, +,,sp|P05023|AT1A1_HUMAN; tr|A0A2R8YEY8|A0A2R8YEY8_HUMAN; sp|P50993|AT1A2_HUMAN; sp|P13637|AT1A3_HUMAN; sp|P20648|ATP4A_HUMAN, , , , , ,T,G,xT,L,T,Q,N,R, , , +,,RRRRRsp|Q8IWI9|MGAP_HUMAN, , , , ,G,A,S,xS,P,S,A,G,S,N,G, +,,sp|Q9UN86|G3BP2_HUMAN,E,D,E,V,F,G,D,xS,E,P,E,L,D,E,E, +,,sp|Q15653|IKBB_HUMAN,P,C,S,S,S,S,D,xS,D,S,G,D,E,G,D, +,,sp|P51398|RT29_HUMAN, , , , , , ,N,xT,S,F,A,Y,P,A,I, +,,sp|P07900|HS90A_HUMAN, , , , ,D,N,S,xT,M,G,Y,M,A,A,K, +,,sp|P25788|PSA3_HUMAN,S,L,K,E,E,D,E,xS,D,D,D,N,M, , , +,,sp|P09211|GSTP1_HUMAN, , , , , , ,A,xS,C,L,Y,G,Q,L,P, +,,sp|P35659|DEK_HUMAN, , , ,N,K,E,E,xS,S,D,D,E,D,K,E, +,,sp|O60343|TBCD4_HUMAN, , , , , ,S,P,xS,A,M,Q,Q,Q,D,G, +,,sp|Q14498|RBM39_HUMAN, , , , , , , ,xS,P,Y,S,G,P,K, , +,,sp|Q9Y5J1|UTP18_HUMAN, , , , , ,T,S,xS,D,D,E,S,E,E,D, +,,sp|Q99880|H2B1L_HUMAN; sp|Q99879|H2B1M_HUMAN; sp|Q99877|H2B1N_HUMAN; sp|Q93079|H2B1H_HUMAN; sp|P62807|H2B1C_HUMAN; sp|P58876|H2B1D_HUMAN; sp|O60814|H2B1K_HUMAN; sp|Q5QNW6|H2B2F_HUMAN; sp|P57053|H2BFS_HUMAN; sp|Q16778|H2B2E_HUMAN; sp|P33778|H2B1B_HUMAN; sp|P23527|H2B1O_HUMAN; sp|P06899|H2B1J_HUMAN; sp|Q8N257|H2B3B_HUMAN, , , , , , , ,xS,F,V,N,D,I,F,E, +,,sp|Q08945|SSRP1_HUMAN,S,Y,D,E,Y,A,D,xS,D,E,D,Q,H,D,A, +,,sp|O95714|HERC2_HUMAN,L,P,A,A,A,Q,P,xS,A,E,D,S,D,T,E, +,,sp|P08238|HS90B_HUMAN, , ,N,P,D,D,I,xT,Q,E,E,Y,G,E,F, +,,sp|P35579|MYH9_HUMAN, ,K,G,A,G,D,G,xS,D,E,E,V,D,G,K, +,,sp|O15530|PDPK1_HUMAN,Q,V,S,S,S,S,S,xS,H,S,L,S,A,S,D, +,,sp|P07910|HNRPC_HUMAN, , , , , ,M,E,xS,E,G,G,A,D,D,S, +,,sp|Q15233|NONO_HUMAN, , , , , , , ,xT,F,N,L,E,K, , , +,,sp|Q96D46|NMD3_HUMAN,A,I,P,V,E,S,D,xT,D,D,E,G,A,P,R, +,,sp|O95714|HERC2_HUMAN,A,Q,P,S,A,E,D,xS,D,T,E,D,D,S,E, +,,sp|Q96EY8|MMAB_HUMAN, , , , ,G,F,S,xS,T,F,T,G,E,R, , +,,sp|P0DP25|CALM3_HUMAN; sp|P0DP24|CALM2_HUMAN; sp|P0DP23|CALM1_HUMAN, , , , ,D,T,D,xS,E,E,E,I,R, , , +,,sp|O60841|IF2P_HUMAN, , , , ,I,N,S,xS,G,E,S,G,D,E,S, +,,sp|Q14676|MDC1_HUMAN, , , , ,D,S,D,xT,D,V,E,E,E,E,L, +,,sp|P06748|NPM_HUMAN, , , , , , ,E,xS,E,D,E,E,E,E,D, +,,sp|P47712|PA24A_HUMAN,V,S,N,D,S,S,D,xS,D,D,E,S,H,E,P, +,,sp|P20674|COX5A_HUMAN, , , , ,G,I,N,xT,L,V,T,Y,D,M,V, +,,sp|Q5T200|ZC3HD_HUMAN, , , , , , , ,xS,P,S,H,L,T,E,D, +,,sp|Q99733|NP1L4_HUMAN,D,A,E,S,E,W,H,xS,E,N,E,E,E,E,K, +,,sp|P51398|RT29_HUMAN, , , , , ,N,T,xS,F,A,Y,P,A,I,R, +,,sp|P62280|RS11_HUMAN, , , , , ,Q,P,xT,I,F,Q,N,K, , , +,,sp|Q7L2H7|EIF3M_HUMAN, , , , , ,W,I,xS,D,W,N,L,T,T,E, +,,sp|Q9UQ80|PA2G4_HUMAN, , , , , , , ,xT,I,I,Q,N,P,T,D, +,,sp|Q13769|THOC5_HUMAN,S,Q,D,D,E,S,D,xS,D,A,E,E,E,Q,T, +,,sp|Q14676|MDC1_HUMAN, , , , , , ,D,xS,D,T,D,V,E,E,E, +,,sp|P01911|2B1F_HUMAN; sp|P04440|DPB1_HUMAN, , , , , ,F,D,xS,D,V,G,E,F,R, , +,,sp|Q5H9R7|PP6R3_HUMAN,Q,Q,F,D,D,G,G,xS,D,E,E,D,I,W,E, +,,sp|P36578|RL4_HUMAN, ,L,D,E,L,Y,G,xT,W,R, , , , , , +,,sp|Q08945|SSRP1_HUMAN, , ,E,G,M,N,P,xS,Y,D,E,Y,A,D,S, +,,sp|P49585|PCY1A_HUMAN, , , , , , , ,xS,P,S,P,S,F,R, , +,,sp|Q15653|IKBB_HUMAN, , ,S,G,P,C,S,xS,S,S,D,S,D,S,G, +,,sp|Q53EZ4|CEP55_HUMAN, , , , , , , ,xS,P,T,A,A,L,N,E, +,,sp|P51531|SMCA2_HUMAN, , ,A,K,P,V,V,xS,D,F,D,S,D,E,E, +,,sp|Q13111|CAF1A_HUMAN, , , , ,S,P,S,xT,T,Y,L,H,T,P,T, +,,sp|Q9BVC4|LST8_HUMAN, ,T,V,Q,H,Q,D,xS,Q,V,N,A,L,E,V, +,,sp|P07900|HS90A_HUMAN, , ,N,P,D,D,I,xT,N,E,E,Y,G,E,F, +,,sp|O15530|PDPK1_HUMAN, ,Q,V,S,S,S,S,xS,S,H,S,L,S,A,S, +,,sp|Q01543|FLI1_HUMAN, , , , , , , ,xS,P,P,L,G,G,A,Q, +,,sp|P29692|EF1D_HUMAN,D,D,I,D,L,F,G,xS,D,N,E,E,E,D,K, +,,sp|P46776|RL27A_HUMAN, , , , , ,N,Q,xS,F,C,P,T,V,N,L, +,,sp|Q9NYB0|TE2IP_HUMAN, , , , , , , ,xS,P,S,S,V,T,G,N, +,,sp|P08238|HS90B_HUMAN, ,K,I,E,D,V,G,xS,D,E,E,D,D,S,G, +,,sp|Q99880|H2B1L_HUMAN; sp|Q99879|H2B1M_HUMAN; sp|Q99877|H2B1N_HUMAN; sp|Q93079|H2B1H_HUMAN; sp|P62807|H2B1C_HUMAN; sp|P58876|H2B1D_HUMAN; sp|O60814|H2B1K_HUMAN; sp|Q5QNW6|H2B2F_HUMAN; sp|P57053|H2BFS_HUMAN; sp|Q16778|H2B2E_HUMAN; sp|P33778|H2B1B_HUMAN; sp|P23527|H2B1O_HUMAN; sp|P06899|H2B1J_HUMAN; sp|Q8N257|H2B3B_HUMAN, , ,Q,V,H,P,D,xT,G,I,S,S,K, , , +,,sp|P60484|PTEN_HUMAN, , , , ,Y,S,D,xT,T,D,S,D,P,E,N, +,,sp|P51858|HDGF_HUMAN, ,G,N,A,E,G,S,xS,D,E,E,G,K,L,V, +,,sp|Q15056|IF4H_HUMAN, , , , ,A,Y,S,xS,F,G,G,G,R, , , +,,sp|P62308|RUXG_HUMAN; sp|A8MWD9|RUXGL_HUMAN, , , , , ,G,N,xS,I,I,M,L,E,A,L, +,,sp|P51532|SMCA4_HUMAN, , ,A,K,P,V,V,xS,D,D,D,S,E,E,E, +,,sp|Q02790|FKBP4_HUMAN, , , ,E,G,T,G,xT,E,M,P,M,I,G,D, +,,sp|Q13111|CAF1A_HUMAN, , , ,S,P,S,T,xT,Y,L,H,T,P,T,P, +,,sp|Q6UN15|FIP1_HUMAN; tr|A0A0B4J203|A0A0B4J203_HUMAN,E,D,D,S,D,S,D,xS,D,D,D,E,D,D,V, +,,sp|P05387|RLA2_HUMAN, ,K,E,E,S,E,E,xS,D,D,D,M,G,F,G, +,,sp|P52756|RBM5_HUMAN,V,A,A,Y,S,G,D,xS,D,N,E,E,E,L,V, +,,sp|O95671|ASML_HUMAN,D,S,I,P,A,A,D,xT,F,E,D,L,S,D,V, +,,sp|Q15653|IKBB_HUMAN, , , ,S,G,P,C,xS,S,S,S,D,S,D,S, +,,RRRRRsp|Q6NYC8|PPR18_HUMAN, ,E,A,L,L,E,E,xS,R,Q,Q,Q,Q,Q,Q, +,,sp|P06748|NPM_HUMAN, , , , , , ,V,xT,L,A,T,L,K, , , +,,sp|Q13111|CAF1A_HUMAN,T,T,Y,L,H,T,P,xT,P,S,E,D,A,A,I, +,,sp|P06454|PTMA_HUMAN,S,D,A,A,V,D,T,xS,S,E,I,T,T,K, , +,,sp|Q99439|CNN2_HUMAN, , , , , ,D,G,xT,I,L,C,T,L,M,N, +,,sp|O15530|PDPK1_HUMAN, , , ,Q,V,S,S,xS,S,S,S,H,S,L,S, +,,sp|P08238|HS90B_HUMAN, , , , ,D,N,S,xT,M,G,Y,M,M,A,K, +,,sp|P51531|SMCA2_HUMAN, ,I,A,K,E,E,E,xS,E,D,E,S,N,E,E, +,,sp|Q92608|DOCK2_HUMAN, , , , , , ,Q,xT,V,I,S,E,N,Y,L, +,,sp|O00170|AIP_HUMAN,L,H,S,D,D,E,G,xT,V,L,D,D,S,R, , +,,sp|O15530|PDPK1_HUMAN, , ,Q,V,S,S,S,xS,S,S,H,S,L,S,A, +,,sp|P07900|HS90A_HUMAN, , , , , , , ,xT,L,V,S,V,T,K, , +,,sp|Q99880|H2B1L_HUMAN; sp|Q99879|H2B1M_HUMAN; sp|Q99877|H2B1N_HUMAN; sp|Q93079|H2B1H_HUMAN; sp|P62807|H2B1C_HUMAN; sp|P58876|H2B1D_HUMAN; sp|O60814|H2B1K_HUMAN; sp|Q5QNW6|H2B2F_HUMAN; sp|P57053|H2BFS_HUMAN, , , , , , ,E,xS,Y,S,V,Y,V,Y,K, +,,sp|Q86UX7|URP2_HUMAN, , , , , ,Y,Y,xS,F,F,D,L,D,P,K, +,,sp|Q6KC79|NIPBL_HUMAN, , , , , ,V,D,xS,D,S,D,S,D,S,E, +,,sp|Q9NRG0|CHRC1_HUMAN,E,N,D,N,D,N,E,xS,D,H,D,E,A,D,S,
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/all stuff/1RSBF.csv Fri Feb 21 13:07:45 2020 -0500 @@ -0,0 +1,457 @@ +Accession Numbers,Amino Acids,A,C,D,E,F,G,H,I,K,L,M,N,P,Q,R,S,T,V,W,Y,Properties,Hydrophobic,Polar,Small,Negative,Postive,Amide,Large Aliphatic,Small Aliphatic,Aromatic,Hydroxy,X,Number of ST,Number of pST +sp|P48735|IDHP_HUMAN,7.522123894,1.769911504,7.079646018,4.646017699,4.424778761,7.743362832,2.876106195,6.415929204,7.96460177,6.85840708,2.654867257,3.318584071,4.203539823,3.982300885,5.530973451,4.867256637,6.85840708,6.194690265,1.991150442,3.097345133,,48.67256637,35.39823009,49.55752212,11.72566372,16.37168142,7.300884956,13.27433628,21.46017699,9.513274336,11.72566372,,53,2,452 +sp|P29401|TKT_HUMAN,11.71749599,1.926163724,5.617977528,5.617977528,3.852327448,7.223113965,2.728731942,7.544141252,6.741573034,7.383627608,2.086677368,3.210272873,4.494382022,4.173354735,4.654895666,6.741573034,5.136436597,5.778491172,0.642054575,2.728731942,,50.88282504,32.74478331,51.8459069,11.23595506,14.12520064,7.383627608,14.92776886,24.71910112,7.223113965,11.87800963,,74,5,623 +sp|P29401|TKT_HUMAN,11.71749599,1.926163724,5.617977528,5.617977528,3.852327448,7.223113965,2.728731942,7.544141252,6.741573034,7.383627608,2.086677368,3.210272873,4.494382022,4.173354735,4.654895666,6.741573034,5.136436597,5.778491172,0.642054575,2.728731942,,50.88282504,32.74478331,51.8459069,11.23595506,14.12520064,7.383627608,14.92776886,24.71910112,7.223113965,11.87800963,,74,2,623 +sp|P30050|RL12_HUMAN,8.484848485,1.818181818,6.060606061,4.848484848,1.212121212,8.484848485,2.424242424,10.3030303,9.090909091,6.666666667,1.212121212,4.242424242,6.666666667,3.636363636,6.060606061,6.060606061,4.848484848,6.666666667,0.606060606,0.606060606,,46.06060606,36.36363636,53.33333333,10.90909091,17.57575758,7.878787879,16.96969697,23.63636364,2.424242424,10.90909091,,18,1,165 +sp|P56556|NDUA6_HUMAN,5.46875,0,5.46875,7.03125,6.25,3.90625,3.90625,3.90625,8.59375,4.6875,4.6875,2.34375,4.6875,3.125,10.15625,3.90625,7.03125,10.9375,1.5625,2.34375,,43.75,40.625,43.75,12.5,22.65625,5.46875,8.59375,20.3125,10.15625,10.9375,,14,4,128 +sp|Q14554|PDIA5_HUMAN,8.285163776,2.504816956,5.780346821,8.092485549,5.202312139,4.624277457,3.66088632,2.504816956,10.40462428,8.670520231,2.119460501,2.697495183,6.165703276,3.082851638,4.046242775,5.009633911,4.238921002,6.936416185,2.312138728,3.66088632,,46.82080925,37.76493256,46.24277457,13.87283237,18.11175337,5.780346821,11.17533719,19.84585742,11.17533719,9.248554913,,48,2,519 +sp|Q00839|HNRPU_HUMAN,7.393939394,1.575757576,4.848484848,10.66666667,3.757575758,13.57575758,1.575757576,2.424242424,8.484848485,5.575757576,2.303030303,5.090909091,5.090909091,5.818181818,5.454545455,4.848484848,3.272727273,4.242424242,0.727272727,3.272727273,,44.84848485,41.93939394,49.93939394,15.51515152,15.51515152,10.90909091,8,25.21212121,7.757575758,8.121212121,,67,5,825 +sp|Q00839|HNRPU_HUMAN,7.393939394,1.575757576,4.848484848,10.66666667,3.757575758,13.57575758,1.575757576,2.424242424,8.484848485,5.575757576,2.303030303,5.090909091,5.090909091,5.818181818,5.454545455,4.848484848,3.272727273,4.242424242,0.727272727,3.272727273,,44.84848485,41.93939394,49.93939394,15.51515152,15.51515152,10.90909091,8,25.21212121,7.757575758,8.121212121,,67,2,825 +sp|Q8IXT5|RB12B_HUMAN,3.196803197,0.599400599,8.091908092,9.99000999,8.391608392,6.193806194,3.796203796,3.996003996,4.095904096,6.193806194,1.498501499,3.196803197,9.99000999,3.296703297,12.68731269,6.293706294,2.197802198,3.896103896,0.699300699,1.698301698,,36.36363636,45.15484515,43.65634366,18.08191808,20.57942058,6.493506494,10.18981019,13.28671329,10.78921079,8.491508492,,85,1,1001 +sp|P52566|GDIR2_HUMAN,3.482587065,0.497512438,8.955223881,10.44776119,2.487562189,5.472636816,2.487562189,2.985074627,11.44278607,8.955223881,2.487562189,2.487562189,6.965174129,1.990049751,2.985074627,4.975124378,7.462686567,7.960199005,1.492537313,3.980099502,,39.80099502,40.7960199,48.25870647,19.40298507,16.91542289,4.47761194,11.94029851,16.91542289,7.960199005,12.43781095,,25,1,201 +sp|Q9H9T3|ELP3_HUMAN,5.301645338,1.828153565,5.118829982,6.76416819,3.10786106,7.678244973,3.10786106,6.032906764,5.850091408,8.775137112,3.290676417,2.010968921,5.301645338,3.473491773,8.226691042,5.667276051,4.936014625,8.043875686,0.548446069,4.936014625,,49.54296161,34.55210238,45.88665448,11.88299817,17.18464351,5.484460695,14.80804388,21.023766,8.592321755,10.60329068,,58,1,547 +sp|Q9UBT2|SAE2_HUMAN,8.28125,1.5625,8.125,7.8125,3.28125,5.46875,1.71875,5.9375,7.5,9.0625,1.71875,5,4.6875,4.21875,5,6.25,4.6875,7.03125,0.9375,1.71875,,45,39.375,51.09375,15.9375,14.21875,9.21875,15,20.78125,5.9375,10.9375,,70,3,640 +sp|Q9Y490|TLN1_HUMAN,15.78118851,1.495474223,4.722550177,7.162534435,1.692247147,6.060606061,1.574183392,3.856749311,6.375442739,9.602518693,2.361275089,3.18772137,3.778040142,7.12317985,4.132231405,7.044470681,6.099960645,6.454151909,0.354191263,1.141282959,,48.79968516,34.27784337,54.62416372,11.88508461,12.08185754,10.31090122,13.459268,28.29594648,3.18772137,13.14443133,,334,1,2541 +sp|Q9NY61|AATF_HUMAN,6.607142857,0.357142857,9.642857143,11.42857143,3.571428571,6.964285714,2.321428571,2.857142857,7.678571429,10.35714286,1.785714286,1.964285714,5,4.642857143,6.428571429,8.035714286,3.928571429,3.928571429,0.892857143,1.607142857,,38.92857143,44.10714286,46.42857143,21.07142857,16.42857143,6.607142857,13.21428571,17.5,6.071428571,11.96428571,,67,3,560 +sp|P29218|IMPA1_HUMAN,8.664259928,2.527075812,5.415162455,7.220216606,3.249097473,7.942238267,1.444043321,7.581227437,5.776173285,5.776173285,4.332129964,3.610108303,3.610108303,3.249097473,3.971119134,6.137184116,5.776173285,10.46931408,1.083032491,2.166064982,,53.79061372,30.68592058,54.15162455,12.63537906,11.19133574,6.859205776,13.35740072,27.07581227,6.498194946,11.9133574,,33,2,277 +sp|P07900|HS90A_HUMAN,4.644808743,0.956284153,7.37704918,13.25136612,3.415300546,4.371584699,1.639344262,6.830601093,10.92896175,8.469945355,2.732240437,4.234972678,2.868852459,3.415300546,4.098360656,5.737704918,5.87431694,5.191256831,0.546448087,3.415300546,,40.57377049,44.94535519,41.2568306,20.6284153,16.66666667,7.650273224,15.30054645,14.20765027,7.37704918,11.61202186,,85,9,732 +sp|P07900|HS90A_HUMAN,4.644808743,0.956284153,7.37704918,13.25136612,3.415300546,4.371584699,1.639344262,6.830601093,10.92896175,8.469945355,2.732240437,4.234972678,2.868852459,3.415300546,4.098360656,5.737704918,5.87431694,5.191256831,0.546448087,3.415300546,,40.57377049,44.94535519,41.2568306,20.6284153,16.66666667,7.650273224,15.30054645,14.20765027,7.37704918,11.61202186,,85,10,732 +sp|P28070|PSB4_HUMAN,8.333333333,0.378787879,4.545454545,5.681818182,3.409090909,10.22727273,1.136363636,4.545454545,1.893939394,9.090909091,4.924242424,3.03030303,4.924242424,3.409090909,7.196969697,8.333333333,5.303030303,6.439393939,1.515151515,5.681818182,,54.54545455,26.89393939,51.51515152,10.22727273,10.22727273,6.439393939,13.63636364,25,10.60606061,13.63636364,,36,3,264 +sp|Q13564|ULA1_HUMAN,7.116104869,1.498127341,5.805243446,8.239700375,4.307116105,5.992509363,2.247191011,7.677902622,6.179775281,9.737827715,1.685393258,5.617977528,3.745318352,4.868913858,4.494382022,6.554307116,4.494382022,5.43071161,0.936329588,3.370786517,,47.75280899,37.45318352,46.25468165,14.04494382,12.92134831,10.48689139,17.41573034,18.53932584,8.61423221,11.04868914,,59,1,534 +sp|P09429|HMGB1_HUMAN,8.837209302,1.395348837,9.302325581,16.74418605,4.186046512,5.11627907,1.395348837,1.860465116,20,1.860465116,2.790697674,1.860465116,6.046511628,0.930232558,3.720930233,5.11627907,2.325581395,2.325581395,0.930232558,3.255813953,,32.55813953,53.95348837,42.3255814,26.04651163,25.11627907,2.790697674,3.720930233,16.27906977,8.372093023,7.441860465,,16,2,215 +sp|P26583|HMGB2_HUMAN,7.177033493,1.435406699,7.177033493,15.78947368,3.827751196,6.220095694,1.913875598,1.435406699,19.13875598,1.913875598,2.870813397,2.392344498,7.177033493,1.913875598,4.306220096,8.133971292,1.913875598,1.435406699,0.956937799,2.870813397,,30.14354067,52.63157895,43.06220096,22.96650718,25.35885167,4.306220096,3.349282297,14.83253589,7.655502392,10.04784689,,21,1,209 +sp|Q71UM5|RS27L_HUMAN,3.571428571,7.142857143,2.380952381,4.761904762,3.571428571,5.952380952,4.761904762,1.19047619,11.9047619,9.523809524,2.380952381,1.19047619,5.952380952,4.761904762,5.952380952,7.142857143,7.142857143,8.333333333,0,2.380952381,,44.04761905,35.71428571,48.80952381,7.142857143,22.61904762,5.952380952,10.71428571,17.85714286,5.952380952,14.28571429,,12,1,84 +sp|P42677|RS27_HUMAN,3.571428571,7.142857143,2.380952381,4.761904762,3.571428571,5.952380952,4.761904762,1.19047619,11.9047619,8.333333333,2.380952381,1.19047619,7.142857143,4.761904762,5.952380952,7.142857143,7.142857143,8.333333333,0,2.380952381,,42.85714286,35.71428571,50,7.142857143,22.61904762,5.952380952,9.523809524,17.85714286,5.952380952,14.28571429,,12,1,84 +sp|P00505|AATM_HUMAN,10.23255814,1.627906977,4.88372093,4.88372093,4.88372093,8.372093023,2.558139535,5.581395349,6.744186047,7.906976744,2.790697674,3.720930233,4.88372093,4.186046512,5.348837209,5.581395349,4.88372093,6.511627907,1.627906977,2.790697674,,52.3255814,32.3255814,50.69767442,9.76744186,14.65116279,7.906976744,13.48837209,25.11627907,9.302325581,10.46511628,,45,1,430 +sp|O43175|SERA_HUMAN,10.13133208,2.43902439,3.752345216,5.816135084,2.814258912,9.380863039,1.500938086,4.502814259,4.87804878,12.19512195,2.43902439,3.564727955,4.87804878,5.065666041,4.127579737,6.003752345,6.566604128,8.255159475,1.125703565,0.562851782,,53.84615385,28.7054409,54.97185741,9.5684803,10.5065666,8.630393996,16.69793621,27.7673546,4.502814259,12.57035647,,67,2,533 +sp|P07437|TBB5_HUMAN,6.756756757,1.801801802,5.855855856,8.108108108,5.18018018,7.882882883,2.252252252,4.054054054,3.378378378,7.207207207,3.828828829,4.72972973,4.504504505,4.72972973,4.954954955,5.855855856,6.981981982,7.432432432,0.900900901,3.603603604,,48.64864865,34.00900901,51.8018018,13.96396396,10.58558559,9.459459459,11.26126126,22.07207207,9.684684685,12.83783784,,57,6,444 +sp|P07437|TBB5_HUMAN,6.756756757,1.801801802,5.855855856,8.108108108,5.18018018,7.882882883,2.252252252,4.054054054,3.378378378,7.207207207,3.828828829,4.72972973,4.504504505,4.72972973,4.954954955,5.855855856,6.981981982,7.432432432,0.900900901,3.603603604,,48.64864865,34.00900901,51.8018018,13.96396396,10.58558559,9.459459459,11.26126126,22.07207207,9.684684685,12.83783784,,57,1,444 +sp|P10599|THIO_HUMAN,7.619047619,4.761904762,6.666666667,9.523809524,8.571428571,4.761904762,0.952380952,3.80952381,11.42857143,5.714285714,2.857142857,2.857142857,2.857142857,4.761904762,0,6.666666667,3.80952381,10.47619048,0.952380952,0.952380952,,50.47619048,36.19047619,50.47619048,16.19047619,12.38095238,7.619047619,9.523809524,22.85714286,10.47619048,10.47619048,,11,1,105 +sp|Q9UQ35|SRRM2_HUMAN,6.649709302,0.472383721,2.325581395,4.651162791,0.690406977,4.978197674,1.453488372,0.981104651,4.723837209,4.469476744,1.199127907,1.453488372,12.24563953,3.488372093,17.00581395,23.32848837,6.25,2.906976744,0.181686047,0.54505814,,23.07412791,35.10174419,60.61046512,6.976744186,23.18313953,4.941860465,5.450581395,14.53488372,1.417151163,29.57848837,,814,12,2752 +sp|Q9UQ35|SRRM2_HUMAN,6.649709302,0.472383721,2.325581395,4.651162791,0.690406977,4.978197674,1.453488372,0.981104651,4.723837209,4.469476744,1.199127907,1.453488372,12.24563953,3.488372093,17.00581395,23.32848837,6.25,2.906976744,0.181686047,0.54505814,,23.07412791,35.10174419,60.61046512,6.976744186,23.18313953,4.941860465,5.450581395,14.53488372,1.417151163,29.57848837,,814,9,2752 +sp|P40926|MDHM_HUMAN,11.53846154,2.366863905,3.846153846,4.733727811,3.550295858,8.284023669,1.479289941,6.213017751,7.692307692,9.171597633,1.775147929,3.846153846,5.917159763,2.662721893,2.958579882,6.50887574,7.100591716,8.875739645,0,1.479289941,,53.25443787,27.21893491,58.28402367,8.579881657,12.13017751,6.50887574,15.38461538,28.69822485,5.029585799,13.60946746,,46,3,338 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+sp|Q92608|DOCK2_HUMAN,4.644808743,1.256830601,5.846994536,7.540983607,4.808743169,4.535519126,2.404371585,6.284153005,7.650273224,10.10928962,4.207650273,3.879781421,3.825136612,5.136612022,5.027322404,6.666666667,5.191256831,6.06557377,1.038251366,3.879781421,,46.83060109,37.4863388,41.91256831,13.38797814,15.08196721,9.016393443,16.39344262,15.24590164,9.726775956,11.8579235,,217,1,1830 +sp|Q86UX7|URP2_HUMAN,7.346326837,1.499250375,5.847076462,7.196401799,3.898050975,6.146926537,2.548725637,4.797601199,5.097451274,11.84407796,1.79910045,2.248875562,5.547226387,5.697151424,7.346326837,7.046476762,3.5982009,5.547226387,2.248875562,2.698650675,,47.82608696,35.982009,44.82758621,13.04347826,14.99250375,7.946026987,16.64167916,19.04047976,8.845577211,10.64467766,,71,1,667 +sp|Q9NRG0|CHRC1_HUMAN,7.633587786,0.763358779,7.633587786,10.6870229,2.290076336,3.816793893,1.526717557,4.580152672,9.923664122,10.6870229,2.290076336,3.816793893,2.290076336,4.580152672,3.816793893,9.923664122,4.580152672,6.106870229,0,3.053435115,,41.22137405,41.98473282,46.5648855,18.32061069,15.26717557,8.396946565,15.26717557,17.55725191,5.34351145,14.50381679,,19,1,131
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/all stuff/2RS.csv Fri Feb 21 13:07:45 2020 -0500 @@ -0,0 +1,536 @@ +Substrate,Species,Reference,-7,-6,-5,-4,-3,-2,-1,0,1,2,3,4,5,6,7,Phosphite +,,sp|Q13283|G3BP1_HUMAN, , , , , , , ,xS,S,S,P,A,P,A,D, +,,sp|Q08043|ACTN3_HUMAN; sp|P35609|ACTN2_HUMAN; sp|P12814|ACTN1_HUMAN; sp|O43707|ACTN4_HUMAN, , , , , ,T,F,xT,A,W,C,N,S,H,L, +,,sp|Q04837|SSBP_HUMAN, , , , , ,Q,A,xT,T,I,I,A,D,N,I, +,,sp|Q15738|NSDHL_HUMAN, , ,V,A,L,A,G,xT,F,H,Y,Y,S,C,E, +,,sp|Q08945|SSRP1_HUMAN, , , , ,R,P,M,xS,A,Y,M,L, , , , +,,sp|Q9Y371|SHLB1_HUMAN, ,L,A,A,D,A,G,xT,F,L,S,R, , , , +,,sp|P09651|ROA1_HUMAN; sp|Q32P51|RA1L2_HUMAN,S,H,F,E,Q,W,G,xT,L,T,D,C,V,V,M, +,,sp|P30740|ILEU_HUMAN, , ,T,F,H,F,N,xT,V,E,E,V,H,S,R, +,,sp|O94979|SC31A_HUMAN,R,P,V,G,A,S,F,xS,F,G,G,K, , , , +,,sp|P07686|HEXB_HUMAN, , ,G,S,Y,S,L,xS,H,V,Y,T,P,N,D, +,,sp|P22626|ROA2_HUMAN, , ,G,F,G,F,V,xT,F,S,S,M,A,E,V, +,,sp|Q8NBS9|TXND5_HUMAN, , , , ,G,Y,P,xT,L,L,L,F,R, , , +,,sp|P60709|ACTB_HUMAN; sp|P63261|ACTG_HUMAN, ,T,V,L,S,G,G,xT,T,M,Y,P,G,I,A, +,,sp|P49247|RPIA_HUMAN,V,L,G,I,G,S,G,xS,T,I,V,H,A,V,Q, +,,sp|Q96IU4|ABHEB_HUMAN,E,T,W,Q,N,L,G,xT,L,H,R, , , , , +,,sp|Q96JH7|VCIP1_HUMAN, , , , , ,S,S,xT,T,F,F,E,L,Q,E, +,,sp|Q13283|G3BP1_HUMAN, , , , , , ,S,xS,S,P,A,P,A,D,I, +,,sp|Q08043|ACTN3_HUMAN; sp|P35609|ACTN2_HUMAN; sp|P12814|ACTN1_HUMAN; sp|O43707|ACTN4_HUMAN, , , , , , ,K,xT,F,T,A,W,C,N,S, +,,sp|Q13509|TBB3_HUMAN; tr|A0A0B4J269|A0A0B4J269_HUMAN, , , , ,M,S,S,xT,F,I,G,N,S,T,A, +,,sp|P49915|GUAA_HUMAN,S,F,Y,N,G,T,T,xT,L,P,I,S,D,E,D, +,,sp|Q15007|FL2D_HUMAN, , , , , , ,S,xT,M,V,D,P,A,I,N, +,,sp|P10809|CH60_HUMAN, , , , ,G,Y,I,xS,P,Y,F,I,N,T,S, +,,sp|O15294|OGT1_HUMAN,L,C,P,T,H,A,D,xS,L,N,N,L,A,N,I, +,,sp|P45880|VDAC2_HUMAN, , ,L,T,F,D,T,xT,F,S,P,N,T,G,K, +,,sp|Q9UKX7|NUP50_HUMAN, , , , ,G,I,G,xT,L,H,L,K,P,T,A, +,,sp|O43312|MTSS1_HUMAN, , , ,R,P,A,S,xT,A,G,L,P,T,T,L, +,,sp|P22314|UBA1_HUMAN, , , , , ,L,Q,xT,S,S,V,L,V,S,G, +,,sp|O75746|CMC1_HUMAN, , , , , ,L,A,xT,A,T,F,A,G,I,E, +,,sp|O43491|E41L2_HUMAN, , , , , , , ,xS,P,T,K,A,P,H,L, +,,sp|Q15005|SPCS2_HUMAN, ,F,F,D,H,S,G,xT,L,V,M,D,A,Y,E, +,,sp|P62995|TRA2B_HUMAN, , , , ,R,P,H,xT,P,T,P,G,I,Y, , +,,sp|Q13596|SNX1_HUMAN, , ,A,V,G,T,Q,xT,L,S,G,A,G,L,L, +,,sp|Q16698|DECR_HUMAN,A,F,I,T,G,G,G,xT,G,L,G,K, , , , +,,sp|P42166|LAP2A_HUMAN,S,D,E,E,R,E,P,xT,P,V,L,G,S,G,A, +,,sp|O43719|HTSF1_HUMAN, , ,V,F,D,D,E,xS,D,E,K,E,D,E,E, +,,sp|P34897|GLYM_HUMAN; sp|P34896|GLYC_HUMAN, , , ,I,S,A,T,xS,I,F,F,E,S,M,P, +,,sp|Q7Z422|SZRD1_HUMAN, , , , , , , ,xS,P,P,K,V,P,I,V, +,,sp|P22626|ROA2_HUMAN, , , , , , ,V,xT,F,S,S,M,A,E,V, +,,sp|P53396|ACLY_HUMAN, , , , , , ,L,xT,L,L,N,P,K, , , +,,sp|P38606|VATA_HUMAN, , , , , ,L,A,xS,F,Y,E,R, , , , +,,sp|Q8IX12|CCAR1_HUMAN,V,M,L,M,A,S,P,xS,M,E,D,L,Y,H,K, +,,sp|P51858|HDGF_HUMAN,A,G,D,L,L,E,D,xS,P,K,R,P,K, , , +,,sp|Q5SW79|CE170_HUMAN,D,L,G,S,L,N,G,xT,F,V,N,D,V,R, , +,,sp|Q9Y277|VDAC3_HUMAN, , , ,V,N,N,A,xS,L,I,G,L,G,Y,T, +,,sp|O75521|ECI2_HUMAN,P,F,S,H,L,G,Q,xS,P,E,G,C,S,S,Y, +,,sp|Q52LJ0|FA98B_HUMAN, , , , , , , ,xT,T,I,T,M,A,H,L, +,,sp|P35659|DEK_HUMAN, , , , , , ,L,xT,M,Q,V,S,S,L,Q, +,,sp|Q15052|ARHG6_HUMAN, , ,I,P,I,A,G,xT,V,V,T,R, , , , +,,sp|P42166|LAP2A_HUMAN, ,G,P,P,D,F,S,xS,D,E,E,R,E,P,T, +,,sp|P49247|RPIA_HUMAN,N,Q,V,L,G,I,G,xS,G,S,T,I,V,H,A, +,,sp|Q9UKX7|NUP50_HUMAN, , , , , , ,S,xT,F,L,F,H,G,N,K, +,,sp|Q9UPN3|MACF1_HUMAN, , , , ,I,S,G,xT,F,S,S,G,W,T,V, +,,sp|P14618|KPYM_HUMAN, ,L,N,F,S,H,G,xT,H,E,Y,H,A,E,T, +,,sp|P49321|NASP_HUMAN, ,P,E,V,N,G,G,xS,G,D,A,V,P,S,G, +,,sp|O75064|DEN4B_HUMAN, ,Y,P,V,P,V,F,xS,T,F,V,L,T,G,A, +,,sp|Q9ULW0|TPX2_HUMAN, , , , , ,G,C,xT,I,V,K,P,F,N,L, +,,sp|Q9H6V9|LDAH_HUMAN, , , , , , ,L,xT,F,Y,Y,G,T,I,D, +,,RRRRRsp|Q8NCX0|CC150_HUMAN, , , , , ,S,H,xS,A,L,V,N,E,L,M, +,,sp|Q6ZNL6|FGD5_HUMAN, ,E,R,P,V,S,M,xS,F,P,L,S,S,P,R, +,,sp|P61981|1433G_HUMAN, , , , , , ,A,xT,V,V,E,S,S,E,K, +,,sp|Q13177|PAK2_HUMAN, , ,S,T,M,V,G,xT,P,Y,W,M,A,P,E, +,,sp|Q9Y3D7|TIM16_HUMAN, , , , , , , ,xS,V,G,G,S,F,Y,L, +,,sp|Q16778|H2B2E_HUMAN; sp|P06899|H2B1J_HUMAN; sp|P33778|H2B1B_HUMAN; sp|P23527|H2B1O_HUMAN; sp|Q8N257|H2B3B_HUMAN; sp|Q6DRA6|H2B2D_HUMAN; sp|Q6DN03|H2B2C_HUMAN, , , , ,E,S,Y,xS,I,Y,V,Y,K, , , +,,sp|Q16594|TAF9_HUMAN, ,L,S,V,G,S,V,xT,S,R,P,S,T,P,T, +,,sp|P06400|RB_HUMAN, , , , , , , ,xS,P,Y,K,F,P,S,S, +,,sp|Q96S55|WRIP1_HUMAN,T,P,T,A,A,E,S,xS,E,G,E,G,E,E,G, +,,sp|P12956|XRCC6_HUMAN, , , ,T,F,N,T,xS,T,G,G,L,L,L,P, +,,sp|P78371|TCPB_HUMAN, , , ,I,H,P,Q,xT,I,I,A,G,W,R, , +,,sp|Q52LJ0|FA98B_HUMAN, , , , , , ,T,xT,I,T,M,A,H,L,L, +,,sp|O15294|OGT1_HUMAN, , , , ,L,C,P,xT,H,A,D,S,L,N,N, +,,sp|P09651|ROA1_HUMAN; sp|Q32P51|RA1L2_HUMAN,K,L,F,I,G,G,L,xS,F,E,T,T,D,E,S, +,,sp|Q13895|BYST_HUMAN, , , , , ,A,A,xT,M,T,A,A,G,H,H, +,,sp|Q9UGU5|HMGX4_HUMAN, , , , , , , ,xS,P,P,T,T,M,L,L, +,,sp|Q15181|IPYR_HUMAN, ,G,I,S,C,M,N,xT,T,L,S,E,S,P,F, +,,sp|P52272|HNRPM_HUMAN, , , , , ,L,G,xS,T,V,F,V,A,N,L, +,,sp|Q9H9Q2|CSN7B_HUMAN, , , , , ,H,L,xT,I,V,S,L,A,S,R, +,,sp|Q9NUL3|STAU2_HUMAN, , , , , ,V,I,xS,G,T,T,L,G,Y,L, +,,sp|Q66LE6|2ABD_HUMAN; sp|Q00005|2ABB_HUMAN; sp|P63151|2ABA_HUMAN, ,G,E,Y,N,V,Y,xS,T,F,Q,S,H,E,P, +,,sp|P24752|THIL_HUMAN, , , ,T,P,I,G,xS,F,L,G,S,L,S,L, +,,sp|P60900|PSA6_HUMAN, , , , , ,H,I,xT,I,F,S,P,E,G,R, +,,sp|P63010|AP2B1_HUMAN; sp|Q10567|AP1B1_HUMAN, , ,L,S,H,A,N,xS,A,V,V,L,S,A,V, +,,sp|P78527|PRKDC_HUMAN, , , , ,S,L,G,xT,I,Q,Q,C,C,D,A, +,,sp|Q99832|TCPH_HUMAN,G,D,G,T,T,S,V,xT,L,L,A,A,E,F,L, +,,sp|P13798|ACPH_HUMAN, , , , , ,A,E,xS,F,F,Q,T,K, , , +,,sp|P53396|ACLY_HUMAN, , , , , ,G,S,xT,F,M,D,H,V,L,R, +,,sp|A0FGR8|ESYT2_HUMAN,G,A,N,T,H,L,S,xT,F,S,F,T,K, , , +,,sp|P57764|GSDMD_HUMAN, , ,T,V,T,I,P,xS,G,S,T,L,A,F,R, +,,sp|P49407|ARRB1_HUMAN,A,D,D,T,V,A,P,xS,S,T,F,C,K, , , +,,sp|O15371|EIF3D_HUMAN, , , , ,I,F,H,xT,V,T,T,T,D,D,P, +,,sp|Q15007|FL2D_HUMAN, , , , , , , ,xS,T,M,V,D,P,A,I, +,,sp|Q9BSJ8|ESYT1_HUMAN, , , , , ,L,G,xT,Q,T,F,C,S,R, , +,,sp|Q96JH7|VCIP1_HUMAN, , , , ,S,S,T,xT,F,F,E,L,Q,E,S, +,,sp|Q99832|TCPH_HUMAN,A,E,V,G,D,G,T,xT,S,V,T,L,L,A,A, +,,sp|Q9UKX7|NUP50_HUMAN, , , , , , , ,xS,T,F,L,F,H,G,N, +,,sp|Q96I25|SPF45_HUMAN, , , , , , , ,xS,P,T,G,P,S,N,S, +,,sp|O60506|HNRPQ_HUMAN, , ,G,Y,A,F,V,xT,F,C,T,K, , , , +,,sp|O00148|DX39A_HUMAN; sp|Q13838|DX39B_HUMAN, , , , , , ,L,xT,L,H,G,L,Q,Q,Y, +,,sp|Q99832|TCPH_HUMAN,E,V,G,D,G,T,T,xS,V,T,L,L,A,A,E, +,,sp|Q14974|IMB1_HUMAN,A,A,V,E,N,L,P,xT,F,L,V,E,L,S,R, +,,sp|Q8WUA2|PPIL4_HUMAN, , , , ,I,N,E,xT,F,V,D,K,D,F,V, +,,sp|Q16658|FSCN1_HUMAN,V,A,R,P,E,P,A,xT,G,Y,T,L,E,F,R, +,,sp|P31323|KAP3_HUMAN, , , , , ,A,A,xT,I,T,A,T,S,P,G, +,,sp|P10809|CH60_HUMAN,G,D,G,T,T,T,A,xT,V,L,A,R, , , , +,,sp|P20290|BTF3_HUMAN, , , , ,V,Q,A,xS,L,A,A,N,T,F,T, +,,sp|O95319|CELF2_HUMAN, , ,G,C,A,F,V,xT,F,S,T,R, , , , +,,sp|Q13126|MTAP_HUMAN, , , , , ,A,E,xS,F,M,F,R, , , , +,,sp|P51692|STA5B_HUMAN; sp|P42229|STA5A_HUMAN,L,I,N,K,P,D,G,xT,F,L,L,R, , , , +,,sp|P16949|STMN1_HUMAN,S,V,P,E,F,P,L,xS,P,P,K, , , , , +,,sp|Q13177|PAK2_HUMAN, , , , , , ,S,xT,M,V,G,T,P,Y,W, +,,sp|Q9Y2X3|NOP58_HUMAN, ,L,I,A,H,A,G,xS,L,L,N,L,A,K, , +,,sp|Q16594|TAF9_HUMAN,L,S,V,G,S,V,T,xS,R,P,S,T,P,T,L, +,,sp|Q66LE6|2ABD_HUMAN; sp|Q00005|2ABB_HUMAN; sp|P63151|2ABA_HUMAN,G,E,Y,N,V,Y,S,xT,F,Q,S,H,E,P,E, +,,sp|P07948|LYN_HUMAN, , ,G,K,D,S,L,xS,D,D,G,V,D,L,K, +,,sp|P31146|COR1A_HUMAN, , , , ,V,S,Q,xT,T,W,D,S,G,F,C, +,,sp|P06493|CDK1_HUMAN, , , ,I,G,E,G,xT,Y,G,V,V,Y,K, , +,,sp|P31146|COR1A_HUMAN, , , ,V,S,Q,T,xT,W,D,S,G,F,C,A, +,,sp|P37802|TAGL2_HUMAN, , , ,I,Q,A,S,xT,M,A,F,K, , , , +,,sp|P22626|ROA2_HUMAN,F,G,F,V,T,F,S,xS,M,A,E,V,D,A,A, +,,sp|Q9H1E3|NUCKS_HUMAN, , ,A,T,V,T,P,xS,P,V,K,G,K, , , +,,sp|Q13263|TIF1B_HUMAN,A,A,S,A,A,A,A,xS,A,A,S,G,S,P,G, +,,sp|P07686|HEXB_HUMAN, , , , , , ,G,xS,Y,S,L,S,H,V,Y, +,,sp|P45880|VDAC2_HUMAN, , , ,V,N,N,S,xS,L,I,G,V,G,Y,T, +,,sp|Q08945|SSRP1_HUMAN, , , , ,I,Y,P,xT,F,L,H,L,H,G,K, +,,sp|P68104|EF1A1_HUMAN, , , , , , ,K,xS,V,E,M,H,H,E,A, +,,sp|P53396|ACLY_HUMAN, , , , , , ,G,xS,T,F,M,D,H,V,L, +,,sp|Q01469|FABP5_HUMAN,T,Q,T,V,C,N,F,xT,D,G,A,L,V,Q,H, +,,sp|Q99436|PSB7_HUMAN, , , , , ,T,G,xT,T,I,A,G,V,V,Y, +,,sp|P14314|GLU2B_HUMAN, , , , ,L,G,G,xS,P,T,S,L,G,T,W, +,,sp|Q16594|TAF9_HUMAN,P,S,T,P,T,L,G,xT,P,T,P,Q,T,M,S, +,,sp|Q99436|PSB7_HUMAN, , , , , , , ,xT,T,I,A,G,V,V,Y, +,,sp|P67809|YBOX1_HUMAN,K,E,N,Q,G,D,E,xT,Q,G,Q,Q,P,P,Q, +,,tr|A0A1W2PRB8|A0A1W2PRB8_HUMAN; sp|Q9H0W9|CK054_HUMAN,K,P,I,G,M,G,G,xT,F,I,I,Q,K, , , +,,sp|P08238|HS90B_HUMAN; sp|P07900|HS90A_HUMAN,D,L,I,N,N,L,G,xT,I,A,K, , , , , +,,sp|P54819|KAD2_HUMAN,L,Q,A,Y,H,T,Q,xT,T,P,L,I,E,Y,Y, +,,sp|P30740|ILEU_HUMAN, , , , , , , ,xT,F,H,F,N,T,V,E, +,,sp|Q8ND56|LS14A_HUMAN, , , , ,S,P,V,xS,T,R,P,L,P,S,A, +,,sp|P31146|COR1A_HUMAN,V,S,Q,T,T,W,D,xS,G,F,C,A,V,N,P, +,,sp|Q9Y4E1|WAC2C_HUMAN; sp|Q641Q2|WAC2A_HUMAN, , , ,S,R,P,T,xS,F,A,D,E,L,A,A, +,,sp|P14314|GLU2B_HUMAN, ,L,G,G,S,P,T,xS,L,G,T,W,G,S,W, +,,sp|P49915|GUAA_HUMAN,P,P,T,D,V,T,P,xT,F,L,T,T,G,V,L, +,,sp|Q96S55|WRIP1_HUMAN, , ,Q,P,A,T,P,xT,A,A,E,S,S,E,G, +,,sp|Q9NVZ3|NECP2_HUMAN,P,A,S,T,G,G,L,xS,L,L,P,P,P,P,G, +,,sp|P12956|XRCC6_HUMAN, , ,T,F,N,T,S,xT,G,G,L,L,L,P,S, +,,sp|P23528|COF1_HUMAN,T,V,D,D,P,Y,A,xT,F,V,K, , , , , +,,sp|Q04837|SSBP_HUMAN, , , , ,Q,A,T,xT,I,I,A,D,N,I,I, +,,sp|Q9ULZ2|STAP1_HUMAN, , , , , ,G,T,xT,L,F,F,Y,T,D,K, +,,sp|O94826|TOM70_HUMAN, , , , , , ,A,xT,F,Y,L,L,I,G,N, +,,sp|Q9BSJ8|ESYT1_HUMAN,N,P,H,L,Q,T,F,xT,F,T,R, , , , , +,,sp|P62805|H4_HUMAN, , , , , , ,K,xT,V,T,A,M,D,V,V, +,,sp|Q9ULW0|TPX2_HUMAN, , , ,A,R,P,N,xT,V,I,S,Q,E,P,F, +,,sp|P55884|EIF3B_HUMAN, , , ,P,R,P,P,xT,L,L,S,Q,E,Q,I, +,,sp|O75663|TIPRL_HUMAN, , , , , , ,G,xT,L,L,G,E,S,L,K, +,,sp|O43312|MTSS1_HUMAN, , , , ,R,P,A,xS,T,A,G,L,P,T,T, +,,sp|P53396|ACLY_HUMAN, , , , ,K,P,A,xS,F,M,T,S,I,C,D, +,,RRRRRsp|Q8NCX0|CC150_HUMAN, , , , , , , ,xS,H,S,A,L,V,N,E, +,,sp|O95619|YETS4_HUMAN, , , , , ,G,V,xT,I,V,K,P,I,V,Y, +,,sp|Q14C86|GAPD1_HUMAN,V,V,S,G,I,S,A,xT,S,E,D,I,P,N,K, +,,sp|P27694|RFA1_HUMAN, , , ,V,V,T,A,xT,L,W,G,E,D,A,D, +,,sp|P53041|PPP5_HUMAN, , , , , ,L,S,xT,L,V,E,T,T,L,K, +,,sp|P10809|CH60_HUMAN,E,A,G,D,G,T,T,xT,A,T,V,L,A,R, , +,,sp|P01911|2B1F_HUMAN;sp|Q30154|DRB5_HUMAN;tr|A0A182DWH4|A0A182DWH4_HUMAN;,Q,V,E,H,P,S,V,xT,S,P,L,T,V,E,W, +,,sp|P60709|ACTB_HUMAN; sp|P63261|ACTG_HUMAN, , , , ,T,V,L,xS,G,G,T,T,M,Y,P, +,,sp|Q9UQ35|SRRM2_HUMAN, , , , , , ,T,xS,P,P,L,L,D,R, , +,,sp|P49189|AL9A1_HUMAN, , , , , , ,M,xS,T,G,T,F,V,V,S, +,,sp|P42166|LAP2A_HUMAN, , ,G,P,P,D,F,xS,S,D,E,E,R,E,P, +,,sp|P46087|NOP2_HUMAN, , ,L,G,V,T,N,xT,I,I,S,H,Y,D,G, +,,sp|P11021|BIP_HUMAN, ,D,N,H,L,L,G,xT,F,D,L,T,G,I,P, +,,sp|P30626|SORCN_HUMAN, , , , , ,A,L,xT,T,M,G,F,R, , , +,,sp|O43491|E41L2_HUMAN, , , , , , , ,xS,Y,T,L,V,V,A,K, +,,sp|P27694|RFA1_HUMAN, , , , , ,V,V,xT,A,T,L,W,G,E,D, +,,sp|Q7Z5L9|I2BP2_HUMAN, , , , ,R,P,A,xS,V,S,S,S,A,A,V, +,,sp|P22314|UBA1_HUMAN, , , ,L,Q,T,S,xS,V,L,V,S,G,L,R, +,,sp|Q13620|CUL4B_HUMAN, , , ,A,F,G,S,xT,I,V,I,N,P,E,K, +,,sp|Q53H12|AGK_HUMAN, , , , , , ,A,xT,V,F,L,N,P,A,A, +,,sp|P01911|2B1F_HUMAN;sp|Q30154|DRB5_HUMAN;tr|A0A182DWH4|A0A182DWH4_HUMAN;,T,C,Q,V,E,H,P,xS,V,T,S,P,L,T,V, +,,sp|P49407|ARRB1_HUMAN,D,T,V,A,P,S,S,xT,F,C,K, , , , , +,,sp|P46087|NOP2_HUMAN, , , , ,L,G,V,xT,N,T,I,I,S,H,Y, +,,sp|P37802|TAGL2_HUMAN, , , , , , , ,xT,L,M,N,L,G,G,L, +,,sp|Q16658|FSCN1_HUMAN,A,P,S,G,P,S,G,xT,L,K, , , , , , +,,tr|A0A1W2PRB8|A0A1W2PRB8_HUMAN; sp|Q9H0W9|CK054_HUMAN, , , , , ,G,G,xT,F,I,I,Q,K, , , +,,sp|Q14156|EFR3A_HUMAN, , , , , , ,L,xT,F,Y,A,V,S,A,P, +,,sp|P22626|ROA2_HUMAN, , , , ,V,T,F,xS,S,M,A,E,V,D,A, +,,sp|P49915|GUAA_HUMAN,H,S,F,Y,N,G,T,xT,T,L,P,I,S,D,E, +,,sp|P60842|IF4A1_HUMAN, , , , , , ,A,xT,Q,A,L,V,L,A,P, +,,sp|P13796|PLSL_HUMAN, , , , ,E,G,E,xS,L,E,D,L,M,K, , +,,sp|O95487|SC24B_HUMAN, , ,D,S,R,P,L,xS,P,I,L,H,I,V,K, +,,sp|P31146|COR1A_HUMAN, , , , , , ,V,xS,Q,T,T,W,D,S,G, +,,sp|Q5JPE7|NOMO2_HUMAN; sp|Q15155|NOMO1_HUMAN; sp|P69849|NOMO3_HUMAN, , , , , , ,I,xT,I,T,G,Y,R, , , +,,sp|P43243|MATR3_HUMAN, , , , , ,L,C,xS,L,F,Y,T,N,E,E, +,,sp|Q9NR09|BIRC6_HUMAN, , , , ,E,T,F,xT,S,W,P,H,V,G,Y, +,,sp|Q96T37|RBM15_HUMAN, , , , , ,D,R,xT,P,P,L,L,Y,R, , +,,sp|P53396|ACLY_HUMAN, , , ,Y,P,G,S,xT,F,M,D,H,V,L,R, +,,sp|Q9NR09|BIRC6_HUMAN, , , , , , ,E,xT,F,T,S,W,P,H,V, +,,tr|A0A0C4DFX4|A0A0C4DFX4_HUMAN; sp|Q6ZRS2|SRCAP_HUMAN,S,P,G,P,S,H,P,xT,F,W,T,Y,T,E,A, +,,sp|Q08043|ACTN3_HUMAN; sp|P35609|ACTN2_HUMAN; sp|P12814|ACTN1_HUMAN; sp|O43707|ACTN4_HUMAN, , , , ,K,T,F,xT,A,W,C,N,S,H,L, +,,sp|A0FGR8|ESYT2_HUMAN, , , , ,G,A,N,xT,H,L,S,T,F,S,F, +,,sp|Q96T68|SETB2_HUMAN, , , , , , ,G,xT,F,V,C,I,Y,S,G, +,,sp|Q9Y3A5|SBDS_HUMAN, , , , ,R,P,Y,xT,V,I,L,I,E,R, , +,,sp|Q96A72|MGN2_HUMAN; sp|P61326|MGN_HUMAN, , , , , ,I,G,xS,L,I,D,V,N,Q,S, +,,sp|Q9UIA9|XPO7_HUMAN, , , , , , , ,xT,T,F,Y,T,A,L,G, +,,sp|P30086|PEBP1_HUMAN, , , , ,R,P,T,xS,I,S,W,D,G,L,D, +,,sp|Q14C86|GAPD1_HUMAN,R,P,S,T,P,G,L,xS,V,V,S,G,I,S,A, +,,sp|P49848|TAF6_HUMAN, , , , , ,F,S,xT,F,I,S,E,G,V,R, +,,sp|P11142|HSP7C_HUMAN,D,I,V,L,V,G,G,xS,T,R, , , , , , +,,sp|O75521|ECI2_HUMAN, , , ,A,T,F,H,xT,P,F,S,H,L,G,Q, +,,sp|Q53QZ3|RHG15_HUMAN, , , , , ,S,S,xS,T,E,L,L,S,H,Y, +,,sp|P06576|ATPB_HUMAN, , , , ,V,A,L,xT,G,L,T,V,A,E,Y, +,,sp|P45880|VDAC2_HUMAN, , , ,L,T,F,D,xT,T,F,S,P,N,T,G, +,,sp|P49407|ARRB1_HUMAN,A,M,E,E,A,D,D,xT,V,A,P,S,S,T,F, +,,sp|Q86UE4|LYRIC_HUMAN,I,P,D,D,Q,K,V,xS,D,D,D,K,E,K,G, +,,sp|P22314|UBA1_HUMAN, , , , ,L,Q,T,xS,S,V,L,V,S,G,L, +,,sp|P62805|H4_HUMAN, , , , , ,T,V,xT,A,M,D,V,V,Y,A, +,,sp|P54886|P5CS_HUMAN, , , , , ,V,G,xT,F,F,S,E,V,K, , +,,sp|Q9Y4E1|WAC2C_HUMAN; sp|Q641Q2|WAC2A_HUMAN, , , , ,S,R,P,xT,S,F,A,D,E,L,A, +,,sp|Q9Y2L1|RRP44_HUMAN, , , , ,H,F,Y,xT,F,T,N,E,H,H,R, +,,sp|Q9NYF8|BCLF1_HUMAN, , , , ,L,L,A,xS,T,L,V,H,S,V,K, +,,sp|O75608|LYPA1_HUMAN, , , , , , , ,xT,L,V,N,P,A,N,V, +,,sp|P29350|PTN6_HUMAN, , , ,G,E,P,W,xT,F,L,V,R, , , , +,,sp|O60508|PRP17_HUMAN, ,S,P,S,S,K,P,xS,L,A,V,A,V,D,S, +,,sp|P49407|ARRB1_HUMAN,D,D,T,V,A,P,S,xS,T,F,C,K, , , , +,,sp|Q99832|TCPH_HUMAN,D,A,E,V,G,D,G,xT,T,S,V,T,L,L,A, +,,sp|Q9BSJ8|ESYT1_HUMAN,G,S,N,P,H,L,Q,xT,F,T,F,T,R, , , +,,sp|P49247|RPIA_HUMAN,L,G,I,G,S,G,S,xT,I,V,H,A,V,Q,R, +,,sp|P35606|COPB2_HUMAN, , ,V,F,N,Y,N,xT,L,E,R, , , , , +,,sp|P55084|ECHB_HUMAN, , , , ,A,A,L,xT,G,L,L,H,R, , , +,,sp|P07737|PROF1_HUMAN, , , , , , ,S,xT,G,G,A,P,T,F,N, +,,sp|P11021|BIP_HUMAN, , , , , , , ,xS,T,M,K,P,V,Q,K, +,,sp|Q99547|MPH6_HUMAN, , , , ,R,Y,E,xT,L,V,G,T,I,G,K, +,,sp|Q7Z4S6|KI21A_HUMAN, , , ,E,K,E,L,xS,P,P,P,G,L,P,S, +,,sp|Q8IX12|CCAR1_HUMAN, , ,V,M,L,M,A,xS,P,S,M,E,D,L,Y, +,,sp|Q15363|TMED2_HUMAN, , , , , , ,Y,xT,F,A,A,H,M,D,G, +,,sp|P53396|ACLY_HUMAN, , , , ,Y,P,G,xS,T,F,M,D,H,V,L, +,,sp|P29401|TKT_HUMAN, , ,S,V,P,T,S,xT,V,F,Y,P,S,D,G, +,,sp|Q9ULW0|TPX2_HUMAN, , , , , ,G,C,xT,I,V,K,P,F, , , +,,sp|Q9NVZ3|NECP2_HUMAN, , ,V,R,P,A,S,xT,G,G,L,S,L,L,P, +,,sp|P54819|KAD2_HUMAN, , ,L,Q,A,Y,H,xT,Q,T,T,P,L,I,E, +,,sp|P12956|XRCC6_HUMAN, , , , , , , ,xT,F,N,T,S,T,G,G, +,,sp|P55036|PSMD4_HUMAN, , , , , , ,I,xT,F,C,T,G,I,R, , +,,sp|O43815|STRN_HUMAN, , ,S,V,I,D,T,xS,T,I,V,R, , , , +,,sp|P30040|ERP29_HUMAN, ,G,A,L,P,L,D,xT,V,T,F,Y,K, , , +,,sp|P11177|ODPB_HUMAN, , , , , , , ,xT,Y,Y,M,S,G,G,L, +,,sp|Q14181|DPOA2_HUMAN, ,S,P,H,Q,L,L,xS,P,S,S,F,S,P,S, +,,sp|Q53EL6|PDCD4_HUMAN,S,G,L,T,V,P,T,xS,P,K, , , , , , +,,sp|P17987|TCPA_HUMAN, ,E,V,G,D,G,T,xT,S,V,V,I,I,A,A, +,,sp|P26196|DDX6_HUMAN, , , , , ,G,V,xT,Q,Y,Y,A,Y,V,T, +,,sp|P09651|ROA1_HUMAN, , , , , ,S,E,xS,P,K,E,P,E,Q,L, +,,sp|Q9ULT8|HECD1_HUMAN, , , , , , , ,xS,T,I,F,Y,Y,V,Q, +,,sp|P40926|MDHM_HUMAN, , , , , , ,L,xT,L,Y,D,I,A,H,T, +,,sp|P78527|PRKDC_HUMAN, , , , , ,L,A,xT,T,I,L,Q,H,W,K, +,,sp|P14866|HNRPL_HUMAN, , , , , ,A,I,xT,H,L,N,N,N,F,M, +,,sp|P22626|ROA2_HUMAN, , , ,V,T,F,S,xS,M,A,E,V,D,A,A, +,,sp|Q14204|DYHC1_HUMAN, , , , , ,Y,A,xT,L,A,T,V,S,R, , +,,sp|Q92871|PMM1_HUMAN; sp|O15305|PMM2_HUMAN, , , , , , ,G,xT,F,I,E,F,R, , , +,,sp|Q6ZU35|K1211_HUMAN, , , , ,R,P,P,xS,P,P,G,P,E,E,R, +,,sp|P11142|HSP7C_HUMAN,I,V,L,V,G,G,S,xT,R, , , , , , , +,,sp|P29401|TKT_HUMAN, , , , , , , ,xS,V,P,T,S,T,V,F, +,,sp|Q14181|DPOA2_HUMAN, , , , , , , ,xS,P,H,Q,L,L,S,P, +,,tr|A0A0C4DFX4|A0A0C4DFX4_HUMAN; sp|Q6ZRS2|SRCAP_HUMAN, , , ,S,P,G,P,xS,H,P,T,F,W,T,Y, +,,sp|Q99832|TCPH_HUMAN, , , , , ,T,C,xT,F,I,L,R, , , , +,,sp|P17844|DDX5_HUMAN, , , , , , , ,xT,T,Y,L,V,L,D,E, +,,sp|O60493|SNX3_HUMAN, , , , , , ,F,xT,T,Y,E,I,R, , , +,,sp|P18124|RL7_HUMAN, , ,Q,I,F,N,G,xT,F,V,K, , , , , +,,tr|A0A1B0GU03|A0A1B0GU03_HUMAN; sp|P07339|CATD_HUMAN, , , , , ,G,I,xT,F,I,A,A,K, , , +,,sp|Q99436|PSB7_HUMAN, , , , ,T,G,T,xT,I,A,G,V,V,Y,K, +,,sp|O60508|PRP17_HUMAN, , , , , ,S,P,xS,S,K,P,S,L,A,V, +,,sp|O15371|EIF3D_HUMAN,I,F,H,T,V,T,T,xT,D,D,P,V,I,R, , +,,sp|P62701|RS4X_HUMAN; sp|Q8TD47|RS4Y2_HUMAN, , , , , , ,L,xT,G,V,F,A,P,R, , +,,sp|O43491|E41L2_HUMAN, , , , , ,S,P,xT,K,A,P,H,L,Q,L, +,,sp|P45880|VDAC2_HUMAN, , , , ,V,N,N,xS,S,L,I,G,V,G,Y, +,,sp|P68104|EF1A1_HUMAN; sp|Q5VTE0|EF1A3_HUMAN, , ,I,G,G,I,G,xT,V,P,V,G,R, , , +,,sp|P78527|PRKDC_HUMAN, , , , , ,L,Y,xS,L,A,L,H,P,N,A, +,,sp|Q16698|DECR_HUMAN, , , ,V,A,F,I,xT,G,G,G,T,G,L,G, +,,sp|P06744|G6PI_HUMAN,E,G,N,R,P,T,N,xS,I,V,F,T,K, , , +,,sp|Q9NUL3|STAU2_HUMAN, , , ,V,I,S,G,xT,T,L,G,Y,L,S,P, +,,sp|Q13263|TIF1B_HUMAN,A,A,A,A,S,A,A,xS,G,S,P,G,P,G,E, +,,sp|Q9NYF8|BCLF1_HUMAN, , , , ,I,D,I,xS,P,S,T,L,R, , , +,,sp|Q99873|ANM1_HUMAN, , , , , , ,A,xT,L,Y,V,T,A,I,E, +,,sp|P55265|DSRAD_HUMAN, , , ,T,L,P,L,xT,G,S,T,F,H,D,Q, +,,sp|Q9ULZ2|STAP1_HUMAN, , , , , , ,G,xT,T,L,F,F,Y,T,D, +,,sp|P29401|TKT_HUMAN, , , , ,S,V,P,xT,S,T,V,F,Y,P,S, +,,sp|P38646|GRP75_HUMAN, , ,L,L,G,Q,F,xT,L,I,G,I,P,P,A, +,,sp|Q14C86|GAPD1_HUMAN,T,P,G,L,S,V,V,xS,G,I,S,A,T,S,E, +,,sp|Q13620|CUL4B_HUMAN, , , , ,A,F,G,xS,T,I,V,I,N,P,E, +,,sp|P61158|ARP3_HUMAN,I,V,L,S,G,G,S,xT,M,F,R, , , , , +,,sp|Q9UK76|JUPI1_HUMAN, , , , , ,R,N,xS,S,E,A,S,S,G,D, +,,sp|Q00059|TFAM_HUMAN, , , , , ,E,L,xT,L,L,G,K,P,K, , +,,sp|P07686|HEXB_HUMAN, , , , ,G,S,Y,xS,L,S,H,V,Y,T,P, +,,sp|Q8WZ42|TITIN_HUMAN, , , , , ,W,T,xT,D,G,S,E,I,K, , +,,sp|Q14204|DYHC1_HUMAN, , , , , , ,V,xT,F,V,N,F,T,V,T, +,,sp|P00338|LDHA_HUMAN, , , , , ,A,D,xT,L,W,G,I,Q,K, , +,,sp|P07954|FUMH_HUMAN, , , ,I,E,Y,D,xT,F,G,E,L,K, , , +,,sp|O15235|RT12_HUMAN, , ,G,V,V,L,C,xT,F,T,R, , , , , +,,sp|Q9BRR9|RHG09_HUMAN,G,S,G,P,A,E,L,xS,A,G,E,D,E,E,E, +,,sp|Q6PI48|SYDM_HUMAN, , , , ,R,Q,N,xT,F,L,V,L,R, , , +,,sp|Q9Y4B6|DCAF1_HUMAN, , , , , ,L,L,xT,L,F,N,P,D,L,A, +,,sp|Q13283|G3BP1_HUMAN, , , , ,Q,Y,Y,xT,L,L,N,Q,A,P,D, +,,sp|Q9BWU0|NADAP_HUMAN, , , , , ,G,T,xS,Y,C,L,F,G,R, , +,,sp|Q13596|SNX1_HUMAN, , , , ,A,V,G,xT,Q,T,L,S,G,A,G, +,,sp|P41250|GARS_HUMAN, , , , , , , ,xT,F,F,S,F,P,A,V, +,,sp|O75083|WDR1_HUMAN, , , , , ,L,Y,xS,I,L,G,T,T,L,K, +,,sp|O75533|SF3B1_HUMAN,G,D,T,P,G,H,A,xT,P,G,H,G,G,A,T, +,,sp|P13861|KAP2_HUMAN, , , , , ,A,A,xT,I,V,A,T,S,E,G, +,,sp|Q71UI9|H2AV_HUMAN; sp|P0C0S5|H2AZ_HUMAN, , , , , , ,A,xT,I,A,G,G,G,V,I, +,,sp|P14618|KPYM_HUMAN, , , , ,L,N,F,xS,H,G,T,H,E,Y,H, +,,sp|P08238|HS90B_HUMAN, , , , , , , ,xT,L,T,L,V,D,T,G, +,,sp|O75534|CSDE1_HUMAN, , , , ,G,T,V,xS,F,H,S,H,S,D,H, +,,sp|Q7Z5L9|I2BP2_HUMAN, ,R,P,A,S,V,S,xS,S,A,A,V,E,H,E, +,,sp|P29401|TKT_HUMAN, , , ,S,V,P,T,xS,T,V,F,Y,P,S,D, +,,sp|Q32P44|EMAL3_HUMAN,P,I,T,M,Y,I,P,xS,G,I,R, , , , , +,,sp|Q08043|ACTN3_HUMAN; sp|P35609|ACTN2_HUMAN; sp|P12814|ACTN1_HUMAN; sp|O43707|ACTN4_HUMAN, , , , , , , ,xT,F,T,A,W,C,N,S, +,,sp|P00505|AATM_HUMAN, , , , ,I,G,A,xS,F,L,Q,R, , , , +,,sp|P22626|ROA2_HUMAN,G,F,G,F,V,T,F,xS,S,M,A,E,V,D,A, +,,sp|Q09472|EP300_HUMAN, , , , , ,L,G,xT,F,L,E,N,R, , , +,,sp|P12956|XRCC6_HUMAN, , , , , , ,R,xT,F,N,T,S,T,G,G, +,,sp|P09651|ROA1_HUMAN; sp|Q32P51|RA1L2_HUMAN; tr|A0A2R8Y4L2|A0A2R8Y4L2_HUMAN, , ,G,F,A,F,V,xT,F,D,D,H,D,S,V, +,,sp|P06744|G6PI_HUMAN,V,F,E,G,N,R,P,xT,N,S,I,V,F,T,K, +,,sp|Q9BTE3|MCMBP_HUMAN, , , , , , ,N,xS,T,F,T,E,H,L,Y, +,,tr|A0A182DWH4|A0A182DWH4_HUMAN, , ,S,G,E,V,Y,xT,C,Q,V,E,H,P,S, +,,sp|P52292|IMA1_HUMAN, , , ,E,A,T,W,xT,M,S,N,I,T,A,G, +,,sp|P08240|SRPRA_HUMAN, , , , ,V,M,G,xT,F,S,T,V,T,S,T, +,,sp|P55265|DSRAD_HUMAN,T,L,P,L,T,G,S,xT,F,H,D,Q,I,A,M, +,,sp|Q9Y5V0|ZN706_HUMAN,A,A,L,I,Y,T,C,xT,V,C,R, , , , , +,,sp|P06748|NPM_HUMAN, , , ,S,I,R,D,xT,P,A,K, , , , , +,,sp|Q9NRW3|ABC3C_HUMAN, , ,A,M,Y,P,G,xT,F,Y,F,Q,F,K, , +,,sp|P36578|RL4_HUMAN,K,L,D,E,L,Y,G,xT,W,R, , , , , , +,,sp|Q15005|SPCS2_HUMAN, , , ,F,F,D,H,xS,G,T,L,V,M,D,A, +,,sp|Q96JH7|VCIP1_HUMAN, , , , , , ,S,xS,T,T,F,F,E,L,Q, +,,sp|P61158|ARP3_HUMAN,N,I,V,L,S,G,G,xS,T,M,F,R, , , , +,,sp|Q92608|DOCK2_HUMAN, , , , , , ,L,xS,Q,T,F,L,Q,L,S, +,,sp|Q9Y2W1|TR150_HUMAN, , , , ,I,D,I,xS,P,S,T,F,R, , , +,,sp|O14980|XPO1_HUMAN, , , , , , ,E,xT,L,V,Y,L,T,H,L, +,,sp|Q9UK76|JUPI1_HUMAN, , , , ,R,N,S,xS,E,A,S,S,G,D,F, +,,sp|P34897|GLYM_HUMAN; sp|P34896|GLYC_HUMAN, , , , ,I,S,A,xT,S,I,F,F,E,S,M, +,,sp|P18433|PTPRA_HUMAN, , , , , ,T,G,xT,F,C,A,L,S,T,V, +,,sp|Q9BWJ5|SF3B5_HUMAN, , , ,Y,T,I,H,xS,Q,L,E,H,L,Q,S, +,,sp|Q13347|EIF3I_HUMAN, , , , , ,D,M,xT,M,F,V,T,A,S,K, +,,sp|Q8ND76|CCNY_HUMAN; sp|Q8N7R7|CCYL1_HUMAN, , , , , ,A,S,xT,I,F,L,S,K, , , +,,sp|Q15181|IPYR_HUMAN,G,I,S,C,M,N,T,xT,L,S,E,S,P,F,K, +,,sp|Q15833|STXB2_HUMAN, ,D,F,Q,G,T,P,xT,F,T,Y,K, , , , +,,sp|P62805|H4_HUMAN, , , , ,K,T,V,xT,A,M,D,V,V,Y,A, +,,sp|P14625|ENPL_HUMAN,A,D,D,K,Y,N,D,xT,F,W,K, , , , , +,,sp|P07437|TBB5_HUMAN; sp|Q13509|TBB3_HUMAN; tr|A0A0B4J269|A0A0B4J269_HUMAN,S,L,G,G,G,T,G,xS,G,M,G,T,L,L,I, +,,sp|P82650|RT22_HUMAN, , , , , ,I,L,xT,P,I,I,F,K, , , +,,sp|Q16594|TAF9_HUMAN,G,S,V,T,S,R,P,xS,T,P,T,L,G,T,P, +,,sp|P14866|HNRPL_HUMAN, , , , ,T,P,A,xS,P,V,V,H,I,R, , +,,sp|P14625|ENPL_HUMAN, , , , , , ,G,xT,T,I,T,L,V,L,K, +,,sp|Q5T4S7|UBR4_HUMAN, , , , , ,L,C,xT,F,T,I,T,Q,K, , +,,sp|Q6IBS0|TWF2_HUMAN, , , , , ,H,Q,xT,L,Q,G,L,A,F,P, +,,sp|P06748|NPM_HUMAN, , , , , ,L,L,xS,I,S,G,K, , , , +,,sp|Q96S55|WRIP1_HUMAN,A,T,P,T,A,A,E,xS,S,E,G,E,G,E,E, +,,sp|P14314|GLU2B_HUMAN, , ,L,G,G,S,P,xT,S,L,G,T,W,G,S, +,,sp|P01911|2B1F_HUMAN; sp|Q30154|DRB5_HUMAN,V,E,H,P,S,V,T,xS,P,L,T,V,E,W,R, +,,sp|P52272|HNRPM_HUMAN,F,G,G,S,F,A,G,xS,F,G,G,A,G,G,H, +,,tr|A0A182DWH4|A0A182DWH4_HUMAN,V,E,H,P,S,V,T,xS,P,L,T,V,E,W,S, +,,sp|O75521|ECI2_HUMAN,A,T,F,H,T,P,F,xS,H,L,G,Q,S,P,E, +,,sp|Q9BTE3|MCMBP_HUMAN, , , , , ,N,S,xT,F,T,E,H,L,Y,R, +,,sp|P68363|TBA1B_HUMAN; sp|Q71U36|TBA1A_HUMAN; sp|Q9BQE3|TBA1C_HUMAN, , , , ,S,F,N,xT,F,F,S,E,T,G,A, +,,sp|Q99613|EIF3C_HUMAN; sp|B5ME19|EIFCL_HUMAN, , ,Q,P,L,L,L,xS,E,D,E,E,D,T,K, +,,sp|Q9NVZ3|NECP2_HUMAN, , , ,V,R,P,A,xS,T,G,G,L,S,L,L, +,,sp|Q99832|TCPH_HUMAN, , , , ,K,T,F,xS,Y,A,G,F,E,M,Q, +,,sp|P60709|ACTB_HUMAN; sp|P63261|ACTG_HUMAN, , , ,A,V,F,P,xS,I,V,G,R, , , , +,,sp|Q86VP6|CAND1_HUMAN, , , , , ,L,G,xT,L,S,A,L,D,I,L, +,,sp|Q08211|DHX9_HUMAN, , , , , ,G,M,xT,L,V,T,P,L,Q,L, +,,sp|P30084|ECHM_HUMAN, , , , ,L,F,Y,xS,T,F,A,T,D,D,R, +,,sp|Q9Y3I0|RTCB_HUMAN, , , , ,S,S,M,xT,F,L,T,R, , , , +,,sp|P16930|FAAA_HUMAN, , , , ,H,L,F,xT,G,P,V,L,S,K, , +,,sp|Q9BRA2|TXD17_HUMAN, , , , , , , ,xT,I,F,A,Y,F,T,G, +,,sp|P12956|XRCC6_HUMAN, , , , ,T,F,N,xT,S,T,G,G,L,L,L, +,,sp|P43686|PRS6B_HUMAN, , , , ,L,I,F,xS,T,I,T,S,K, , , +,,sp|P53597|SUCA_HUMAN, , ,Q,G,T,F,H,xS,Q,Q,A,L,E,Y,G, +,,sp|P52292|IMA1_HUMAN, , , , , ,E,A,xT,W,T,M,S,N,I,T, +,,sp|P54819|KAD2_HUMAN,Q,A,Y,H,T,Q,T,xT,P,L,I,E,Y,Y,R, +,,sp|P27797|CALR_HUMAN, , , , , ,G,Q,xT,L,V,V,Q,F,T,V, +,,sp|Q99426|TBCB_HUMAN, , , , , , , ,xS,L,T,I,A,E,F,K, +,,sp|Q14697|GANAB_HUMAN, , , , , , ,L,xS,F,Q,H,D,P,E,T, +,,sp|P30086|PEBP1_HUMAN, , , , , ,R,P,xT,S,I,S,W,D,G,L, +,,sp|O60508|PRP17_HUMAN, , , , ,S,P,S,xS,K,P,S,L,A,V,A, +,,sp|Q13315|ATM_HUMAN, , , ,D,R,E,F,xS,T,F,Y,E,S,L,K, +,,sp|P51991|ROA3_HUMAN, , , ,W,G,T,L,xT,D,C,V,V,M,R,D, +,,sp|Q13895|BYST_HUMAN, , , ,A,A,T,M,xT,A,A,G,H,H,A,E, +,,sp|P55884|EIF3B_HUMAN, , , , ,I,S,V,xS,F,Y,H,V,K, , , +,,sp|Q99575|POP1_HUMAN, , , ,Y,I,T,A,xS,T,F,A,Q,A,R, , +,,sp|P49588|SYAC_HUMAN, , , , , ,I,G,xT,I,Y,G,D,L,K, , +,,sp|Q7Z5L9|I2BP2_HUMAN,R,P,A,S,V,S,S,xS,A,A,V,E,H,E,Q, +,,sp|P23588|IF4B_HUMAN, , , , , ,A,A,xS,I,F,G,G,A,K,P, +,,sp|Q9UIA9|XPO7_HUMAN, , , , , , ,T,xT,F,Y,T,A,L,G,R, +,,sp|P07437|TBB5_HUMAN; sp|Q13509|TBB3_HUMAN; tr|A0A0B4J269|A0A0B4J269_HUMAN,G,T,G,S,G,M,G,xT,L,L,I,S,K, , , +,,sp|P17987|TCPA_HUMAN,E,V,G,D,G,T,T,xS,V,V,I,I,A,A,E, +,,sp|O15042|SR140_HUMAN, , , , , ,L,Y,xS,I,L,Q,G,D,S,P, +,,sp|Q9UKM9|RALY_HUMAN, , , , ,G,R,L,xS,P,V,P,V,P,R, , +,,sp|P30086|PEBP1_HUMAN, , ,R,P,T,S,I,xS,W,D,G,L,D,S,G, +,,sp|Q13586|STIM1_HUMAN, , ,N,T,L,F,G,xT,F,H,V,A,H,S,S, +,,sp|Q7Z5L9|I2BP2_HUMAN, , ,R,P,A,S,V,xS,S,S,A,A,V,E,H, +,,sp|Q96JH7|VCIP1_HUMAN, , , , , , , ,xS,S,T,T,F,F,E,L, +,,sp|P17987|TCPA_HUMAN, , ,E,V,G,D,G,xT,T,S,V,V,I,I,A, +,,sp|P06737|PYGL_HUMAN, , , , , , , ,xT,F,A,Y,T,N,H,T, +,,sp|Q16594|TAF9_HUMAN,S,V,T,S,R,P,S,xT,P,T,L,G,T,P,T, +,,sp|P30084|ECHM_HUMAN, , , ,L,F,Y,S,xT,F,A,T,D,D,R,K, +,,sp|P09651|ROA1_HUMAN; tr|A0A2R8Y4L2|A0A2R8Y4L2_HUMAN, , , , , ,Y,H,xT,V,N,G,H,N,C,E, +,,sp|Q9NZL9|MAT2B_HUMAN, , ,G,T,F,H,W,xS,G,N,E,Q,M,T,K, +,,sp|P06748|NPM_HUMAN, , , , , , , ,xT,V,S,L,G,A,G,A, +,,sp|Q14C86|GAPD1_HUMAN,L,S,V,V,S,G,I,xS,A,T,S,E,D,I,P, +,,sp|Q9NPJ3|ACO13_HUMAN, , , , , , ,I,xT,L,V,S,A,A,P,G, +,,sp|Q9H7N4|SFR19_HUMAN, , , ,Q,R,S,P,xS,P,A,P,A,P,A,P, +,,sp|Q03252|LMNB2_HUMAN,G,G,P,A,T,P,L,xS,P,T,R, , , , , +,,sp|Q9HCC0|MCCB_HUMAN, , , , ,K,Q,G,xT,I,F,L,A,G,P,P, +,,sp|O15371|EIF3D_HUMAN, , ,I,F,H,T,V,xT,T,T,D,D,P,V,I, +,,sp|Q9UI08|EVL_HUMAN, , , ,Y,N,Q,A,xT,P,T,F,H,Q,W,R, +,,sp|Q13283|G3BP1_HUMAN, , , , , ,S,S,xS,P,A,P,A,D,I,A, +,,sp|O75064|DEN4B_HUMAN,Y,P,V,P,V,F,S,xT,F,V,L,T,G,A,A, +,,sp|Q16594|TAF9_HUMAN, , , ,L,S,V,G,xS,V,T,S,R,P,S,T, +,,sp|Q13177|PAK2_HUMAN, , , , , , , ,xS,T,M,V,G,T,P,Y, +,,sp|P20290|BTF3_HUMAN,Q,A,S,L,A,A,N,xT,F,T,I,T,G,H,A, +,,sp|Q8WVB6|CTF18_HUMAN, , , ,L,R,P,V,xS,T,Q,L,Y,S,T,R, +,,sp|Q9ULT8|HECD1_HUMAN, , , , , , ,S,xT,I,F,Y,Y,V,Q,K, +,,sp|P25789|PSA4_HUMAN, , , ,V,E,I,A,xT,L,T,R, , , , , +,,sp|Q9H7N4|SFR19_HUMAN, , , , , ,Q,R,xS,P,S,P,A,P,A,P, +,,sp|Q9BWJ5|SF3B5_HUMAN, , , , , , ,Y,xT,I,H,S,Q,L,E,H, +,,sp|P30101|PDIA3_HUMAN,Y,G,V,S,G,Y,P,xT,L,K, , , , , , +,,sp|Q6ZNL6|FGD5_HUMAN, , , ,E,R,P,V,xS,M,S,F,P,L,S,S, +,,sp|P55265|DSRAD_HUMAN, ,T,L,P,L,T,G,xS,T,F,H,D,Q,I,A, +,,sp|O60573|IF4E2_HUMAN, , , , ,Q,I,G,xT,F,A,S,V,E,Q,F, +,,sp|P34932|HSP74_HUMAN,P,Q,A,A,E,Q,G,xT,D,T,A,V,P,S,D, +,,sp|Q8WV74|NUDT8_HUMAN, , , ,A,R,P,A,xS,A,A,V,L,V,P,L, +,,sp|P22087|FBRL_HUMAN; sp|A6NHQ2|FBLL1_HUMAN,I,V,A,L,N,A,H,xT,F,L,R, , , , , +,,sp|P55265|DSRAD_HUMAN, , , , , , , ,xT,L,P,L,T,G,S,T, +,,sp|Q15181|IPYR_HUMAN, , , , , ,G,I,xS,C,M,N,T,T,L,S, +,,sp|P60709|ACTB_HUMAN; sp|P63261|ACTG_HUMAN, , , ,A,V,F,P,xS,I,V,G,R,P,R, , +,,sp|P06737|PYGL_HUMAN, , , ,T,F,A,Y,xT,N,H,T,V,L,P,E, +,,sp|P38646|GRP75_HUMAN, , , , ,Q,A,V,xT,N,P,N,N,T,F,Y, +,,sp|P61960|UFM1_HUMAN, , , , , , ,I,xT,L,T,S,D,P,R, , +,,sp|Q8IYB3|SRRM1_HUMAN, , , , , ,E,K,xT,P,E,L,P,E,P,S, +,,sp|P49915|GUAA_HUMAN,A,H,S,F,Y,N,G,xT,T,T,L,P,I,S,D, +,,sp|Q14690|RRP5_HUMAN, , , , , ,A,G,xT,Y,F,S,N,Q,A,V, +,,sp|P07900|HS90A_HUMAN, , , , , , , ,xT,L,T,I,V,D,T,G, +,,sp|O14980|XPO1_HUMAN, ,E,T,L,V,Y,L,xT,H,L,D,Y,V,D,T, +,,sp|P04075|ALDOA_HUMAN,H,E,E,I,A,M,A,xT,V,T,A,L,R, , , +,,sp|O75521|ECI2_HUMAN, , , , , , ,A,xT,F,H,T,P,F,S,H, +,,sp|P07737|PROF1_HUMAN, , , , , , , ,xS,T,G,G,A,P,T,F, +,,sp|P08865|RSSA_HUMAN,A,S,Y,V,N,L,P,xT,I,A,L,C,N,T,D, +,,sp|P60709|ACTB_HUMAN; sp|P63261|ACTG_HUMAN,T,V,L,S,G,G,T,xT,M,Y,P,G,I,A,D, +,,sp|P13639|EF2_HUMAN, , , , , , , ,xT,I,L,M,M,G,R, , +,,sp|Q16594|TAF9_HUMAN,T,S,R,P,S,T,P,xT,L,G,T,P,T,P,Q, +,,sp|P62807|H2B1C_HUMAN; sp|P57053|H2BFS_HUMAN; sp|O60814|H2B1K_HUMAN; sp|Q99880|H2B1L_HUMAN; sp|Q99879|H2B1M_HUMAN; sp|Q99877|H2B1N_HUMAN; sp|Q93079|H2B1H_HUMAN; sp|Q5QNW6|H2B2F_HUMAN; sp|P58876|H2B1D_HUMAN, , , , ,E,S,Y,xS,V,Y,V,Y,K, , , +,,sp|Q15005|SPCS2_HUMAN, , , , , , ,L,xT,F,I,S,G,R, , , +,,sp|Q9UKJ3|GPTC8_HUMAN, , ,S,P,S,Q,Y,xS,E,E,E,E,E,E,D, +,,sp|Q9UKJ3|GPTC8_HUMAN, , , , , ,S,P,xS,Q,Y,S,E,E,E,E, +,,sp|O60583|CCNT2_HUMAN, , , , , , , ,xS,P,V,G,L,S,S,D, +,,sp|Q14554|PDIA5_HUMAN, , , , ,G,Q,G,xT,I,C,W,V,D,C,G, +,,sp|Q96QH2|PRAM_HUMAN, , , , , , , ,xS,P,Q,P,E,L,S,T, +,,sp|Q9UI08|EVL_HUMAN, , , , , , , ,xS,P,L,Q,S,Q,P,H, +,,sp|P53999|TCP4_HUMAN, , , ,E,L,V,S,xS,S,S,S,G,S,D,S, +,,sp|Q6PJG6|BRAT1_HUMAN, , , , , , ,G,xS,P,N,T,A,S,A,E, +,,sp|P49450|CENPA_HUMAN, , , , , , , ,xS,P,S,P,T,P,T,P, +,,sp|O00231|PSD11_HUMAN, , , , , ,A,Q,xS,L,L,S,T,D,R, , +,,sp|Q9NR82|KCNQ5_HUMAN, , , , ,S,P,S,xT,D,I,T,A,E,G,S, +,,tr|H3BQZ7|H3BQZ7_HUMAN; sp|Q1KMD3|HNRL2_HUMAN, , , , , , , ,xS,G,D,E,T,P,G,S, +,,sp|Q07002|CDK18_HUMAN,L,G,E,G,T,Y,A,xT,V,F,K, , , , , +,,sp|P45973|CBX5_HUMAN, , , , ,T,A,D,xS,S,S,S,E,D,E,E, +,,sp|Q14739|LBR_HUMAN, , , , , , , ,xS,P,G,R,P,P,K, , +,,sp|Q9BQE3|TBA1C_HUMAN; sp|Q71U36|TBA1A_HUMAN; sp|P68363|TBA1B_HUMAN, , , , ,G,H,Y,xT,I,G,K, , , , , +,,sp|P53999|TCP4_HUMAN,E,L,V,S,S,S,S,xS,G,S,D,S,D,S,E, +,,sp|P19338|NUCL_HUMAN, , , , ,K,E,D,xS,D,E,E,E,D,D,D, +,,sp|P53999|TCP4_HUMAN, , ,E,L,V,S,S,xS,S,S,G,S,D,S,D, +,,sp|Q9Y2W1|TR150_HUMAN, , , ,S,P,P,S,xT,G,S,T,Y,G,S,S, +,,sp|Q92804|RBP56_HUMAN, , , ,Q,S,S,Y,xS,Q,Q,P,Y,N,N,Q, +,,sp|P53999|TCP4_HUMAN, , , , ,E,L,V,xS,S,S,S,S,G,S,D, +,,sp|Q9HCN4|GPN1_HUMAN,A,A,A,E,L,Q,A,xS,G,G,P,R, , , , +,,sp|P19338|NUCL_HUMAN, , , ,K,V,V,V,xS,P,T,K, , , , , +,,sp|P31943|HNRH1_HUMAN; sp|P55795|HNRH2_HUMAN, , ,H,T,G,P,N,xS,P,D,T,A,N,D,G, +,,sp|O94888|UBXN7_HUMAN, , , , , , , ,xS,P,H,K,D,L,G,H, +,,sp|Q99618|CDCA3_HUMAN, , , , , ,S,P,xS,A,G,I,L,R, , , +,,sp|Q9UQ35|SRRM2_HUMAN, , ,S,C,F,E,S,xS,P,D,P,E,L,K, , +,,sp|Q9Y2W1|TR150_HUMAN; sp|Q9NYF8|BCLF1_HUMAN, , , , , , , ,xS,P,E,I,H,R, , , +,,sp|Q9NWQ8|PHAG1_HUMAN, , , , , ,S,P,xS,S,C,N,D,L,Y,A, +,,sp|Q8ND76|CCNY_HUMAN, , , , , ,S,A,xS,A,D,N,L,T,L,P, +,,sp|Q9Y2W1|TR150_HUMAN, ,S,P,P,S,T,G,xS,T,Y,G,S,S,Q,K, +,,sp|P25205|MCM3_HUMAN, , , ,G,G,Y,T,xS,G,T,F,R, , , , +,,sp|P27824|CALX_HUMAN,E,D,E,I,L,N,R,xS,P,R, , , , , , +,,sp|P61978|HNRPK_HUMAN, , ,D,Y,D,D,M,xS,P,R, , , , , , +,,sp|Q9Y2W1|TR150_HUMAN, , , , ,S,P,P,xS,T,G,S,T,Y,G,S, +,,sp|Q9HCE3|ZN532_HUMAN, , , , , , , ,xS,P,E,S,Q,N,L,I, +,,sp|P18615|NELFE_HUMAN, , , , , , , ,xS,I,S,A,D,D,D,L, +,,sp|P08575|PTPRC_HUMAN,D,E,S,S,D,D,D,xS,D,S,E,E,P,S,K, +,,sp|Q15036|SNX17_HUMAN, , , , , , , ,xS,P,P,L,L,E,S,P, +,,sp|Q6JBY9|CPZIP_HUMAN, , , , , ,S,Q,xS,D,C,G,E,L,G,D, +,,sp|Q96RU3|FNBP1_HUMAN, , , , , ,T,V,xS,D,N,S,L,S,N,S, +,,sp|Q9Y2W1|TR150_HUMAN,T,G,S,T,Y,G,S,xS,Q,K,E,E,S,A,A, +,,sp|P18615|NELFE_HUMAN, , , , , ,S,I,xS,A,D,D,D,L,Q,E, +,,sp|Q7Z6Z7|HUWE1_HUMAN, , , , , , ,G,xS,G,T,A,S,D,D,E, +,,sp|Q96I25|SPF45_HUMAN, , ,R,P,D,P,D,xS,D,E,D,E,D,Y,E, +,,sp|Q15366|PCBP2_HUMAN, , , , , , ,P,xS,S,S,P,V,I,F,A, +,,sp|P85037|FOXK1_HUMAN, , , , , ,E,G,xS,P,I,P,H,D,P,E, +,,sp|Q13098|CSN1_HUMAN, , , , , , , ,xS,P,P,R,E,G,S,Q, +,,sp|P08575|PTPRC_HUMAN,E,H,D,S,D,E,S,xS,D,D,D,S,D,S,E, +,,sp|P16401|H15_HUMAN; sp|P16402|H13_HUMAN; sp|Q02539|H11_HUMAN; sp|P16403|H12_HUMAN; sp|P10412|H14_HUMAN; sp|P22492|H1T_HUMAN, ,G,T,G,A,S,G,xS,F,K, , , , , , +,,sp|P60174|TPIS_HUMAN, , , ,D,C,G,A,xT,W,V,V,L,G,H, , +,,sp|Q9Y2W1|TR150_HUMAN,S,T,G,S,T,Y,G,xS,S,Q,K,E,E,S,A, +,,sp|Q15287|RNPS1_HUMAN, , , , , , , ,xS,P,S,P,K,P,T,K, +,,sp|Q05193|DYN1_HUMAN, , , , , , , ,xS,P,T,S,S,P,T,P, +,,sp|P07948|LYN_HUMAN, , , , ,G,K,D,xS,L,S,D,D,G,V,D, +,,sp|Q5SSJ5|HP1B3_HUMAN, , , , , ,G,A,xS,G,S,F,V,V,V,Q, +,,sp|P49585|PCY1A_HUMAN, , , , , ,S,P,xS,P,S,F,R, , , , +,,sp|Q7Z6Z7|HUWE1_HUMAN, , , , ,G,S,G,xT,A,S,D,D,E,F,E, +,,sp|Q92610|ZN592_HUMAN, , , , , , , ,xS,P,L,E,A,T,R, , +,,sp|Q03164|KMT2A_HUMAN, , , , , , , ,xS,P,T,V,P,S,Q,N, +,,sp|Q07666|KHDR1_HUMAN, , , , , , , ,xS,G,S,M,D,P,S,G, +,,sp|Q16629|SRSF7_HUMAN, , , , , , , ,xS,P,S,G,S,P,R, , +,,sp|P08575|PTPRC_HUMAN,S,E,H,D,S,D,E,xS,S,D,D,D,S,D,S, +,,sp|Q5T7W0|ZN618_HUMAN, , , , , , , ,xS,P,P,A,V,V,E,E, +,,sp|Q9H0E3|SP130_HUMAN, , , , , , , ,xS,P,P,K,E,Y,I,D, +,,sp|Q5VTE0|EF1A3_HUMAN; sp|P68104|EF1A1_HUMAN, , , , , ,S,T,xT,T,G,H,L,I,Y,K, +,,sp|Q92804|RBP56_HUMAN, , , , , ,Q,S,xS,Y,S,Q,Q,P,Y,N, +,,sp|Q9Y2W1|TR150_HUMAN,S,P,P,S,T,G,S,xT,Y,G,S,S,Q,K,E, +,,sp|Q13098|CSN1_HUMAN, ,S,P,P,R,E,G,xS,Q,G,E,L,T,P,A, +,,sp|P61313|RL15_HUMAN, , , , , , ,N,xT,L,Q,L,H,R, , , +,,tr|A0A0B4J1V8|A0A0B4J1V8_HUMAN; sp|Q9NQ55|SSF1_HUMAN, , , , ,V,G,G,xS,D,E,E,A,S,G,I, +,,sp|P49736|MCM2_HUMAN, ,G,N,D,P,L,T,xS,S,P,G,R, , , , +,,RRRRRsp|O15229|KMO_HUMAN, , , , ,E,A,A,xT,L,L,D,K, , , , +,,sp|P19013|K2C4_HUMAN,R,G,A,F,S,S,V,xS,M,S,G,G,A,G,R, +,,sp|O15530|PDPK1_HUMAN, , , , , , , ,xT,Q,T,E,S,S,T,P, +,,sp|P06748|NPM_HUMAN, , , , , ,G,P,xS,S,V,E,D,I,K, , +,,sp|Q92793|CBP_HUMAN, , , , , , , ,xS,P,L,S,Q,G,D,S, +,,sp|Q9Y6K9|NEMO_HUMAN, , , , , , , ,xS,P,P,E,E,P,P,D, +,,sp|P53999|TCP4_HUMAN,V,S,S,S,S,S,G,xS,D,S,D,S,E,V,D, +,,sp|Q99613|EIF3C_HUMAN; sp|B5ME19|EIFCL_HUMAN, , , , ,T,C,H,xS,F,I,I,N,E,K, , +,,sp|O75534|CSDE1_HUMAN, , , , , , ,G,xT,V,S,F,H,S,H,S, +,,sp|Q13547|HDAC1_HUMAN,C,E,E,E,F,S,D,xS,E,E,E,G,E,G,G, +,,sp|P53999|TCP4_HUMAN, ,E,L,V,S,S,S,xS,S,G,S,D,S,D,S, +,,sp|Q9H0F6|SHRPN_HUMAN, , , , , , , ,xS,P,G,N,L,T,E,R, +,,sp|P53999|TCP4_HUMAN,S,S,S,S,G,S,D,xS,D,S,E,V,D,K,K, +,,sp|P31930|QCR1_HUMAN, , , ,N,R,P,G,xS,A,L,E,K, , , , +,,sp|Q05BQ5|MBTD1_HUMAN,L,I,C,V,A,T,V,xT,R, , , , , , , +,,sp|Q5VUA4|ZN318_HUMAN, , , , , ,S,P,xT,V,L,C,Q,K, , , +,,sp|Q92688|AN32B_HUMAN, , , , ,K,R,E,xT,D,D,E,G,E,D,D,
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/all stuff/2RSBF.csv Fri Feb 21 13:07:45 2020 -0500 @@ -0,0 +1,437 @@ +Accession Numbers,Amino Acids,A,C,D,E,F,G,H,I,K,L,M,N,P,Q,R,S,T,V,W,Y,Properties,Hydrophobic,Polar,Small,Negative,Postive,Amide,Large Aliphatic,Small Aliphatic,Aromatic,Hydroxy,X,Number of ST,Number of pST +sp|Q13283|G3BP1_HUMAN,4.721030043,0.214592275,5.150214592,10.30042918,4.077253219,8.369098712,2.575107296,3.004291845,4.077253219,5.364806867,2.360515021,4.506437768,10.51502146,6.43776824,7.939914163,5.793991416,3.004291845,9.442060086,0.214592275,1.931330472,,39.69957082,40.98712446,51.7167382,15.45064378,14.59227468,10.94420601,8.369098712,22.53218884,6.223175966,8.798283262,,41,4,466 +sp|Q13283|G3BP1_HUMAN,4.721030043,0.214592275,5.150214592,10.30042918,4.077253219,8.369098712,2.575107296,3.004291845,4.077253219,5.364806867,2.360515021,4.506437768,10.51502146,6.43776824,7.939914163,5.793991416,3.004291845,9.442060086,0.214592275,1.931330472,,39.69957082,40.98712446,51.7167382,15.45064378,14.59227468,10.94420601,8.369098712,22.53218884,6.223175966,8.798283262,,41,3,466 +sp|O43707|ACTN4_HUMAN,8.452250274,0.878155873,6.915477497,9.549945115,3.293084523,4.500548847,3.402854007,6.586169045,6.366630077,9.220636663,2.634467618,5.049396268,3.183315038,6.147091109,5.598243688,5.159165752,4.500548847,4.061470911,1.756311745,2.744237102,,44.1273326,43.02963776,42.70032931,16.46542261,15.36772777,11.19648738,15.80680571,17.01427003,7.79363337,9.659714599,,88,4,911 +sp|P35609|ACTN2_HUMAN,8.389261745,1.118568233,6.040268456,10.29082774,3.131991051,3.914988814,2.572706935,7.382550336,5.928411633,9.395973154,3.243847875,5.14541387,3.131991051,6.15212528,6.711409396,4.250559284,4.8098434,3.691275168,1.789709172,2.908277405,,44.96644295,42.84116331,40.49217002,16.3310962,15.21252796,11.29753915,16.77852349,15.99552573,7.829977629,9.060402685,,81,4,894 +sp|Q08043|ACTN3_HUMAN,9.10099889,1.442841287,5.882352941,9.766925638,3.32963374,5.549389567,2.219755827,5.216426193,5.216426193,10.65482797,3.107658158,4.328523862,3.218645949,5.993340733,7.325194229,4.217536071,4.439511654,4.772475028,1.886792453,2.330743618,,47.3917869,40.73251942,42.95227525,15.64927858,14.76137625,10.32186459,15.87125416,19.42286349,7.547169811,8.657047725,,78,4,901 +sp|P12814|ACTN1_HUMAN,7.959641256,1.121076233,6.950672646,9.417040359,3.251121076,4.596412556,3.02690583,6.838565022,6.053811659,9.417040359,3.02690583,4.820627803,3.3632287,5.829596413,6.053811659,4.035874439,5.605381166,3.923766816,1.793721973,2.914798206,,44.84304933,42.15246637,42.37668161,16.367713,15.13452915,10.65022422,16.25560538,16.47982063,7.959641256,9.641255605,,86,4,892 +sp|Q04837|SSBP_HUMAN,2.702702703,0,5.405405405,6.756756757,3.378378378,6.081081081,2.027027027,5.405405405,5.405405405,8.783783784,2.027027027,4.054054054,2.702702703,6.081081081,10.13513514,6.756756757,6.756756757,10.13513514,1.351351351,4.054054054,,43.91891892,39.86486486,44.59459459,12.16216216,17.56756757,10.13513514,14.18918919,18.91891892,8.783783784,13.51351351,,20,2,148 +sp|Q15738|NSDHL_HUMAN,7.238605898,1.340482574,4.557640751,5.361930295,5.09383378,6.434316354,2.680965147,5.898123324,5.361930295,9.115281501,2.680965147,5.09383378,6.166219839,4.557640751,5.09383378,4.289544236,6.166219839,8.310991957,0.536193029,4.021447721,,50.67024129,32.7077748,49.59785523,9.919571046,13.13672922,9.651474531,15.01340483,21.98391421,9.651474531,10.45576408,,39,1,373 +sp|Q08945|SSRP1_HUMAN,4.37235543,0.846262341,6.911142454,10.43723554,4.936530324,6.629055007,1.833568406,4.090267983,10.71932299,6.770098731,2.3977433,3.94922426,3.526093089,3.102961918,6.064880113,10.1551481,4.513399154,4.795486601,0.846262341,3.102961918,,38.78702398,43.01833568,45.69816643,17.348378,18.61777151,7.052186178,10.86036671,15.79689704,8.885754584,14.66854725,,104,3,709 +sp|Q08945|SSRP1_HUMAN,4.37235543,0.846262341,6.911142454,10.43723554,4.936530324,6.629055007,1.833568406,4.090267983,10.71932299,6.770098731,2.3977433,3.94922426,3.526093089,3.102961918,6.064880113,10.1551481,4.513399154,4.795486601,0.846262341,3.102961918,,38.78702398,43.01833568,45.69816643,17.348378,18.61777151,7.052186178,10.86036671,15.79689704,8.885754584,14.66854725,,104,1,709 +sp|Q9Y371|SHLB1_HUMAN,8.493150685,1.369863014,4.931506849,7.945205479,3.01369863,5.205479452,1.095890411,4.931506849,6.849315068,12.05479452,2.465753425,6.02739726,3.287671233,4.931506849,4.931506849,7.397260274,7.123287671,4.109589041,0.547945205,3.287671233,,45.47945205,36.71232877,47.94520548,12.87671233,12.87671233,10.95890411,16.98630137,17.80821918,6.849315068,14.52054795,,53,1,365 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+sp|Q05BQ5|MBTD1_HUMAN,6.52866242,3.184713376,5.414012739,6.050955414,4.458598726,6.687898089,2.547770701,4.777070064,7.643312102,7.006369427,2.388535032,3.503184713,5.732484076,4.140127389,4.299363057,8.917197452,4.777070064,6.210191083,2.229299363,3.503184713,,46.97452229,33.59872611,50.95541401,11.46496815,14.49044586,7.643312102,11.78343949,19.42675159,10.1910828,13.69426752,,86,1,628 +sp|Q5VUA4|ZN318_HUMAN,5.660377358,1.272487933,5.353225099,9.039052216,2.36946029,5.748135147,2.413339184,3.641948223,7.415533129,8.205353225,1.360245722,3.027643703,9.477841158,3.598069329,6.625713032,12.76875823,4.782799473,5.089951733,0.482667837,1.667397982,,35.49802545,37.47257569,53.18121983,14.39227731,16.45458534,6.625713032,11.84730145,16.49846424,4.519526108,17.5515577,,400,2,2279 +sp|Q92688|AN32B_HUMAN,2.390438247,1.195219124,15.13944223,22.31075697,2.788844622,6.374501992,0.796812749,2.390438247,6.772908367,13.14741036,1.195219124,5.179282869,2.788844622,0.796812749,3.984063745,4.38247012,2.788844622,4.38247012,0,1.195219124,,35.05976096,54.98007968,44.62151394,37.4501992,11.55378486,5.976095618,15.53784861,13.14741036,3.984063745,7.171314741,,18,1,251
--- a/all stuff/Commonality and Difference finderMADE 7 TO 7 1-15-2019.R Fri Apr 19 16:55:29 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,1281 +0,0 @@ -#I should make an SOP for this. Problems we encountered: no x in the xY motif, and the kilodemon -#the output files have both Y and xY, they shouldn't why is that happening? make it not happen -#make sure that accession numbers stay locked to each motif, somehow -#output should look just like the KALIP input - -#ff you want ONLY FULL MOTIFS, put "YES" here, please use all caps -FullMotifsOnly_questionmark<-"NO" -#If you want ONLY TRUNCATED MOTIFS, put "YES" here, please use all caps -TruncatedMotifsOnly_questionmark<-"NO" -#if you want to find the overlap, put a "YES" here (all caps), if you want to find the non-overlap, put "NO" (all caps) -Are_You_Looking_For_Commonality<-"NO" - - -#put the names of your input files here -FirstSubstrateSet<- read.csv("Galaxy63-BTK_PLUS-R1_Substrates.csv", stringsAsFactors=FALSE) -Firstsubbackfreq<- read.csv("Galaxy64-BTK_PLUS-R1_SubstrateBackgroundFrequency.csv", header=FALSE, stringsAsFactors=FALSE) - -SecondSubstrateSet<- read.csv("Galaxy65-BTK_PLUS_R2_Substrates.csv", stringsAsFactors=FALSE) -Secondsubbackfreq<- read.csv("Galaxy66-BTK_PLUS_R2_SubstrateBackgroundFrequency.csv", header=FALSE, stringsAsFactors=FALSE) - -ThirdSubstrateSet<- read.csv("Galaxy69-BTK_PLUS_R3_Substrates.csv", stringsAsFactors=FALSE) -Thirdsubbackfreq<- read.csv("Galaxy70-BTK_PLUS_R3_SubstrateBackgroundFrequency.csv", header=FALSE, stringsAsFactors=FALSE) - -#then put the names of your output files here -Shared_motifs_table<-"180719_GALAXY-BTK-plus-rep-OVLP-7to7-substrates.csv" -Shared_subbackfreq_table<-"180719_GALAXY-BTK-plus-rep-OVLP-7to7-SubBackFreq.csv" - -# Shared_motifs_table<-"Shared motifs 7-27-17.csv" -# Shared_subbackfreq_table<-"SubstrateBackgrounFrequency-for-shared-motifs 4 7-27-17.csv" - -First_unshared_motifs_table<-"R1 substrates.csv" -First_unshared_subbackfreq<-"R1 SBF.csv" - -Second_unshared_motifs_table<-"R2 subs.csv" -Second_unshared_subbackfreq<-"R2 SBf.csv" - -Third_unshared_motifs_table<-"R3 subs.csv" -Third_unshared_subbackfreq<-"R3 SBF.csv" - -#final note, this code is going to be unworkable if you want to make a Venn diagram of more than 3 circles. I think I'll poke around -#other languages to see if any of them can do it. -#################################################################################################################################### - - - - - -FirstxY<-rep("xY",times=nrow(FirstSubstrateSet)) -FirstSubstrateSet[,11]<-FirstxY - -SecondxY<-rep("xY",times=nrow(SecondSubstrateSet)) -SecondSubstrateSet[,11]<-SecondxY - -ThirdxY<-rep("xY",times=nrow(ThirdSubstrateSet)) -ThirdSubstrateSet[,11]<-ThirdxY - - - - - - - - - - - -#################################################################################################################################### -#################################################################################################################################### -# better version of this code written in C: what happens when two kinases share a motif, but they found that motif in two -# separate proteins thus two separate accession numbers? -# It should actually output the shared motif and BOTH accession numbers. Right now it does not, it only maps out the second -# accession number. So that needs to be fixed BUT you need to keep the commonality between a motif and its accession number -#################################################################################################################################### -#################################################################################################################################### -#################################################################################################################################### -#################################################################################################################################### - -#Create the motif sets, deciding wether or not you're looking for truncated or full here -#full only -if (Are_You_Looking_For_Commonality=="YES"){ - if (FullMotifsOnly_questionmark=="YES"){ - FTLwtmotifs=matrix(,nrow = nrow(FirstSubstrateSet),ncol=1) - FTLwtAccessionNumbers=matrix(,nrow = nrow(FirstSubstrateSet),ncol=1) - leftspaces<-c() - rightspaces<-c() - for (i in 1:nrow(FirstSubstrateSet)){ - FTLwtletters<-FirstSubstrateSet[i,4:18] - FTLwtletters<-FTLwtletters[FTLwtletters !="XXXXX"] - FTLwtletters<-paste(FTLwtletters, sep="", collapse="") - - - YYYmotif <- unlist(strsplit(FTLwtletters, split = "")) - YYYposition <- match(x = "x", table = YYYmotif) - #position itself tells me how much is to the left of that X by what it's number is. x at position 4 tells me that there are - #just 3 letters to the left of x - - YYYLettersToTheLeft <- YYYposition - 1 - #how many letters to the right SHOULD just be length(motif)-position-1 if it's 5 long and x is at 3 then Y is at 4 and there is - #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1 - YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1 - #then sanity check, we're currently looking only at +/-4, but this spot allows for up to +/- 7 as well, just depends on what the - #variable the user puts in is - - if (YYYLettersToTheLeft > 6 && YYYLettersToTheRight > 6) { - motif<-YYYmotif - #save that motif, which is the Y and +/- 4 amino acids, including truncation - motif<-motif[!motif %in% "x"] - motif<-paste(motif, sep="", collapse="") - FTLwtletters<-motif - FTLwtmotifs[i,1]<-FTLwtletters - FTLwtAccessionNumbers[i,1]<-FirstSubstrateSet[i,3] - - } - - } - # FTLwtmotifs <- FTLwtmotifs[!is.na(FTLwtmotifs)] - # FTLwtmotifs<-matrix(FTLwtmotifs,ncol = 1) - # - - D835Ymotifs=matrix(,nrow = nrow(SecondSubstrateSet),ncol=1) - D835YAccessionNumbers<-matrix(,nrow = nrow(SecondSubstrateSet),ncol = 1) - - for (i in 1:nrow(SecondSubstrateSet)){ - D835letters<-SecondSubstrateSet[i,4:18] - D835letters<-D835letters[D835letters !="XXXXX"] - D835letters<-paste(D835letters, sep="", collapse="") - - - YYYmotif <- unlist(strsplit(D835letters, split = "")) - YYYposition <- match(x = "x", table = YYYmotif) - #position itself tells me how much is to the left of that X by what it's number is. x at position 4 tells me that there are - #just 3 letters to the left of x - - YYYLettersToTheLeft <- YYYposition - 1 - #how many letters to the right SHOULD just be length(motif)-position-1 if it's 5 long and x is at 3 then Y is at 4 and there is - #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1 - YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1 - #then sanity check, we're currently looking only at +/-4, but this spot allows for up to +/- 7 as well, just depends on what the - #variable the user puts in is - - if (YYYLettersToTheLeft > 6 && YYYLettersToTheRight > 6) { - motif<-YYYmotif - #add blank spaces if the motif has less than 4 letters to the left/right - motif<-c(leftspaces,YYYmotif,rightspaces) - #save that motif, which is the Y and +/- 4 amino acids, including truncation - motif<-motif[!motif %in% "x"] - motif<-paste(motif, sep="", collapse="") - D835letters<-motif - D835Ymotifs[i,1]<-D835letters - D835YAccessionNumbers[i,1]<-SecondSubstrateSet[i,3] - - } - } - - ITDmotifs=matrix(,nrow = nrow(ThirdSubstrateSet),ncol=1) - ITDAccessionNumbers<-matrix(,nrow = nrow(ThirdSubstrateSet)) - - for (i in 1:nrow(ThirdSubstrateSet)){ - ITDletters<-ThirdSubstrateSet[i,4:18] - ITDletters<-ITDletters[ITDletters !="XXXXX"] - ITDletters<-paste(ITDletters, sep="", collapse="") - YYYmotif <- unlist(strsplit(ITDletters, split = "")) - YYYposition <- match(x = "x", table = YYYmotif) - #position itself tells me how much is to the left of that X by what it's number is. x at position 4 tells me that there are - #just 3 letters to the left of x - - YYYLettersToTheLeft <- YYYposition - 1 - #how many letters to the right SHOULD just be length(motif)-position-1 if it's 5 long and x is at 3 then Y is at 4 and there is - #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1 - YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1 - #then sanity check, we're currently looking only at +/-4, but this spot allows for up to +/- 7 as well, just depends on what the - #variable the user puts in is - - if (YYYLettersToTheLeft > 6 && YYYLettersToTheRight > 6) { - motif<-YYYmotif - #add blank spaces if the motif has less than 4 letters to the left/right - motif<-c(leftspaces,YYYmotif,rightspaces) - #save that motif, which is the Y and +/- 4 amino acids, including truncation - motif<-motif[!motif %in% "x"] - motif<-paste(motif, sep="", collapse="") - ITDletters<-motif - ITDmotifs[i,1]<-ITDletters - ITDAccessionNumbers[i,1]<-ThirdSubstrateSet[i,3] - - } - } - - } - - ##############################################3 - #Truncated only - if (TruncatedMotifsOnly_questionmark=="YES"){ - FTLwtmotifs=matrix(,nrow = nrow(FirstSubstrateSet),ncol=1) - FTLwtAccessionNumbers=matrix(,nrow = nrow(FirstSubstrateSet),ncol=1) - - for (i in 1:nrow(FirstSubstrateSet)){ - FTLwtletters<-FirstSubstrateSet[i,4:18] - FTLwtletters<-FTLwtletters[FTLwtletters !="XXXXX"] - FTLwtletters<-paste(FTLwtletters, sep="", collapse="") - - - YYYmotif <- unlist(strsplit(FTLwtletters, split = "")) - YYYposition <- match(x = "x", table = YYYmotif) - #position itself tells me how much is to the left of that X by what it's number is. x at position 4 tells me that there are - #just 3 letters to the left of x - - YYYLettersToTheLeft <- YYYposition - 1 - #how many letters to the right SHOULD just be length(motif)-position-1 if it's 5 long and x is at 3 then Y is at 4 and there is - #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1 - YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1 - #then sanity check, we're currently looking only at +/-4, but this spot allows for up to +/- 7 as well, just depends on what the - #variable the user puts in is - - if (YYYLettersToTheLeft < 7 | YYYLettersToTheRight < 7) { - leftspaces<-rep(" ",times=(7-YYYLettersToTheLeft)) - rightspaces<-rep(" ",times=7-(YYYLettersToTheRight)) - #add blank spaces if the motif has less than 4 letters to the left/right - motif<-c(leftspaces,YYYmotif,rightspaces) - #save that motif, which is the Y and +/- 4 amino acids, including truncation - motif<-motif[!motif %in% "x"] - motif<-paste(motif, sep="", collapse="") - FTLwtletters<-motif - FTLwtmotifs[i,1]<-FTLwtletters - FTLwtAccessionNumbers[i,1]<-FirstSubstrateSet[i,3] - } - - } - - D835Ymotifs=matrix(,nrow = nrow(SecondSubstrateSet),ncol=1) - D835YAccessionNumbers<-matrix(,nrow = nrow(SecondSubstrateSet),ncol = 1) - - for (i in 1:nrow(SecondSubstrateSet)){ - D835letters<-SecondSubstrateSet[i,4:18] - D835letters<-D835letters[D835letters !="XXXXX"] - D835letters<-paste(D835letters, sep="", collapse="") - - - YYYmotif <- unlist(strsplit(D835letters, split = "")) - YYYposition <- match(x = "x", table = YYYmotif) - #position itself tells me how much is to the left of that X by what it's number is. x at position 4 tells me that there are - #just 3 letters to the left of x - - YYYLettersToTheLeft <- YYYposition - 1 - #how many letters to the right SHOULD just be length(motif)-position-1 if it's 5 long and x is at 3 then Y is at 4 and there is - #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1 - YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1 - #then sanity check, we're currently looking only at +/-4, but this spot allows for up to +/- 7 as well, just depends on what the - #variable the user puts in is - - if (YYYLettersToTheLeft < 7 | YYYLettersToTheRight < 7) { - leftspaces<-rep(" ",times=(7-YYYLettersToTheLeft)) - rightspaces<-rep(" ",times=7-(YYYLettersToTheRight)) - #add blank spaces if the motif has less than 4 letters to the left/right - motif<-c(leftspaces,YYYmotif,rightspaces) - #save that motif, which is the Y and +/- 4 amino acids, including truncation - motif<-motif[!motif %in% "x"] - motif<-paste(motif, sep="", collapse="") - D835letters<-motif - D835YAccessionNumbers[i,1]<-SecondSubstrateSet[i,3] - D835Ymotifs[i,1]<-D835letters - } - } - - ITDmotifs=matrix(,nrow = nrow(ThirdSubstrateSet),ncol=1) - ITDAccessionNumbers<-matrix(,nrow = nrow(ThirdSubstrateSet)) - - for (i in 1:nrow(ThirdSubstrateSet)){ - ITDletters<-ThirdSubstrateSet[i,4:18] - ITDletters<-ITDletters[ITDletters !="XXXXX"] - ITDletters<-paste(ITDletters, sep="", collapse="") - YYYmotif <- unlist(strsplit(ITDletters, split = "")) - YYYposition <- match(x = "x", table = YYYmotif) - #position itself tells me how much is to the left of that X by what it's number is. x at position 4 tells me that there are - #just 3 letters to the left of x - - YYYLettersToTheLeft <- YYYposition - 1 - #how many letters to the right SHOULD just be length(motif)-position-1 if it's 5 long and x is at 3 then Y is at 4 and there is - #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1 - YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1 - #then sanity check, we're currently looking only at +/-4, but this spot allows for up to +/- 7 as well, just depends on what the - #variable the user puts in is - - if (YYYLettersToTheLeft < 7 | YYYLettersToTheRight < 7) { - leftspaces<-rep(" ",times=(7-YYYLettersToTheLeft)) - rightspaces<-rep(" ",times=7-(YYYLettersToTheRight)) - #add blank spaces if the motif has less than 4 letters to the left/right - motif<-c(leftspaces,YYYmotif,rightspaces) - #save that motif, which is the Y and +/- 4 amino acids, including truncation - motif<-motif[!motif %in% "x"] - motif<-paste(motif, sep="", collapse="") - ITDletters<-motif - ITDAccessionNumbers[i,1]<-ThirdSubstrateSet[i,3] - ITDmotifs[i,1]<-ITDletters - } - } - - } - - ############################################### - #ALL motifs, full and truncated - - if (FullMotifsOnly_questionmark!="YES"&&TruncatedMotifsOnly_questionmark!="YES"){ - FTLwtmotifs=matrix(,nrow = nrow(FirstSubstrateSet),ncol=1) - FTLwtAccessionNumbers=matrix(,nrow = nrow(FirstSubstrateSet),ncol=1) - - for (i in 1:nrow(FirstSubstrateSet)){ - FTLwtletters<-FirstSubstrateSet[i,4:18] - FTLwtletters<-FTLwtletters[FTLwtletters !="XXXXX"] - FTLwtletters<-paste(FTLwtletters, sep="", collapse="") - leftspaces<-c() - rightspaces<-c() - - YYYmotif <- unlist(strsplit(FTLwtletters, split = "")) - YYYposition <- match(x = "x", table = YYYmotif) - #position itself tells me how much is to the left of that X by what it's number is. x at position 4 tells me that there are - #just 3 letters to the left of x - - YYYLettersToTheLeft <- YYYposition - 1 - #how many letters to the right SHOULD just be length(motif)-position-1 if it's 5 long and x is at 3 then Y is at 4 and there is - #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1 - YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1 - #then sanity check, we're currently looking only at +/-4, but this spot allows for up to +/- 7 as well, just depends on what the - #variable the user puts in is - - - if (YYYLettersToTheLeft < 7 | YYYLettersToTheRight < 7) { - leftspaces<-rep(" ",times=(7-YYYLettersToTheLeft)) - rightspaces<-rep(" ",times=7-(YYYLettersToTheRight)) - #add blank spaces if the motif has less than 4 letters to the left/right - motif<-c(leftspaces,YYYmotif,rightspaces) - #save that motif, which is the Y and +/- 4 amino acids, including truncation - motif<-motif[!motif %in% "x"] - motif<-paste(motif, sep="", collapse="") - FTLwtletters<-motif - FTLwtmotifs[i,1]<-FTLwtletters - FTLwtAccessionNumbers[i,1]<-FirstSubstrateSet[i,3] - } - - if(YYYLettersToTheLeft>6 && YYYLettersToTheRight>6){ - motif<-YYYmotif - #add blank spaces if the motif has less than 4 letters to the left/right - motif<-c(leftspaces,YYYmotif,rightspaces) - #save that motif, which is the Y and +/- 4 amino acids, including truncation - motif<-motif[!motif %in% "x"] - motif<-paste(motif, sep="", collapse="") - FTLwtletters<-motif - FTLwtmotifs[i,1]<-FTLwtletters - FTLwtAccessionNumbers[i,1]<-FirstSubstrateSet[i,3] - - - } - - } - - D835Ymotifs=matrix(,nrow = nrow(SecondSubstrateSet),ncol=1) - D835YAccessionNumbers<-matrix(,nrow = nrow(SecondSubstrateSet),ncol = 1) - - for (i in 1:nrow(SecondSubstrateSet)){ - D835letters<-SecondSubstrateSet[i,4:18] - D835letters<-D835letters[D835letters !="XXXXX"] - D835letters<-paste(D835letters, sep="", collapse="") - leftspaces<-c() - rightspaces<-c() - - YYYmotif <- unlist(strsplit(D835letters, split = "")) - YYYposition <- match(x = "x", table = YYYmotif) - #position itself tells me how much is to the left of that X by what it's number is. x at position 4 tells me that there are - #just 3 letters to the left of x - - YYYLettersToTheLeft <- YYYposition - 1 - #how many letters to the right SHOULD just be length(motif)-position-1 if it's 5 long and x is at 3 then Y is at 4 and there is - #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1 - YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1 - #then sanity check, we're currently looking only at +/-4, but this spot allows for up to +/- 7 as well, just depends on what the - #variable the user puts in is - if (YYYLettersToTheLeft < 7 | YYYLettersToTheRight < 7) { - leftspaces<-rep(" ",times=(7-YYYLettersToTheLeft)) - rightspaces<-rep(" ",times=7-(YYYLettersToTheRight)) - #add blank spaces if the motif has less than 4 letters to the left/right - motif<-c(leftspaces,YYYmotif,rightspaces) - #save that motif, which is the Y and +/- 4 amino acids, including truncation - motif<-motif[!motif %in% "x"] - motif<-paste(motif, sep="", collapse="") - D835letters<-motif - D835Ymotifs[i,1]<-D835letters - D835YAccessionNumbers[i,1]<-FirstSubstrateSet[i,3] - } - - if(YYYLettersToTheLeft>6 && YYYLettersToTheRight>6){ - motif<-YYYmotif - #add blank spaces if the motif has less than 4 letters to the left/right - motif<-c(leftspaces,YYYmotif,rightspaces) - #save that motif, which is the Y and +/- 4 amino acids, including truncation - motif<-motif[!motif %in% "x"] - motif<-paste(motif, sep="", collapse="") - D835letters<-motif - D835Ymotifs[i,1]<-D835letters - D835YAccessionNumbers[i,1]<-FirstSubstrateSet[i,3] - } - } - - - ITDmotifs=matrix(,nrow = nrow(ThirdSubstrateSet),ncol=1) - ITDAccessionNumbers<-matrix(,nrow = nrow(ThirdSubstrateSet)) - - for (i in 1:nrow(ThirdSubstrateSet)){ - ITDletters<-ThirdSubstrateSet[i,4:18] - ITDletters<-ITDletters[ITDletters !="XXXXX"] - ITDletters<-paste(ITDletters, sep="", collapse="") - YYYmotif <- unlist(strsplit(ITDletters, split = "")) - leftspaces<-c() - rightspaces<-c() - YYYposition <- match(x = "x", table = YYYmotif) - #position itself tells me how much is to the left of that X by what it's number is. x at position 4 tells me that there are - #just 3 letters to the left of x - - YYYLettersToTheLeft <- YYYposition - 1 - #how many letters to the right SHOULD just be length(motif)-position-1 if it's 5 long and x is at 3 then Y is at 4 and there is - #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1 - YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1 - #then sanity check, we're currently looking only at +/-4, but this spot allows for up to +/- 7 as well, just depends on what the - #variable the user puts in is - if (YYYLettersToTheLeft < 7 | YYYLettersToTheRight < 7) { - leftspaces<-rep(" ",times=(7-YYYLettersToTheLeft)) - rightspaces<-rep(" ",times=7-(YYYLettersToTheRight)) - #add blank spaces if the motif has less than 4 letters to the left/right - motif<-c(leftspaces,YYYmotif,rightspaces) - #save that motif, which is the Y and +/- 4 amino acids, including truncation - motif<-motif[!motif %in% "x"] - motif<-paste(motif, sep="", collapse="") - ITDletters<-motif - ITDmotifs[i,1]<-ITDletters - ITDAccessionNumbers[i,1]<-FirstSubstrateSet[i,3] - } - - if(YYYLettersToTheLeft>6 && YYYLettersToTheRight>6){ - motif<-YYYmotif - #add blank spaces if the motif has less than 4 letters to the left/right - motif<-c(leftspaces,YYYmotif,rightspaces) - #save that motif, which is the Y and +/- 4 amino acids, including truncation - motif<-motif[!motif %in% "x"] - motif<-paste(motif, sep="", collapse="") - ITDletters<-motif - ITDmotifs[i,1]<-ITDletters - ITDAccessionNumbers[i,1]<-FirstSubstrateSet[i,3] - } - } - - } - ############################################################################################################################# - ############################################################################################################################# - ############################################################################################################################# - ############################################################################################################################# - ############################################################################################################################# - - #now look for either commonality or difference. Actually could you look for both... - - if (Are_You_Looking_For_Commonality=="YES"){ - - columnalheader<-c(as.character(Thirdsubbackfreq[1:36,1])) - columnalheader<-matrix(columnalheader,nrow = 1) - write.table(x=columnalheader, - file=Shared_subbackfreq_table, - quote=FALSE, sep=",", - row.names=FALSE,col.names = FALSE, na="", append=TRUE) - - FirstOverlapmotifs<-c() - for (i in 1:nrow(ITDmotifs)){ - for (j in 1:nrow(D835Ymotifs)){ - if (is.na(ITDmotifs[i,1])!=TRUE&&is.na(D835Ymotifs[j,1])!=TRUE){ - if (ITDmotifs[i,1]==D835Ymotifs[j,1]){ - FirstOverlapmotifs<-c(FirstOverlapmotifs,D835Ymotifs[j,1]) - } - } - } - } - - AllAccessionNumbers<-c() - columnalheader<-c(rep(NA,36)) - FinalMatrix<-matrix(data =columnalheader,nrow = 1) - - FinalMotifs<-c(rep(NA,20)) - FinalMotifsMatrix<-matrix(data = FinalMotifs,nrow = 1) - - - for (l in 1:length(FirstOverlapmotifs)) { - AccessionNumber<-00000000000 - for (k in 1:nrow(FTLwtmotifs)) { - AccessionNumber<-0000000000000 - if(is.na(FTLwtmotifs[k])!=TRUE){ - #I don't remember why, but I felt it necessary to destroy the accession number multiple times to ensure it is - #destroyed immediately after use - if (FirstOverlapmotifs[l] == FTLwtmotifs[k]) { - substratematrix<-FirstSubstrateSet[k,1:20] - substratematrix<-as.matrix(substratematrix,nrow=1) - FinalMotifsMatrix<-rbind(FinalMotifsMatrix,substratematrix) - #when you find a match between the venn diagrams, save the substrate info you get into a matrix - - AccessionNumber <- as.character(FirstSubstrateSet[k, 3]) - #then take the accession number - - for (m in 1:ncol(Firstsubbackfreq)) { - AN <- as.character(Firstsubbackfreq[1, m]) - if (grepl(pattern = AN, - x = AccessionNumber, - fixed = TRUE) == TRUE) { - outputmatrix <- as.character(Firstsubbackfreq[, m]) - outputmatrix <- matrix(outputmatrix, nrow = 1) - #with that accession number, find a match in the subbackfreq file and save it here - FinalMatrix<-rbind(FinalMatrix,outputmatrix) - } - } - } - } - } - } - - - TrueMatrix<-FinalMatrix[!duplicated(FinalMatrix),] - TrueFinalMotifsMatrix<-FinalMotifsMatrix[!duplicated(FinalMotifsMatrix),] - - TrueFinalMotifsMatrix<-TrueFinalMotifsMatrix[2:nrow(TrueFinalMotifsMatrix),] - TrueMatrix<-TrueMatrix[2:nrow(TrueMatrix),] - - write.table( - x = TrueFinalMotifsMatrix, - file = Shared_motifs_table, - quote = FALSE, - sep = ",", - row.names = FALSE, - col.names = TRUE, - na = "", - append = TRUE - ) - - - write.table( - x = TrueMatrix, - file = Shared_subbackfreq_table, - quote = FALSE, - sep = ",", - row.names = FALSE, - col.names = FALSE, - na = "", - append = TRUE - ) - } -} - -if (Are_You_Looking_For_Commonality=="NO"){ - if (FullMotifsOnly_questionmark=="YES"){ - FTLwtmotifs=rep(NA,times=nrow(FirstSubstrateSet)) - FTLwtAccessionNumbers=rep(NA,times=nrow(FirstSubstrateSet)) - leftspaces<-c() - rightspaces<-c() - for (i in 1:nrow(FirstSubstrateSet)){ - FTLwtletters<-FirstSubstrateSet[i,4:18] - FTLwtletters<-FTLwtletters[FTLwtletters !="XXXXX"] - FTLwtletters<-paste(FTLwtletters, sep="", collapse="") - - - YYYmotif <- unlist(strsplit(FTLwtletters, split = "")) - YYYposition <- match(x = "x", table = YYYmotif) - #position itself tells me how much is to the left of that X by what it's number is. x at position 4 tells me that there are - #just 3 letters to the left of x - - YYYLettersToTheLeft <- YYYposition - 1 - #how many letters to the right SHOULD just be length(motif)-position-1 if it's 5 long and x is at 3 then Y is at 4 and there is - #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1 - YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1 - #then sanity check, we're currently looking only at +/-4, but this spot allows for up to +/- 7 as well, just depends on what the - #variable the user puts in is - - if (YYYLettersToTheLeft > 6 && YYYLettersToTheRight > 6) { - motif<-YYYmotif - #save that motif, which is the Y and +/- 4 amino acids, including truncation - motif<-motif[!motif %in% "x"] - motif<-paste(motif, sep="", collapse="") - FTLwtletters<-motif - FTLwtmotifs[i]<-FTLwtletters - FTLwtAccessionNumbers[i]<-FirstSubstrateSet[i,3] - } - - } - # FTLwtmotifs <- FTLwtmotifs[!is.na(FTLwtmotifs)] - # FTLwtmotifs<-matrix(FTLwtmotifs,ncol = 1) - # - - D835Ymotifs=rep(NA,times=nrow(FirstSubstrateSet)) - D835YAccessionNumbers=rep(NA,times=nrow(FirstSubstrateSet)) - - for (i in 1:nrow(SecondSubstrateSet)){ - D835letters<-SecondSubstrateSet[i,4:18] - D835letters<-D835letters[D835letters !="XXXXX"] - D835letters<-paste(D835letters, sep="", collapse="") - - - YYYmotif <- unlist(strsplit(D835letters, split = "")) - YYYposition <- match(x = "x", table = YYYmotif) - #position itself tells me how much is to the left of that X by what it's number is. x at position 4 tells me that there are - #just 3 letters to the left of x - - YYYLettersToTheLeft <- YYYposition - 1 - #how many letters to the right SHOULD just be length(motif)-position-1 if it's 5 long and x is at 3 then Y is at 4 and there is - #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1 - YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1 - #then sanity check, we're currently looking only at +/-4, but this spot allows for up to +/- 7 as well, just depends on what the - #variable the user puts in is - - if (YYYLettersToTheLeft > 6 && YYYLettersToTheRight > 6) { - motif<-YYYmotif - #add blank spaces if the motif has less than 4 letters to the left/right - motif<-c(leftspaces,YYYmotif,rightspaces) - #save that motif, which is the Y and +/- 4 amino acids, including truncation - motif<-motif[!motif %in% "x"] - motif<-paste(motif, sep="", collapse="") - D835letters<-motif - D835Ymotifs[i]<-D835letters - D835YAccessionNumbers[i]<-SecondSubstrateSet[i,3] - } - } - - ITDmotifs=rep(NA,times=nrow(FirstSubstrateSet)) - ITDAccessionNumbers=rep(NA,times=nrow(FirstSubstrateSet)) - - for (i in 1:nrow(ThirdSubstrateSet)){ - ITDletters<-ThirdSubstrateSet[i,4:18] - ITDletters<-ITDletters[ITDletters !="XXXXX"] - ITDletters<-paste(ITDletters, sep="", collapse="") - YYYmotif <- unlist(strsplit(ITDletters, split = "")) - YYYposition <- match(x = "x", table = YYYmotif) - #position itself tells me how much is to the left of that X by what it's number is. x at position 4 tells me that there are - #just 3 letters to the left of x - - YYYLettersToTheLeft <- YYYposition - 1 - #how many letters to the right SHOULD just be length(motif)-position-1 if it's 5 long and x is at 3 then Y is at 4 and there is - #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1 - YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1 - #then sanity check, we're currently looking only at +/-4, but this spot allows for up to +/- 7 as well, just depends on what the - #variable the user puts in is - - if (YYYLettersToTheLeft > 6 && YYYLettersToTheRight > 6) { - motif<-YYYmotif - #add blank spaces if the motif has less than 4 letters to the left/right - motif<-c(leftspaces,YYYmotif,rightspaces) - #save that motif, which is the Y and +/- 4 amino acids, including truncation - motif<-motif[!motif %in% "x"] - motif<-paste(motif, sep="", collapse="") - ITDletters<-motif - ITDmotifs[i]<-ITDletters - ITDAccessionNumbers[i]<-ThirdSubstrateSet[i,3] - - } - } - names(ITDmotifs)<-ITDAccessionNumbers - names(D835Ymotifs)<-D835YAccessionNumbers - names(FTLwtmotifs)<-FTLwtAccessionNumbers - } - - - ##############################################3 - #Truncated only - if (TruncatedMotifsOnly_questionmark=="YES"){ - FTLwtmotifs=matrix(,nrow = nrow(FirstSubstrateSet),ncol=1) - FTLwtAccessionNumbers=matrix(,nrow = nrow(FirstSubstrateSet),ncol=1) - - for (i in 1:nrow(FirstSubstrateSet)){ - FTLwtletters<-FirstSubstrateSet[i,4:18] - FTLwtletters<-FTLwtletters[FTLwtletters !="XXXXX"] - FTLwtletters<-paste(FTLwtletters, sep="", collapse="") - - - YYYmotif <- unlist(strsplit(FTLwtletters, split = "")) - YYYposition <- match(x = "x", table = YYYmotif) - #position itself tells me how much is to the left of that X by what it's number is. x at position 4 tells me that there are - #just 3 letters to the left of x - - YYYLettersToTheLeft <- YYYposition - 1 - #how many letters to the right SHOULD just be length(motif)-position-1 if it's 5 long and x is at 3 then Y is at 4 and there is - #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1 - YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1 - #then sanity check, we're currently looking only at +/-4, but this spot allows for up to +/- 7 as well, just depends on what the - #variable the user puts in is - - if (YYYLettersToTheLeft < 7 | YYYLettersToTheRight < 7) { - leftspaces<-rep(" ",times=(7-YYYLettersToTheLeft)) - rightspaces<-rep(" ",times=7-(YYYLettersToTheRight)) - #add blank spaces if the motif has less than 4 letters to the left/right - motif<-c(leftspaces,YYYmotif,rightspaces) - #save that motif, which is the Y and +/- 4 amino acids, including truncation - motif<-motif[!motif %in% "x"] - motif<-paste(motif, sep="", collapse="") - FTLwtletters<-motif - FTLwtmotifs[i,1]<-FTLwtletters - FTLwtAccessionNumbers[i,1]<-FirstSubstrateSet[i,3] - } - - } - - D835Ymotifs=matrix(,nrow = nrow(SecondSubstrateSet),ncol=1) - D835YAccessionNumbers<-matrix(,nrow = nrow(SecondSubstrateSet),ncol = 1) - i=2 - for (i in 1:nrow(SecondSubstrateSet)){ - D835letters<-SecondSubstrateSet[i,4:18] - D835letters<-D835letters[D835letters !="XXXXX"] - D835letters<-paste(D835letters, sep="", collapse="") - - - YYYmotif <- unlist(strsplit(D835letters, split = "")) - YYYposition <- match(x = "x", table = YYYmotif) - #position itself tells me how much is to the left of that X by what it's number is. x at position 4 tells me that there are - #just 3 letters to the left of x - - YYYLettersToTheLeft <- YYYposition - 1 - #how many letters to the right SHOULD just be length(motif)-position-1 if it's 5 long and x is at 3 then Y is at 4 and there is - #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1 - YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1 - #then sanity check, we're currently looking only at +/-4, but this spot allows for up to +/- 7 as well, just depends on what the - #variable the user puts in is - - if (YYYLettersToTheLeft < 7 | YYYLettersToTheRight < 7) { - leftspaces<-rep(" ",times=(7-YYYLettersToTheLeft)) - rightspaces<-rep(" ",times=7-(YYYLettersToTheRight)) - #add blank spaces if the motif has less than 4 letters to the left/right - motif<-c(leftspaces,YYYmotif,rightspaces) - #save that motif, which is the Y and +/- 4 amino acids, including truncation - motif<-motif[!motif %in% "x"] - motif<-paste(motif, sep="", collapse="") - D835letters<-motif - D835YAccessionNumbers[i,1]<-SecondSubstrateSet[i,3] - D835Ymotifs[i,1]<-D835letters - } - } - - ITDmotifs=matrix(,nrow = nrow(ThirdSubstrateSet),ncol=1) - ITDAccessionNumbers<-matrix(,nrow = nrow(ThirdSubstrateSet)) - - for (i in 1:nrow(ThirdSubstrateSet)){ - ITDletters<-ThirdSubstrateSet[i,4:18] - ITDletters<-ITDletters[ITDletters !="XXXXX"] - ITDletters<-paste(ITDletters, sep="", collapse="") - YYYmotif <- unlist(strsplit(ITDletters, split = "")) - YYYposition <- match(x = "x", table = YYYmotif) - #position itself tells me how much is to the left of that X by what it's number is. x at position 4 tells me that there are - #just 3 letters to the left of x - - YYYLettersToTheLeft <- YYYposition - 1 - #how many letters to the right SHOULD just be length(motif)-position-1 if it's 5 long and x is at 3 then Y is at 4 and there is - #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1 - YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1 - #then sanity check, we're currently looking only at +/-4, but this spot allows for up to +/- 7 as well, just depends on what the - #variable the user puts in is - - if (YYYLettersToTheLeft < 7 | YYYLettersToTheRight < 7) { - leftspaces<-rep(" ",times=(7-YYYLettersToTheLeft)) - rightspaces<-rep(" ",times=7-(YYYLettersToTheRight)) - #add blank spaces if the motif has less than 4 letters to the left/right - motif<-c(leftspaces,YYYmotif,rightspaces) - #save that motif, which is the Y and +/- 4 amino acids, including truncation - motif<-motif[!motif %in% "x"] - motif<-paste(motif, sep="", collapse="") - ITDletters<-motif - ITDAccessionNumbers[i,1]<-ThirdSubstrateSet[i,3] - ITDmotifs[i,1]<-ITDletters - } - } - names(FTLwtmotifs)<-FTLwtAccessionNumbers - names(D835Ymotifs)<-D835YAccessionNumbers - names(ITDmotifs)<-ITDAccessionNumbers - } - - ############################################### - #ALL motifs, full and truncated - - if (FullMotifsOnly_questionmark!="YES"&&TruncatedMotifsOnly_questionmark!="YES"){ - FTLwtmotifs=matrix(,nrow = nrow(FirstSubstrateSet),ncol=1) - FTLwtAccessionNumbers=matrix(,nrow = nrow(FirstSubstrateSet),ncol=1) - - for (i in 1:nrow(FirstSubstrateSet)){ - FTLwtletters<-FirstSubstrateSet[i,4:18] - FTLwtletters<-FTLwtletters[FTLwtletters !="XXXXX"] - FTLwtletters<-paste(FTLwtletters, sep="", collapse="") - leftspaces<-c() - rightspaces<-c() - - YYYmotif <- unlist(strsplit(FTLwtletters, split = "")) - YYYposition <- match(x = "x", table = YYYmotif) - #position itself tells me how much is to the left of that X by what it's number is. x at position 4 tells me that there are - #just 3 letters to the left of x - - YYYLettersToTheLeft <- YYYposition - 1 - #how many letters to the right SHOULD just be length(motif)-position-1 if it's 5 long and x is at 3 then Y is at 4 and there is - #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1 - YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1 - #then sanity check, we're currently looking only at +/-4, but this spot allows for up to +/- 7 as well, just depends on what the - #variable the user puts in is - - - if (YYYLettersToTheLeft < 7 | YYYLettersToTheRight < 7) { - leftspaces<-rep(" ",times=(7-YYYLettersToTheLeft)) - rightspaces<-rep(" ",times=7-(YYYLettersToTheRight)) - #add blank spaces if the motif has less than 4 letters to the left/right - motif<-c(leftspaces,YYYmotif,rightspaces) - #save that motif, which is the Y and +/- 4 amino acids, including truncation - motif<-motif[!motif %in% "x"] - motif<-paste(motif, sep="", collapse="") - FTLwtletters<-motif - FTLwtmotifs[i,1]<-FTLwtletters - FTLwtAccessionNumbers[i,1]<-FirstSubstrateSet[i,3] - } - - if(YYYLettersToTheLeft>6 && YYYLettersToTheRight>6){ - motif<-YYYmotif - #add blank spaces if the motif has less than 4 letters to the left/right - motif<-c(leftspaces,YYYmotif,rightspaces) - #save that motif, which is the Y and +/- 4 amino acids, including truncation - motif<-motif[!motif %in% "x"] - motif<-paste(motif, sep="", collapse="") - FTLwtletters<-motif - FTLwtmotifs[i,1]<-FTLwtletters - FTLwtAccessionNumbers[i,1]<-FirstSubstrateSet[i,3] - - - } - - } - - D835Ymotifs=matrix(,nrow = nrow(SecondSubstrateSet),ncol=1) - D835YAccessionNumbers<-matrix(,nrow = nrow(SecondSubstrateSet),ncol = 1) - - for (i in 1:nrow(SecondSubstrateSet)){ - D835letters<-SecondSubstrateSet[i,4:18] - D835letters<-D835letters[D835letters !="XXXXX"] - D835letters<-paste(D835letters, sep="", collapse="") - leftspaces<-c() - rightspaces<-c() - - YYYmotif <- unlist(strsplit(D835letters, split = "")) - YYYposition <- match(x = "x", table = YYYmotif) - #position itself tells me how much is to the left of that X by what it's number is. x at position 4 tells me that there are - #just 3 letters to the left of x - - YYYLettersToTheLeft <- YYYposition - 1 - #how many letters to the right SHOULD just be length(motif)-position-1 if it's 5 long and x is at 3 then Y is at 4 and there is - #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1 - YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1 - #then sanity check, we're currently looking only at +/-4, but this spot allows for up to +/- 7 as well, just depends on what the - #variable the user puts in is - if (YYYLettersToTheLeft < 7 | YYYLettersToTheRight < 7) { - leftspaces<-rep(" ",times=(7-YYYLettersToTheLeft)) - rightspaces<-rep(" ",times=7-(YYYLettersToTheRight)) - #add blank spaces if the motif has less than 4 letters to the left/right - motif<-c(leftspaces,YYYmotif,rightspaces) - #save that motif, which is the Y and +/- 4 amino acids, including truncation - motif<-motif[!motif %in% "x"] - motif<-paste(motif, sep="", collapse="") - D835letters<-motif - D835Ymotifs[i,1]<-D835letters - D835YAccessionNumbers[i,1]<-FirstSubstrateSet[i,3] - } - - if(YYYLettersToTheLeft>6 && YYYLettersToTheRight>6){ - motif<-YYYmotif - #add blank spaces if the motif has less than 4 letters to the left/right - motif<-c(leftspaces,YYYmotif,rightspaces) - #save that motif, which is the Y and +/- 4 amino acids, including truncation - motif<-motif[!motif %in% "x"] - motif<-paste(motif, sep="", collapse="") - D835letters<-motif - D835Ymotifs[i,1]<-D835letters - D835YAccessionNumbers[i,1]<-FirstSubstrateSet[i,3] - } - } - - - ITDmotifs=matrix(,nrow = nrow(ThirdSubstrateSet),ncol=1) - ITDAccessionNumbers<-matrix(,nrow = nrow(ThirdSubstrateSet)) - - for (i in 1:nrow(ThirdSubstrateSet)){ - ITDletters<-ThirdSubstrateSet[i,4:18] - ITDletters<-ITDletters[ITDletters !="XXXXX"] - ITDletters<-paste(ITDletters, sep="", collapse="") - YYYmotif <- unlist(strsplit(ITDletters, split = "")) - leftspaces<-c() - rightspaces<-c() - YYYposition <- match(x = "x", table = YYYmotif) - #position itself tells me how much is to the left of that X by what it's number is. x at position 4 tells me that there are - #just 3 letters to the left of x - - YYYLettersToTheLeft <- YYYposition - 1 - #how many letters to the right SHOULD just be length(motif)-position-1 if it's 5 long and x is at 3 then Y is at 4 and there is - #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1 - YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1 - #then sanity check, we're currently looking only at +/-4, but this spot allows for up to +/- 7 as well, just depends on what the - #variable the user puts in is - if (YYYLettersToTheLeft < 7 | YYYLettersToTheRight < 7) { - leftspaces<-rep(" ",times=(7-YYYLettersToTheLeft)) - rightspaces<-rep(" ",times=7-(YYYLettersToTheRight)) - #add blank spaces if the motif has less than 4 letters to the left/right - motif<-c(leftspaces,YYYmotif,rightspaces) - #save that motif, which is the Y and +/- 4 amino acids, including truncation - motif<-motif[!motif %in% "x"] - motif<-paste(motif, sep="", collapse="") - ITDletters<-motif - ITDmotifs[i,1]<-ITDletters - ITDAccessionNumbers[i,1]<-FirstSubstrateSet[i,3] - } - - if(YYYLettersToTheLeft>6 && YYYLettersToTheRight>6){ - motif<-YYYmotif - #add blank spaces if the motif has less than 4 letters to the left/right - motif<-c(leftspaces,YYYmotif,rightspaces) - #save that motif, which is the Y and +/- 4 amino acids, including truncation - motif<-motif[!motif %in% "x"] - motif<-paste(motif, sep="", collapse="") - ITDletters<-motif - ITDmotifs[i,1]<-ITDletters - ITDAccessionNumbers[i,1]<-FirstSubstrateSet[i,3] - } - } - names(FTLwtmotifs)<-FTLwtAccessionNumbers - names(D835Ymotifs)<-D835YAccessionNumbers - names(ITDmotifs)<-ITDAccessionNumbers - } - - - FTLwtmotifsFINAL<-FTLwtmotifs[!FTLwtmotifs %in% D835Ymotifs] - FTLwtmotifsFINAL<-FTLwtmotifsFINAL[!FTLwtmotifsFINAL %in% ITDmotifs] - FTLwtmotifsFINAL<-FTLwtmotifsFINAL[!duplicated(FTLwtmotifsFINAL)] - - - ITDmotifsFINAL<-ITDmotifs[!ITDmotifs %in% D835Ymotifs] - ITDmotifsFINAL<-ITDmotifsFINAL[!ITDmotifsFINAL %in% FTLwtmotifs] - ITDmotifsFINAL<-ITDmotifsFINAL[!duplicated(ITDmotifsFINAL)] - - - D835YmotifsFINAL<-D835Ymotifs[!D835Ymotifs %in% FTLwtmotifs] - D835YmotifsFINAL<-D835YmotifsFINAL[!D835YmotifsFINAL %in% ITDmotifs] - D835YmotifsFINAL<-D835YmotifsFINAL[!duplicated(D835YmotifsFINAL)] - - - columnalheader<-c(rep(NA,35)) - FTLFinalMatrix<-matrix(data =columnalheader,nrow = 1) - - for (k in 1:length(FTLwtmotifsFINAL)) { - AN<-00000 - #I don't remember why, but I felt it necessary to destroy the accession number multiple times to ensure it is - #destroyed immediately after use - for (m in 1:ncol(Firstsubbackfreq)) { - AN <- as.character(Firstsubbackfreq[1, m]) - if (grepl(pattern = AN, - x = names(FTLwtmotifsFINAL[k]), - fixed = TRUE) == TRUE) { - outputmatrix <- as.character(Firstsubbackfreq[, m]) - outputmatrix <- matrix(outputmatrix, nrow = 1) - #with that accession number, find a match in the subbackfreq file and save it here - FTLFinalMatrix<-rbind(FTLFinalMatrix,outputmatrix) - } - } - } - FTLFinalMatrix<-FTLFinalMatrix[!duplicated(FTLFinalMatrix),] - - columnalheader<-c(rep(NA,35)) - ITDFinalMatrix<-matrix(data =columnalheader,nrow = 1) - - for (k in 1:length(ITDmotifsFINAL)) { - AN<-00000 - #I don't remember why, but I felt it necessary to destroy the accession number multiple times to ensure it is - #destroyed immediately after use - for (m in 1:ncol(Thirdsubbackfreq)) { - AN <- as.character(Thirdsubbackfreq[1, m]) - if (grepl(pattern = AN, - x = names(ITDmotifsFINAL[k]), - fixed = TRUE) == TRUE) { - outputmatrix <- as.character(Thirdsubbackfreq[, m]) - outputmatrix <- matrix(outputmatrix, nrow = 1) - #with that accession number, find a match in the subbackfreq file and save it here - ITDFinalMatrix<-rbind(ITDFinalMatrix,outputmatrix) - } - } - } - ITDFinalMatrix<-ITDFinalMatrix[!duplicated(ITDFinalMatrix),] - - columnalheader<-c(rep(NA,35)) - D835YFinalMatrix<-matrix(data =columnalheader,nrow = 1) - - for (k in 1:length(D835YmotifsFINAL)) { - #I don't remember why, but I felt it necessary to destroy the accession number multiple times to ensure it is - #destroyed immediately after use - for (m in 1:ncol(Secondsubbackfreq)) { - AN <- as.character(Secondsubbackfreq[1, m]) - if (grepl(pattern = AN, - x = names(D835YmotifsFINAL[k]), - fixed = TRUE) == TRUE) { - outputmatrix <- as.character(Secondsubbackfreq[, m]) - outputmatrix <- matrix(outputmatrix, nrow = 1) - #with that accession number, find a match in the subbackfreq file and save it here - D835YFinalMatrix<-rbind(D835YFinalMatrix,outputmatrix) - } - } - } - D835YFinalMatrix<-D835YFinalMatrix[!duplicated(D835YFinalMatrix),] - - FTLoutputmatrix<-matrix(data=c(FTLwtmotifsFINAL,names(FTLwtmotifsFINAL)),ncol = 2) - - - write.table(x=FTLoutputmatrix, - file=First_unshared_motifs_table, - quote=FALSE, sep=",", - row.names=FALSE,col.names = FALSE, na="", append=TRUE) - - columnalheader<-c("Accession Numbers",as.character(Thirdsubbackfreq[1:35,1])) - columnalheader<-matrix(columnalheader,nrow = 1) - write.table(x=columnalheader, - file=First_unshared_subbackfreq, - quote=FALSE, sep=",", - row.names=FALSE,col.names = FALSE, na="", append=TRUE) - - write.table(x=FTLFinalMatrix, - file=First_unshared_subbackfreq, - quote=FALSE, sep=",", - row.names=FALSE,col.names = FALSE, na="", append=TRUE) - - ############################################################################################################ - - D835Youtputmatrix<-matrix(data=c(D835YmotifsFINAL,names(D835YmotifsFINAL)),ncol = 2) - - write.table(x=D835Youtputmatrix, - file=Second_unshared_motifs_table, - quote=FALSE, sep=",", - row.names=FALSE,col.names = FALSE, na="", append=TRUE) - - columnalheader<-c("Accession Numbers",as.character(Thirdsubbackfreq[1:35,1])) - columnalheader<-matrix(columnalheader,nrow = 1) - write.table(x=columnalheader, - file=Second_unshared_subbackfreq, - quote=FALSE, sep=",", - row.names=FALSE,col.names = FALSE, na="", append=TRUE) - - write.table(x=D835YFinalMatrix, - file=Second_unshared_subbackfreq, - quote=FALSE, sep=",", - row.names=FALSE,col.names = FALSE, na="", append=TRUE) - - ############################################################################################################ - - ITDoutputmatrix<-matrix(data = c(ITDmotifsFINAL,names(ITDmotifsFINAL)),ncol = 2) - - write.table(x=ITDoutputmatrix, - file=Third_unshared_motifs_table, - quote=FALSE, sep=",", - row.names=FALSE,col.names = FALSE, na="", append=TRUE) - - columnalheader<-c("Accession Numbers",as.character(Thirdsubbackfreq[1:35,1])) - columnalheader<-matrix(columnalheader,nrow = 1) - write.table(x=columnalheader, - file=Third_unshared_subbackfreq, - quote=FALSE, sep=",", - row.names=FALSE,col.names = FALSE, na="", append=TRUE) - - write.table(x=ITDFinalMatrix, - file=Third_unshared_subbackfreq, - quote=FALSE, sep=",", - row.names=FALSE,col.names = FALSE, na="", append=TRUE) - -} - -# if (Are_You_Looking_For_Commonality=="NO"){ -# -# -# FTLwtmotifsFULLMATRIX<-cbind(FTLwtmotifs,FTLwtAccessionNumbers) -# ITDmotifsFULLMATRIX<-cbind(ITDmotifs,ITDAccessionNumbers) -# D835YmotifsFULLMATRIX<-cbind(D835Ymotifs,D835YAccessionNumbers) -# # ?duplicated -# -# FTLwtmotifsFINAL<-FTLwtmotifs[!FTLwtmotifs %in% D835Ymotifs] -# FTLwtmotifsFINAL<-FTLwtmotifsFINAL[!FTLwtmotifsFINAL %in% ITDmotifs] -# FTLwtmotifsFINAL<-matrix(data=FTLwtmotifsFINAL, ncol = 1) -# -# ITDmotifsFINAL<-ITDmotifs[!ITDmotifs %in% D835Ymotifs] -# ITDmotifsFINAL<-ITDmotifsFINAL[!ITDmotifsFINAL %in% FTLwtmotifs] -# ITDmotifsFINAL<-matrix(data=ITDmotifsFINAL, ncol = 1) -# -# D835YmotifsFINAL<-D835Ymotifs[!D835Ymotifs %in% FTLwtmotifs] -# D835YmotifsFINAL<-D835YmotifsFINAL[!D835YmotifsFINAL %in% ITDmotifs] -# D835YmotifsFINAL<-matrix(data=D835YmotifsFINAL, ncol = 1) -# -# FTLnondupeAccessionNumbers<-c() -# -# for (z in 1:nrow(FTLwtmotifsFINAL)) { -# for (w in 1:nrow(FTLwtmotifsFULLMATRIX)) { -# if (is.na(FTLwtmotifsFULLMATRIX[w,1])!=TRUE) -# if (FTLwtmotifsFINAL[z]==FTLwtmotifsFULLMATRIX[w,1]){ -# FTLnondupeAccessionNumbers<-c(FTLnondupeAccessionNumbers,FTLwtmotifsFULLMATRIX[w,2]) -# } -# } -# } -# -# -# #find accession numbers here, put a matrix of those things, amino acid %, but only after I've unduped them -# FTLnondupeAccessionNumbers<-FTLnondupeAccessionNumbers[!duplicated(FTLnondupeAccessionNumbers)] -# -# columnalheader<-c(rep(NA,35)) -# FTLFinalMatrix<-matrix(data =columnalheader,nrow = 1) -# -# for (k in 1:length(FTLnondupeAccessionNumbers)) { -# #I don't remember why, but I felt it necessary to destroy the accession number multiple times to ensure it is -# #destroyed immediately after use -# for (m in 1:ncol(Firstsubbackfreq)) { -# AN <- as.character(Firstsubbackfreq[1, m]) -# if (grepl(pattern = AN, -# x = FTLnondupeAccessionNumbers[k], -# fixed = TRUE) == TRUE) { -# outputmatrix <- as.character(Firstsubbackfreq[, m]) -# outputmatrix <- matrix(outputmatrix, nrow = 1) -# #with that accession number, find a match in the subbackfreq file and save it here -# FTLFinalMatrix<-rbind(FTLFinalMatrix,outputmatrix) -# } -# } -# } -# ITDnondupeAccessionNumbers<-c() -# -# for (z in 1:nrow(ITDmotifsFINAL)) { -# for (w in 1:nrow(ITDmotifsFULLMATRIX)) { -# if (is.na(ITDmotifsFULLMATRIX[w,1])!=TRUE) -# if (ITDmotifsFINAL[z]==ITDmotifsFULLMATRIX[w,1]){ -# ITDnondupeAccessionNumbers<-c(ITDnondupeAccessionNumbers,ITDmotifsFULLMATRIX[w,2]) -# } -# } -# } -# -# -# #find accession numbers here, put a matrix of those things, amino acid %, but only after I've unduped them -# ITDnondupeAccessionNumbers<-ITDnondupeAccessionNumbers[!duplicated(ITDnondupeAccessionNumbers)] -# -# columnalheader<-c(rep(NA,35)) -# ITDFinalMatrix<-matrix(data =columnalheader,nrow = 1) -# -# for (k in 1:length(ITDnondupeAccessionNumbers)) { -# #I don't remember why, but I felt it necessary to destroy the accession number multiple times to ensure it is -# #destroyed immediately after use -# for (m in 1:ncol(Thirdsubbackfreq)) { -# AN <- as.character(Thirdsubbackfreq[1, m]) -# if (grepl(pattern = AN, -# x = ITDnondupeAccessionNumbers[k], -# fixed = TRUE) == TRUE) { -# outputmatrix <- as.character(Thirdsubbackfreq[, m]) -# outputmatrix <- matrix(outputmatrix, nrow = 1) -# #with that accession number, find a match in the subbackfreq file and save it here -# ITDFinalMatrix<-rbind(ITDFinalMatrix,outputmatrix) -# } -# } -# } -# -# -# D835YnondupeAccessionNumbers<-c() -# -# for (z in 1:nrow(D835YmotifsFINAL)) { -# for (w in 1:nrow(D835YmotifsFULLMATRIX)) { -# if (is.na(D835YmotifsFULLMATRIX[w,1])!=TRUE) -# if (D835YmotifsFINAL[z]==D835YmotifsFULLMATRIX[w,1]){ -# D835YnondupeAccessionNumbers<-c(D835YnondupeAccessionNumbers,D835YmotifsFULLMATRIX[w,2]) -# } -# } -# } -# -# -# #find accession numbers here, put a matrix of those things, amino acid %, but only after I've unduped them -# D835YnondupeAccessionNumbers<-D835YnondupeAccessionNumbers[!duplicated(D835YnondupeAccessionNumbers)] -# -# columnalheader<-c(rep(NA,35)) -# D835YFinalMatrix<-matrix(data =columnalheader,nrow = 1) -# -# for (k in 1:length(D835YnondupeAccessionNumbers)) { -# #I don't remember why, but I felt it necessary to destroy the accession number multiple times to ensure it is -# #destroyed immediately after use -# for (m in 1:ncol(Secondsubbackfreq)) { -# AN <- as.character(Secondsubbackfreq[1, m]) -# if (grepl(pattern = AN, -# x = D835YnondupeAccessionNumbers[k], -# fixed = TRUE) == TRUE) { -# outputmatrix <- as.character(Secondsubbackfreq[, m]) -# outputmatrix <- matrix(outputmatrix, nrow = 1) -# #with that accession number, find a match in the subbackfreq file and save it here -# D835YFinalMatrix<-rbind(D835YFinalMatrix,outputmatrix) -# } -# } -# } -# -# -# -# # FinalFTLmotifs<-FTLwtmotifsFINAL[!duplicated(FTLwtmotifsFINAL)] -# # FinalFTLAccessionNumbers<-FTLnondupeAccessionNumbers[!duplicated(FTLnondupeAccessionNumbers)] -# # necessaryNAs<-rep(NA,times=(length(FinalFTLmotifs)-length(FinalFTLAccessionNumbers))) -# # FinalFTLAccessionNumbers<-c(FinalFTLAccessionNumbers,necessaryNAs) -# # TRUEFTLoutputmatrix<-cbind(FinalFTLmotifs,FinalFTLAccessionNumbers) -# # TRUEFTLoutputmatrix -# -# write.table(x=FTLwtmotifsFINAL, -# file=First_unshared_motifs_table, -# quote=FALSE, sep=",", -# row.names=FALSE,col.names = FALSE, na="", append=TRUE) -# -# columnalheader<-c("Accession Numbers",as.character(Thirdsubbackfreq[1:35,1])) -# columnalheader<-matrix(columnalheader,nrow = 1) -# write.table(x=columnalheader, -# file=First_unshared_subbackfreq, -# quote=FALSE, sep=",", -# row.names=FALSE,col.names = FALSE, na="", append=TRUE) -# -# write.table(x=FTLFinalMatrix, -# file=First_unshared_subbackfreq, -# quote=FALSE, sep=",", -# row.names=FALSE,col.names = FALSE, na="", append=TRUE) -# -# -# -# -# -# -# -# -# -# -# -# -# write.table(x=D835YmotifsFINAL, -# file=Second_unshared_motifs_table, -# quote=FALSE, sep=",", -# row.names=FALSE,col.names = FALSE, na="", append=TRUE) -# -# columnalheader<-c("Accession Numbers",as.character(Thirdsubbackfreq[1:35,1])) -# columnalheader<-matrix(columnalheader,nrow = 1) -# write.table(x=columnalheader, -# file=Second_unshared_subbackfreq, -# quote=FALSE, sep=",", -# row.names=FALSE,col.names = FALSE, na="", append=TRUE) -# -# write.table(x=D835YFinalMatrix, -# file=Second_unshared_subbackfreq, -# quote=FALSE, sep=",", -# row.names=FALSE,col.names = FALSE, na="", append=TRUE) -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# write.table(x=ITDmotifsFINAL, -# file=Third_unshared_motifs_table, -# quote=FALSE, sep=",", -# row.names=FALSE,col.names = FALSE, na="", append=TRUE) -# -# columnalheader<-c("Accession Numbers",as.character(Thirdsubbackfreq[1:35,1])) -# columnalheader<-matrix(columnalheader,nrow = 1) -# write.table(x=columnalheader, -# file=Third_unshared_subbackfreq, -# quote=FALSE, sep=",", -# row.names=FALSE,col.names = FALSE, na="", append=TRUE) -# -# write.table(x=ITDFinalMatrix, -# file=Third_unshared_subbackfreq, -# quote=FALSE, sep=",", -# row.names=FALSE,col.names = FALSE, na="", append=TRUE) -# -# -# -# -# -# -# }
--- a/all stuff/Commonality and Difference finderMADE 7 TO 7.R Fri Apr 19 16:55:29 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,1281 +0,0 @@ -#I should make an SOP for this. Problems we encountered: no x in the xY motif, and the kilodemon -#the output files have both Y and xY, they shouldn't why is that happening? make it not happen -#make sure that accession numbers stay locked to each motif, somehow -#output should look just like the KALIP input - -#ff you want ONLY FULL MOTIFS, put "YES" here, please use all caps -FullMotifsOnly_questionmark<-"NO" -#If you want ONLY TRUNCATED MOTIFS, put "YES" here, please use all caps -TruncatedMotifsOnly_questionmark<-"NO" -#if you want to find the overlap, put a "YES" here (all caps), if you want to find the non-overlap, put "NO" (all caps) -Are_You_Looking_For_Commonality<-"YES" - - -#put the names of your input files here -FirstSubstrateSet<- read.csv("Galaxy63-BTK_PLUS-R1_Substrates.csv", stringsAsFactors=FALSE) -Firstsubbackfreq<- read.csv("Galaxy64-BTK_PLUS-R1_SubstrateBackgroundFrequency.csv", header=FALSE, stringsAsFactors=FALSE) - -SecondSubstrateSet<- read.csv("Galaxy65-BTK_PLUS_R2_Substrates.csv", stringsAsFactors=FALSE) -Secondsubbackfreq<- read.csv("Galaxy66-BTK_PLUS_R2_SubstrateBackgroundFrequency.csv", header=FALSE, stringsAsFactors=FALSE) - -ThirdSubstrateSet<- read.csv("Galaxy69-BTK_PLUS_R3_Substrates.csv", stringsAsFactors=FALSE) -Thirdsubbackfreq<- read.csv("Galaxy70-BTK_PLUS_R3_SubstrateBackgroundFrequency.csv", header=FALSE, stringsAsFactors=FALSE) - -#then put the names of your output files here -Shared_motifs_table<-"180719_GALAXY-BTK-plus-rep-OVLP-7to7-substrates.csv" -Shared_subbackfreq_table<-"180719_GALAXY-BTK-plus-rep-OVLP-7to7-SubBackFreq.csv" - -# Shared_motifs_table<-"Shared motifs 7-27-17.csv" -# Shared_subbackfreq_table<-"SubstrateBackgrounFrequency-for-shared-motifs 4 7-27-17.csv" - -First_unshared_motifs_table<-"R1 substrates.csv" -First_unshared_subbackfreq<-"R1 SBF.csv" - -Second_unshared_motifs_table<-"R2 subs.csv" -Second_unshared_subbackfreq<-"R2 SBf.csv" - -Third_unshared_motifs_table<-"R3 subs.csv" -Third_unshared_subbackfreq<-"R3 SBF.csv" - -#final note, this code is going to be unworkable if you want to make a Venn diagram of more than 3 circles. I think I'll poke around -#other languages to see if any of them can do it. -#################################################################################################################################### - - - - - -FirstxY<-rep("xY",times=nrow(FirstSubstrateSet)) -FirstSubstrateSet[,11]<-FirstxY - -SecondxY<-rep("xY",times=nrow(SecondSubstrateSet)) -SecondSubstrateSet[,11]<-SecondxY - -ThirdxY<-rep("xY",times=nrow(ThirdSubstrateSet)) -ThirdSubstrateSet[,11]<-ThirdxY - - - - - - - - - - - -#################################################################################################################################### -#################################################################################################################################### -# better version of this code written in C: what happens when two kinases share a motif, but they found that motif in two -# separate proteins thus two separate accession numbers? -# It should actually output the shared motif and BOTH accession numbers. Right now it does not, it only maps out the second -# accession number. So that needs to be fixed BUT you need to keep the commonality between a motif and its accession number -#################################################################################################################################### -#################################################################################################################################### -#################################################################################################################################### -#################################################################################################################################### - -#Create the motif sets, deciding wether or not you're looking for truncated or full here -#full only -if (Are_You_Looking_For_Commonality=="YES"){ - if (FullMotifsOnly_questionmark=="YES"){ - FTLwtmotifs=matrix(,nrow = nrow(FirstSubstrateSet),ncol=1) - FTLwtAccessionNumbers=matrix(,nrow = nrow(FirstSubstrateSet),ncol=1) - leftspaces<-c() - rightspaces<-c() - for (i in 1:nrow(FirstSubstrateSet)){ - FTLwtletters<-FirstSubstrateSet[i,4:18] - FTLwtletters<-FTLwtletters[FTLwtletters !="XXXXX"] - FTLwtletters<-paste(FTLwtletters, sep="", collapse="") - - - YYYmotif <- unlist(strsplit(FTLwtletters, split = "")) - YYYposition <- match(x = "x", table = YYYmotif) - #position itself tells me how much is to the left of that X by what it's number is. x at position 4 tells me that there are - #just 3 letters to the left of x - - YYYLettersToTheLeft <- YYYposition - 1 - #how many letters to the right SHOULD just be length(motif)-position-1 if it's 5 long and x is at 3 then Y is at 4 and there is - #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1 - YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1 - #then sanity check, we're currently looking only at +/-4, but this spot allows for up to +/- 7 as well, just depends on what the - #variable the user puts in is - - if (YYYLettersToTheLeft > 6 && YYYLettersToTheRight > 6) { - motif<-YYYmotif - #save that motif, which is the Y and +/- 4 amino acids, including truncation - motif<-motif[!motif %in% "x"] - motif<-paste(motif, sep="", collapse="") - FTLwtletters<-motif - FTLwtmotifs[i,1]<-FTLwtletters - FTLwtAccessionNumbers[i,1]<-FirstSubstrateSet[i,3] - - } - - } - # FTLwtmotifs <- FTLwtmotifs[!is.na(FTLwtmotifs)] - # FTLwtmotifs<-matrix(FTLwtmotifs,ncol = 1) - # - - D835Ymotifs=matrix(,nrow = nrow(SecondSubstrateSet),ncol=1) - D835YAccessionNumbers<-matrix(,nrow = nrow(SecondSubstrateSet),ncol = 1) - - for (i in 1:nrow(SecondSubstrateSet)){ - D835letters<-SecondSubstrateSet[i,4:18] - D835letters<-D835letters[D835letters !="XXXXX"] - D835letters<-paste(D835letters, sep="", collapse="") - - - YYYmotif <- unlist(strsplit(D835letters, split = "")) - YYYposition <- match(x = "x", table = YYYmotif) - #position itself tells me how much is to the left of that X by what it's number is. x at position 4 tells me that there are - #just 3 letters to the left of x - - YYYLettersToTheLeft <- YYYposition - 1 - #how many letters to the right SHOULD just be length(motif)-position-1 if it's 5 long and x is at 3 then Y is at 4 and there is - #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1 - YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1 - #then sanity check, we're currently looking only at +/-4, but this spot allows for up to +/- 7 as well, just depends on what the - #variable the user puts in is - - if (YYYLettersToTheLeft > 6 && YYYLettersToTheRight > 6) { - motif<-YYYmotif - #add blank spaces if the motif has less than 4 letters to the left/right - motif<-c(leftspaces,YYYmotif,rightspaces) - #save that motif, which is the Y and +/- 4 amino acids, including truncation - motif<-motif[!motif %in% "x"] - motif<-paste(motif, sep="", collapse="") - D835letters<-motif - D835Ymotifs[i,1]<-D835letters - D835YAccessionNumbers[i,1]<-SecondSubstrateSet[i,3] - - } - } - - ITDmotifs=matrix(,nrow = nrow(ThirdSubstrateSet),ncol=1) - ITDAccessionNumbers<-matrix(,nrow = nrow(ThirdSubstrateSet)) - - for (i in 1:nrow(ThirdSubstrateSet)){ - ITDletters<-ThirdSubstrateSet[i,4:18] - ITDletters<-ITDletters[ITDletters !="XXXXX"] - ITDletters<-paste(ITDletters, sep="", collapse="") - YYYmotif <- unlist(strsplit(ITDletters, split = "")) - YYYposition <- match(x = "x", table = YYYmotif) - #position itself tells me how much is to the left of that X by what it's number is. x at position 4 tells me that there are - #just 3 letters to the left of x - - YYYLettersToTheLeft <- YYYposition - 1 - #how many letters to the right SHOULD just be length(motif)-position-1 if it's 5 long and x is at 3 then Y is at 4 and there is - #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1 - YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1 - #then sanity check, we're currently looking only at +/-4, but this spot allows for up to +/- 7 as well, just depends on what the - #variable the user puts in is - - if (YYYLettersToTheLeft > 6 && YYYLettersToTheRight > 6) { - motif<-YYYmotif - #add blank spaces if the motif has less than 4 letters to the left/right - motif<-c(leftspaces,YYYmotif,rightspaces) - #save that motif, which is the Y and +/- 4 amino acids, including truncation - motif<-motif[!motif %in% "x"] - motif<-paste(motif, sep="", collapse="") - ITDletters<-motif - ITDmotifs[i,1]<-ITDletters - ITDAccessionNumbers[i,1]<-ThirdSubstrateSet[i,3] - - } - } - - } - - ##############################################3 - #Truncated only - if (TruncatedMotifsOnly_questionmark=="YES"){ - FTLwtmotifs=matrix(,nrow = nrow(FirstSubstrateSet),ncol=1) - FTLwtAccessionNumbers=matrix(,nrow = nrow(FirstSubstrateSet),ncol=1) - - for (i in 1:nrow(FirstSubstrateSet)){ - FTLwtletters<-FirstSubstrateSet[i,4:18] - FTLwtletters<-FTLwtletters[FTLwtletters !="XXXXX"] - FTLwtletters<-paste(FTLwtletters, sep="", collapse="") - - - YYYmotif <- unlist(strsplit(FTLwtletters, split = "")) - YYYposition <- match(x = "x", table = YYYmotif) - #position itself tells me how much is to the left of that X by what it's number is. x at position 4 tells me that there are - #just 3 letters to the left of x - - YYYLettersToTheLeft <- YYYposition - 1 - #how many letters to the right SHOULD just be length(motif)-position-1 if it's 5 long and x is at 3 then Y is at 4 and there is - #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1 - YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1 - #then sanity check, we're currently looking only at +/-4, but this spot allows for up to +/- 7 as well, just depends on what the - #variable the user puts in is - - if (YYYLettersToTheLeft < 7 | YYYLettersToTheRight < 7) { - leftspaces<-rep(" ",times=(7-YYYLettersToTheLeft)) - rightspaces<-rep(" ",times=7-(YYYLettersToTheRight)) - #add blank spaces if the motif has less than 4 letters to the left/right - motif<-c(leftspaces,YYYmotif,rightspaces) - #save that motif, which is the Y and +/- 4 amino acids, including truncation - motif<-motif[!motif %in% "x"] - motif<-paste(motif, sep="", collapse="") - FTLwtletters<-motif - FTLwtmotifs[i,1]<-FTLwtletters - FTLwtAccessionNumbers[i,1]<-FirstSubstrateSet[i,3] - } - - } - - D835Ymotifs=matrix(,nrow = nrow(SecondSubstrateSet),ncol=1) - D835YAccessionNumbers<-matrix(,nrow = nrow(SecondSubstrateSet),ncol = 1) - - for (i in 1:nrow(SecondSubstrateSet)){ - D835letters<-SecondSubstrateSet[i,4:18] - D835letters<-D835letters[D835letters !="XXXXX"] - D835letters<-paste(D835letters, sep="", collapse="") - - - YYYmotif <- unlist(strsplit(D835letters, split = "")) - YYYposition <- match(x = "x", table = YYYmotif) - #position itself tells me how much is to the left of that X by what it's number is. x at position 4 tells me that there are - #just 3 letters to the left of x - - YYYLettersToTheLeft <- YYYposition - 1 - #how many letters to the right SHOULD just be length(motif)-position-1 if it's 5 long and x is at 3 then Y is at 4 and there is - #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1 - YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1 - #then sanity check, we're currently looking only at +/-4, but this spot allows for up to +/- 7 as well, just depends on what the - #variable the user puts in is - - if (YYYLettersToTheLeft < 7 | YYYLettersToTheRight < 7) { - leftspaces<-rep(" ",times=(7-YYYLettersToTheLeft)) - rightspaces<-rep(" ",times=7-(YYYLettersToTheRight)) - #add blank spaces if the motif has less than 4 letters to the left/right - motif<-c(leftspaces,YYYmotif,rightspaces) - #save that motif, which is the Y and +/- 4 amino acids, including truncation - motif<-motif[!motif %in% "x"] - motif<-paste(motif, sep="", collapse="") - D835letters<-motif - D835YAccessionNumbers[i,1]<-SecondSubstrateSet[i,3] - D835Ymotifs[i,1]<-D835letters - } - } - - ITDmotifs=matrix(,nrow = nrow(ThirdSubstrateSet),ncol=1) - ITDAccessionNumbers<-matrix(,nrow = nrow(ThirdSubstrateSet)) - - for (i in 1:nrow(ThirdSubstrateSet)){ - ITDletters<-ThirdSubstrateSet[i,4:18] - ITDletters<-ITDletters[ITDletters !="XXXXX"] - ITDletters<-paste(ITDletters, sep="", collapse="") - YYYmotif <- unlist(strsplit(ITDletters, split = "")) - YYYposition <- match(x = "x", table = YYYmotif) - #position itself tells me how much is to the left of that X by what it's number is. x at position 4 tells me that there are - #just 3 letters to the left of x - - YYYLettersToTheLeft <- YYYposition - 1 - #how many letters to the right SHOULD just be length(motif)-position-1 if it's 5 long and x is at 3 then Y is at 4 and there is - #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1 - YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1 - #then sanity check, we're currently looking only at +/-4, but this spot allows for up to +/- 7 as well, just depends on what the - #variable the user puts in is - - if (YYYLettersToTheLeft < 7 | YYYLettersToTheRight < 7) { - leftspaces<-rep(" ",times=(7-YYYLettersToTheLeft)) - rightspaces<-rep(" ",times=7-(YYYLettersToTheRight)) - #add blank spaces if the motif has less than 4 letters to the left/right - motif<-c(leftspaces,YYYmotif,rightspaces) - #save that motif, which is the Y and +/- 4 amino acids, including truncation - motif<-motif[!motif %in% "x"] - motif<-paste(motif, sep="", collapse="") - ITDletters<-motif - ITDAccessionNumbers[i,1]<-ThirdSubstrateSet[i,3] - ITDmotifs[i,1]<-ITDletters - } - } - - } - - ############################################### - #ALL motifs, full and truncated - - if (FullMotifsOnly_questionmark!="YES"&&TruncatedMotifsOnly_questionmark!="YES"){ - FTLwtmotifs=matrix(,nrow = nrow(FirstSubstrateSet),ncol=1) - FTLwtAccessionNumbers=matrix(,nrow = nrow(FirstSubstrateSet),ncol=1) - - for (i in 1:nrow(FirstSubstrateSet)){ - FTLwtletters<-FirstSubstrateSet[i,4:18] - FTLwtletters<-FTLwtletters[FTLwtletters !="XXXXX"] - FTLwtletters<-paste(FTLwtletters, sep="", collapse="") - leftspaces<-c() - rightspaces<-c() - - YYYmotif <- unlist(strsplit(FTLwtletters, split = "")) - YYYposition <- match(x = "x", table = YYYmotif) - #position itself tells me how much is to the left of that X by what it's number is. x at position 4 tells me that there are - #just 3 letters to the left of x - - YYYLettersToTheLeft <- YYYposition - 1 - #how many letters to the right SHOULD just be length(motif)-position-1 if it's 5 long and x is at 3 then Y is at 4 and there is - #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1 - YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1 - #then sanity check, we're currently looking only at +/-4, but this spot allows for up to +/- 7 as well, just depends on what the - #variable the user puts in is - - - if (YYYLettersToTheLeft < 7 | YYYLettersToTheRight < 7) { - leftspaces<-rep(" ",times=(7-YYYLettersToTheLeft)) - rightspaces<-rep(" ",times=7-(YYYLettersToTheRight)) - #add blank spaces if the motif has less than 4 letters to the left/right - motif<-c(leftspaces,YYYmotif,rightspaces) - #save that motif, which is the Y and +/- 4 amino acids, including truncation - motif<-motif[!motif %in% "x"] - motif<-paste(motif, sep="", collapse="") - FTLwtletters<-motif - FTLwtmotifs[i,1]<-FTLwtletters - FTLwtAccessionNumbers[i,1]<-FirstSubstrateSet[i,3] - } - - if(YYYLettersToTheLeft>6 && YYYLettersToTheRight>6){ - motif<-YYYmotif - #add blank spaces if the motif has less than 4 letters to the left/right - motif<-c(leftspaces,YYYmotif,rightspaces) - #save that motif, which is the Y and +/- 4 amino acids, including truncation - motif<-motif[!motif %in% "x"] - motif<-paste(motif, sep="", collapse="") - FTLwtletters<-motif - FTLwtmotifs[i,1]<-FTLwtletters - FTLwtAccessionNumbers[i,1]<-FirstSubstrateSet[i,3] - - - } - - } - - D835Ymotifs=matrix(,nrow = nrow(SecondSubstrateSet),ncol=1) - D835YAccessionNumbers<-matrix(,nrow = nrow(SecondSubstrateSet),ncol = 1) - - for (i in 1:nrow(SecondSubstrateSet)){ - D835letters<-SecondSubstrateSet[i,4:18] - D835letters<-D835letters[D835letters !="XXXXX"] - D835letters<-paste(D835letters, sep="", collapse="") - leftspaces<-c() - rightspaces<-c() - - YYYmotif <- unlist(strsplit(D835letters, split = "")) - YYYposition <- match(x = "x", table = YYYmotif) - #position itself tells me how much is to the left of that X by what it's number is. x at position 4 tells me that there are - #just 3 letters to the left of x - - YYYLettersToTheLeft <- YYYposition - 1 - #how many letters to the right SHOULD just be length(motif)-position-1 if it's 5 long and x is at 3 then Y is at 4 and there is - #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1 - YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1 - #then sanity check, we're currently looking only at +/-4, but this spot allows for up to +/- 7 as well, just depends on what the - #variable the user puts in is - if (YYYLettersToTheLeft < 7 | YYYLettersToTheRight < 7) { - leftspaces<-rep(" ",times=(7-YYYLettersToTheLeft)) - rightspaces<-rep(" ",times=7-(YYYLettersToTheRight)) - #add blank spaces if the motif has less than 4 letters to the left/right - motif<-c(leftspaces,YYYmotif,rightspaces) - #save that motif, which is the Y and +/- 4 amino acids, including truncation - motif<-motif[!motif %in% "x"] - motif<-paste(motif, sep="", collapse="") - D835letters<-motif - D835Ymotifs[i,1]<-D835letters - D835YAccessionNumbers[i,1]<-FirstSubstrateSet[i,3] - } - - if(YYYLettersToTheLeft>6 && YYYLettersToTheRight>6){ - motif<-YYYmotif - #add blank spaces if the motif has less than 4 letters to the left/right - motif<-c(leftspaces,YYYmotif,rightspaces) - #save that motif, which is the Y and +/- 4 amino acids, including truncation - motif<-motif[!motif %in% "x"] - motif<-paste(motif, sep="", collapse="") - D835letters<-motif - D835Ymotifs[i,1]<-D835letters - D835YAccessionNumbers[i,1]<-FirstSubstrateSet[i,3] - } - } - - - ITDmotifs=matrix(,nrow = nrow(ThirdSubstrateSet),ncol=1) - ITDAccessionNumbers<-matrix(,nrow = nrow(ThirdSubstrateSet)) - - for (i in 1:nrow(ThirdSubstrateSet)){ - ITDletters<-ThirdSubstrateSet[i,4:18] - ITDletters<-ITDletters[ITDletters !="XXXXX"] - ITDletters<-paste(ITDletters, sep="", collapse="") - YYYmotif <- unlist(strsplit(ITDletters, split = "")) - leftspaces<-c() - rightspaces<-c() - YYYposition <- match(x = "x", table = YYYmotif) - #position itself tells me how much is to the left of that X by what it's number is. x at position 4 tells me that there are - #just 3 letters to the left of x - - YYYLettersToTheLeft <- YYYposition - 1 - #how many letters to the right SHOULD just be length(motif)-position-1 if it's 5 long and x is at 3 then Y is at 4 and there is - #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1 - YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1 - #then sanity check, we're currently looking only at +/-4, but this spot allows for up to +/- 7 as well, just depends on what the - #variable the user puts in is - if (YYYLettersToTheLeft < 7 | YYYLettersToTheRight < 7) { - leftspaces<-rep(" ",times=(7-YYYLettersToTheLeft)) - rightspaces<-rep(" ",times=7-(YYYLettersToTheRight)) - #add blank spaces if the motif has less than 4 letters to the left/right - motif<-c(leftspaces,YYYmotif,rightspaces) - #save that motif, which is the Y and +/- 4 amino acids, including truncation - motif<-motif[!motif %in% "x"] - motif<-paste(motif, sep="", collapse="") - ITDletters<-motif - ITDmotifs[i,1]<-ITDletters - ITDAccessionNumbers[i,1]<-FirstSubstrateSet[i,3] - } - - if(YYYLettersToTheLeft>6 && YYYLettersToTheRight>6){ - motif<-YYYmotif - #add blank spaces if the motif has less than 4 letters to the left/right - motif<-c(leftspaces,YYYmotif,rightspaces) - #save that motif, which is the Y and +/- 4 amino acids, including truncation - motif<-motif[!motif %in% "x"] - motif<-paste(motif, sep="", collapse="") - ITDletters<-motif - ITDmotifs[i,1]<-ITDletters - ITDAccessionNumbers[i,1]<-FirstSubstrateSet[i,3] - } - } - - } - ############################################################################################################################# - ############################################################################################################################# - ############################################################################################################################# - ############################################################################################################################# - ############################################################################################################################# - - #now look for either commonality or difference. Actually could you look for both... - - if (Are_You_Looking_For_Commonality=="YES"){ - - columnalheader<-c(as.character(Thirdsubbackfreq[1:36,1])) - columnalheader<-matrix(columnalheader,nrow = 1) - write.table(x=columnalheader, - file=Shared_subbackfreq_table, - quote=FALSE, sep=",", - row.names=FALSE,col.names = FALSE, na="", append=TRUE) - - FirstOverlapmotifs<-c() - for (i in 1:nrow(ITDmotifs)){ - for (j in 1:nrow(D835Ymotifs)){ - if (is.na(ITDmotifs[i,1])!=TRUE&&is.na(D835Ymotifs[j,1])!=TRUE){ - if (ITDmotifs[i,1]==D835Ymotifs[j,1]){ - FirstOverlapmotifs<-c(FirstOverlapmotifs,D835Ymotifs[j,1]) - } - } - } - } - - AllAccessionNumbers<-c() - columnalheader<-c(rep(NA,36)) - FinalMatrix<-matrix(data =columnalheader,nrow = 1) - - FinalMotifs<-c(rep(NA,20)) - FinalMotifsMatrix<-matrix(data = FinalMotifs,nrow = 1) - - - for (l in 1:length(FirstOverlapmotifs)) { - AccessionNumber<-00000000000 - for (k in 1:nrow(FTLwtmotifs)) { - AccessionNumber<-0000000000000 - if(is.na(FTLwtmotifs[k])!=TRUE){ - #I don't remember why, but I felt it necessary to destroy the accession number multiple times to ensure it is - #destroyed immediately after use - if (FirstOverlapmotifs[l] == FTLwtmotifs[k]) { - substratematrix<-FirstSubstrateSet[k,1:20] - substratematrix<-as.matrix(substratematrix,nrow=1) - FinalMotifsMatrix<-rbind(FinalMotifsMatrix,substratematrix) - #when you find a match between the venn diagrams, save the substrate info you get into a matrix - - AccessionNumber <- as.character(FirstSubstrateSet[k, 3]) - #then take the accession number - - for (m in 1:ncol(Firstsubbackfreq)) { - AN <- as.character(Firstsubbackfreq[1, m]) - if (grepl(pattern = AN, - x = AccessionNumber, - fixed = TRUE) == TRUE) { - outputmatrix <- as.character(Firstsubbackfreq[, m]) - outputmatrix <- matrix(outputmatrix, nrow = 1) - #with that accession number, find a match in the subbackfreq file and save it here - FinalMatrix<-rbind(FinalMatrix,outputmatrix) - } - } - } - } - } - } - - - TrueMatrix<-FinalMatrix[!duplicated(FinalMatrix),] - TrueFinalMotifsMatrix<-FinalMotifsMatrix[!duplicated(FinalMotifsMatrix),] - - TrueFinalMotifsMatrix<-TrueFinalMotifsMatrix[2:nrow(TrueFinalMotifsMatrix),] - TrueMatrix<-TrueMatrix[2:nrow(TrueMatrix),] - - write.table( - x = TrueFinalMotifsMatrix, - file = Shared_motifs_table, - quote = FALSE, - sep = ",", - row.names = FALSE, - col.names = TRUE, - na = "", - append = TRUE - ) - - - write.table( - x = TrueMatrix, - file = Shared_subbackfreq_table, - quote = FALSE, - sep = ",", - row.names = FALSE, - col.names = FALSE, - na = "", - append = TRUE - ) - } -} - -if (Are_You_Looking_For_Commonality=="NO"){ - if (FullMotifsOnly_questionmark=="YES"){ - FTLwtmotifs=rep(NA,times=nrow(FirstSubstrateSet)) - FTLwtAccessionNumbers=rep(NA,times=nrow(FirstSubstrateSet)) - leftspaces<-c() - rightspaces<-c() - for (i in 1:nrow(FirstSubstrateSet)){ - FTLwtletters<-FirstSubstrateSet[i,4:18] - FTLwtletters<-FTLwtletters[FTLwtletters !="XXXXX"] - FTLwtletters<-paste(FTLwtletters, sep="", collapse="") - - - YYYmotif <- unlist(strsplit(FTLwtletters, split = "")) - YYYposition <- match(x = "x", table = YYYmotif) - #position itself tells me how much is to the left of that X by what it's number is. x at position 4 tells me that there are - #just 3 letters to the left of x - - YYYLettersToTheLeft <- YYYposition - 1 - #how many letters to the right SHOULD just be length(motif)-position-1 if it's 5 long and x is at 3 then Y is at 4 and there is - #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1 - YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1 - #then sanity check, we're currently looking only at +/-4, but this spot allows for up to +/- 7 as well, just depends on what the - #variable the user puts in is - - if (YYYLettersToTheLeft > 6 && YYYLettersToTheRight > 6) { - motif<-YYYmotif - #save that motif, which is the Y and +/- 4 amino acids, including truncation - motif<-motif[!motif %in% "x"] - motif<-paste(motif, sep="", collapse="") - FTLwtletters<-motif - FTLwtmotifs[i]<-FTLwtletters - FTLwtAccessionNumbers[i]<-FirstSubstrateSet[i,3] - } - - } - # FTLwtmotifs <- FTLwtmotifs[!is.na(FTLwtmotifs)] - # FTLwtmotifs<-matrix(FTLwtmotifs,ncol = 1) - # - - D835Ymotifs=rep(NA,times=nrow(FirstSubstrateSet)) - D835YAccessionNumbers=rep(NA,times=nrow(FirstSubstrateSet)) - - for (i in 1:nrow(SecondSubstrateSet)){ - D835letters<-SecondSubstrateSet[i,4:18] - D835letters<-D835letters[D835letters !="XXXXX"] - D835letters<-paste(D835letters, sep="", collapse="") - - - YYYmotif <- unlist(strsplit(D835letters, split = "")) - YYYposition <- match(x = "x", table = YYYmotif) - #position itself tells me how much is to the left of that X by what it's number is. x at position 4 tells me that there are - #just 3 letters to the left of x - - YYYLettersToTheLeft <- YYYposition - 1 - #how many letters to the right SHOULD just be length(motif)-position-1 if it's 5 long and x is at 3 then Y is at 4 and there is - #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1 - YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1 - #then sanity check, we're currently looking only at +/-4, but this spot allows for up to +/- 7 as well, just depends on what the - #variable the user puts in is - - if (YYYLettersToTheLeft > 6 && YYYLettersToTheRight > 6) { - motif<-YYYmotif - #add blank spaces if the motif has less than 4 letters to the left/right - motif<-c(leftspaces,YYYmotif,rightspaces) - #save that motif, which is the Y and +/- 4 amino acids, including truncation - motif<-motif[!motif %in% "x"] - motif<-paste(motif, sep="", collapse="") - D835letters<-motif - D835Ymotifs[i]<-D835letters - D835YAccessionNumbers[i]<-SecondSubstrateSet[i,3] - } - } - - ITDmotifs=rep(NA,times=nrow(FirstSubstrateSet)) - ITDAccessionNumbers=rep(NA,times=nrow(FirstSubstrateSet)) - - for (i in 1:nrow(ThirdSubstrateSet)){ - ITDletters<-ThirdSubstrateSet[i,4:18] - ITDletters<-ITDletters[ITDletters !="XXXXX"] - ITDletters<-paste(ITDletters, sep="", collapse="") - YYYmotif <- unlist(strsplit(ITDletters, split = "")) - YYYposition <- match(x = "x", table = YYYmotif) - #position itself tells me how much is to the left of that X by what it's number is. x at position 4 tells me that there are - #just 3 letters to the left of x - - YYYLettersToTheLeft <- YYYposition - 1 - #how many letters to the right SHOULD just be length(motif)-position-1 if it's 5 long and x is at 3 then Y is at 4 and there is - #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1 - YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1 - #then sanity check, we're currently looking only at +/-4, but this spot allows for up to +/- 7 as well, just depends on what the - #variable the user puts in is - - if (YYYLettersToTheLeft > 6 && YYYLettersToTheRight > 6) { - motif<-YYYmotif - #add blank spaces if the motif has less than 4 letters to the left/right - motif<-c(leftspaces,YYYmotif,rightspaces) - #save that motif, which is the Y and +/- 4 amino acids, including truncation - motif<-motif[!motif %in% "x"] - motif<-paste(motif, sep="", collapse="") - ITDletters<-motif - ITDmotifs[i]<-ITDletters - ITDAccessionNumbers[i]<-ThirdSubstrateSet[i,3] - - } - } - names(ITDmotifs)<-ITDAccessionNumbers - names(D835Ymotifs)<-D835YAccessionNumbers - names(FTLwtmotifs)<-FTLwtAccessionNumbers - } - - - ##############################################3 - #Truncated only - if (TruncatedMotifsOnly_questionmark=="YES"){ - FTLwtmotifs=matrix(,nrow = nrow(FirstSubstrateSet),ncol=1) - FTLwtAccessionNumbers=matrix(,nrow = nrow(FirstSubstrateSet),ncol=1) - - for (i in 1:nrow(FirstSubstrateSet)){ - FTLwtletters<-FirstSubstrateSet[i,4:18] - FTLwtletters<-FTLwtletters[FTLwtletters !="XXXXX"] - FTLwtletters<-paste(FTLwtletters, sep="", collapse="") - - - YYYmotif <- unlist(strsplit(FTLwtletters, split = "")) - YYYposition <- match(x = "x", table = YYYmotif) - #position itself tells me how much is to the left of that X by what it's number is. x at position 4 tells me that there are - #just 3 letters to the left of x - - YYYLettersToTheLeft <- YYYposition - 1 - #how many letters to the right SHOULD just be length(motif)-position-1 if it's 5 long and x is at 3 then Y is at 4 and there is - #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1 - YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1 - #then sanity check, we're currently looking only at +/-4, but this spot allows for up to +/- 7 as well, just depends on what the - #variable the user puts in is - - if (YYYLettersToTheLeft < 7 | YYYLettersToTheRight < 7) { - leftspaces<-rep(" ",times=(7-YYYLettersToTheLeft)) - rightspaces<-rep(" ",times=7-(YYYLettersToTheRight)) - #add blank spaces if the motif has less than 4 letters to the left/right - motif<-c(leftspaces,YYYmotif,rightspaces) - #save that motif, which is the Y and +/- 4 amino acids, including truncation - motif<-motif[!motif %in% "x"] - motif<-paste(motif, sep="", collapse="") - FTLwtletters<-motif - FTLwtmotifs[i,1]<-FTLwtletters - FTLwtAccessionNumbers[i,1]<-FirstSubstrateSet[i,3] - } - - } - - D835Ymotifs=matrix(,nrow = nrow(SecondSubstrateSet),ncol=1) - D835YAccessionNumbers<-matrix(,nrow = nrow(SecondSubstrateSet),ncol = 1) - i=2 - for (i in 1:nrow(SecondSubstrateSet)){ - D835letters<-SecondSubstrateSet[i,4:18] - D835letters<-D835letters[D835letters !="XXXXX"] - D835letters<-paste(D835letters, sep="", collapse="") - - - YYYmotif <- unlist(strsplit(D835letters, split = "")) - YYYposition <- match(x = "x", table = YYYmotif) - #position itself tells me how much is to the left of that X by what it's number is. x at position 4 tells me that there are - #just 3 letters to the left of x - - YYYLettersToTheLeft <- YYYposition - 1 - #how many letters to the right SHOULD just be length(motif)-position-1 if it's 5 long and x is at 3 then Y is at 4 and there is - #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1 - YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1 - #then sanity check, we're currently looking only at +/-4, but this spot allows for up to +/- 7 as well, just depends on what the - #variable the user puts in is - - if (YYYLettersToTheLeft < 7 | YYYLettersToTheRight < 7) { - leftspaces<-rep(" ",times=(7-YYYLettersToTheLeft)) - rightspaces<-rep(" ",times=7-(YYYLettersToTheRight)) - #add blank spaces if the motif has less than 4 letters to the left/right - motif<-c(leftspaces,YYYmotif,rightspaces) - #save that motif, which is the Y and +/- 4 amino acids, including truncation - motif<-motif[!motif %in% "x"] - motif<-paste(motif, sep="", collapse="") - D835letters<-motif - D835YAccessionNumbers[i,1]<-SecondSubstrateSet[i,3] - D835Ymotifs[i,1]<-D835letters - } - } - - ITDmotifs=matrix(,nrow = nrow(ThirdSubstrateSet),ncol=1) - ITDAccessionNumbers<-matrix(,nrow = nrow(ThirdSubstrateSet)) - - for (i in 1:nrow(ThirdSubstrateSet)){ - ITDletters<-ThirdSubstrateSet[i,4:18] - ITDletters<-ITDletters[ITDletters !="XXXXX"] - ITDletters<-paste(ITDletters, sep="", collapse="") - YYYmotif <- unlist(strsplit(ITDletters, split = "")) - YYYposition <- match(x = "x", table = YYYmotif) - #position itself tells me how much is to the left of that X by what it's number is. x at position 4 tells me that there are - #just 3 letters to the left of x - - YYYLettersToTheLeft <- YYYposition - 1 - #how many letters to the right SHOULD just be length(motif)-position-1 if it's 5 long and x is at 3 then Y is at 4 and there is - #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1 - YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1 - #then sanity check, we're currently looking only at +/-4, but this spot allows for up to +/- 7 as well, just depends on what the - #variable the user puts in is - - if (YYYLettersToTheLeft < 7 | YYYLettersToTheRight < 7) { - leftspaces<-rep(" ",times=(7-YYYLettersToTheLeft)) - rightspaces<-rep(" ",times=7-(YYYLettersToTheRight)) - #add blank spaces if the motif has less than 4 letters to the left/right - motif<-c(leftspaces,YYYmotif,rightspaces) - #save that motif, which is the Y and +/- 4 amino acids, including truncation - motif<-motif[!motif %in% "x"] - motif<-paste(motif, sep="", collapse="") - ITDletters<-motif - ITDAccessionNumbers[i,1]<-ThirdSubstrateSet[i,3] - ITDmotifs[i,1]<-ITDletters - } - } - names(FTLwtmotifs)<-FTLwtAccessionNumbers - names(D835Ymotifs)<-D835YAccessionNumbers - names(ITDmotifs)<-ITDAccessionNumbers - } - - ############################################### - #ALL motifs, full and truncated - - if (FullMotifsOnly_questionmark!="YES"&&TruncatedMotifsOnly_questionmark!="YES"){ - FTLwtmotifs=matrix(,nrow = nrow(FirstSubstrateSet),ncol=1) - FTLwtAccessionNumbers=matrix(,nrow = nrow(FirstSubstrateSet),ncol=1) - - for (i in 1:nrow(FirstSubstrateSet)){ - FTLwtletters<-FirstSubstrateSet[i,4:18] - FTLwtletters<-FTLwtletters[FTLwtletters !="XXXXX"] - FTLwtletters<-paste(FTLwtletters, sep="", collapse="") - leftspaces<-c() - rightspaces<-c() - - YYYmotif <- unlist(strsplit(FTLwtletters, split = "")) - YYYposition <- match(x = "x", table = YYYmotif) - #position itself tells me how much is to the left of that X by what it's number is. x at position 4 tells me that there are - #just 3 letters to the left of x - - YYYLettersToTheLeft <- YYYposition - 1 - #how many letters to the right SHOULD just be length(motif)-position-1 if it's 5 long and x is at 3 then Y is at 4 and there is - #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1 - YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1 - #then sanity check, we're currently looking only at +/-4, but this spot allows for up to +/- 7 as well, just depends on what the - #variable the user puts in is - - - if (YYYLettersToTheLeft < 7 | YYYLettersToTheRight < 7) { - leftspaces<-rep(" ",times=(7-YYYLettersToTheLeft)) - rightspaces<-rep(" ",times=7-(YYYLettersToTheRight)) - #add blank spaces if the motif has less than 4 letters to the left/right - motif<-c(leftspaces,YYYmotif,rightspaces) - #save that motif, which is the Y and +/- 4 amino acids, including truncation - motif<-motif[!motif %in% "x"] - motif<-paste(motif, sep="", collapse="") - FTLwtletters<-motif - FTLwtmotifs[i,1]<-FTLwtletters - FTLwtAccessionNumbers[i,1]<-FirstSubstrateSet[i,3] - } - - if(YYYLettersToTheLeft>6 && YYYLettersToTheRight>6){ - motif<-YYYmotif - #add blank spaces if the motif has less than 4 letters to the left/right - motif<-c(leftspaces,YYYmotif,rightspaces) - #save that motif, which is the Y and +/- 4 amino acids, including truncation - motif<-motif[!motif %in% "x"] - motif<-paste(motif, sep="", collapse="") - FTLwtletters<-motif - FTLwtmotifs[i,1]<-FTLwtletters - FTLwtAccessionNumbers[i,1]<-FirstSubstrateSet[i,3] - - - } - - } - - D835Ymotifs=matrix(,nrow = nrow(SecondSubstrateSet),ncol=1) - D835YAccessionNumbers<-matrix(,nrow = nrow(SecondSubstrateSet),ncol = 1) - - for (i in 1:nrow(SecondSubstrateSet)){ - D835letters<-SecondSubstrateSet[i,4:18] - D835letters<-D835letters[D835letters !="XXXXX"] - D835letters<-paste(D835letters, sep="", collapse="") - leftspaces<-c() - rightspaces<-c() - - YYYmotif <- unlist(strsplit(D835letters, split = "")) - YYYposition <- match(x = "x", table = YYYmotif) - #position itself tells me how much is to the left of that X by what it's number is. x at position 4 tells me that there are - #just 3 letters to the left of x - - YYYLettersToTheLeft <- YYYposition - 1 - #how many letters to the right SHOULD just be length(motif)-position-1 if it's 5 long and x is at 3 then Y is at 4 and there is - #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1 - YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1 - #then sanity check, we're currently looking only at +/-4, but this spot allows for up to +/- 7 as well, just depends on what the - #variable the user puts in is - if (YYYLettersToTheLeft < 7 | YYYLettersToTheRight < 7) { - leftspaces<-rep(" ",times=(7-YYYLettersToTheLeft)) - rightspaces<-rep(" ",times=7-(YYYLettersToTheRight)) - #add blank spaces if the motif has less than 4 letters to the left/right - motif<-c(leftspaces,YYYmotif,rightspaces) - #save that motif, which is the Y and +/- 4 amino acids, including truncation - motif<-motif[!motif %in% "x"] - motif<-paste(motif, sep="", collapse="") - D835letters<-motif - D835Ymotifs[i,1]<-D835letters - D835YAccessionNumbers[i,1]<-FirstSubstrateSet[i,3] - } - - if(YYYLettersToTheLeft>6 && YYYLettersToTheRight>6){ - motif<-YYYmotif - #add blank spaces if the motif has less than 4 letters to the left/right - motif<-c(leftspaces,YYYmotif,rightspaces) - #save that motif, which is the Y and +/- 4 amino acids, including truncation - motif<-motif[!motif %in% "x"] - motif<-paste(motif, sep="", collapse="") - D835letters<-motif - D835Ymotifs[i,1]<-D835letters - D835YAccessionNumbers[i,1]<-FirstSubstrateSet[i,3] - } - } - - - ITDmotifs=matrix(,nrow = nrow(ThirdSubstrateSet),ncol=1) - ITDAccessionNumbers<-matrix(,nrow = nrow(ThirdSubstrateSet)) - - for (i in 1:nrow(ThirdSubstrateSet)){ - ITDletters<-ThirdSubstrateSet[i,4:18] - ITDletters<-ITDletters[ITDletters !="XXXXX"] - ITDletters<-paste(ITDletters, sep="", collapse="") - YYYmotif <- unlist(strsplit(ITDletters, split = "")) - leftspaces<-c() - rightspaces<-c() - YYYposition <- match(x = "x", table = YYYmotif) - #position itself tells me how much is to the left of that X by what it's number is. x at position 4 tells me that there are - #just 3 letters to the left of x - - YYYLettersToTheLeft <- YYYposition - 1 - #how many letters to the right SHOULD just be length(motif)-position-1 if it's 5 long and x is at 3 then Y is at 4 and there is - #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1 - YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1 - #then sanity check, we're currently looking only at +/-4, but this spot allows for up to +/- 7 as well, just depends on what the - #variable the user puts in is - if (YYYLettersToTheLeft < 7 | YYYLettersToTheRight < 7) { - leftspaces<-rep(" ",times=(7-YYYLettersToTheLeft)) - rightspaces<-rep(" ",times=7-(YYYLettersToTheRight)) - #add blank spaces if the motif has less than 4 letters to the left/right - motif<-c(leftspaces,YYYmotif,rightspaces) - #save that motif, which is the Y and +/- 4 amino acids, including truncation - motif<-motif[!motif %in% "x"] - motif<-paste(motif, sep="", collapse="") - ITDletters<-motif - ITDmotifs[i,1]<-ITDletters - ITDAccessionNumbers[i,1]<-FirstSubstrateSet[i,3] - } - - if(YYYLettersToTheLeft>6 && YYYLettersToTheRight>6){ - motif<-YYYmotif - #add blank spaces if the motif has less than 4 letters to the left/right - motif<-c(leftspaces,YYYmotif,rightspaces) - #save that motif, which is the Y and +/- 4 amino acids, including truncation - motif<-motif[!motif %in% "x"] - motif<-paste(motif, sep="", collapse="") - ITDletters<-motif - ITDmotifs[i,1]<-ITDletters - ITDAccessionNumbers[i,1]<-FirstSubstrateSet[i,3] - } - } - names(FTLwtmotifs)<-FTLwtAccessionNumbers - names(D835Ymotifs)<-D835YAccessionNumbers - names(ITDmotifs)<-ITDAccessionNumbers - } - - - FTLwtmotifsFINAL<-FTLwtmotifs[!FTLwtmotifs %in% D835Ymotifs] - FTLwtmotifsFINAL<-FTLwtmotifsFINAL[!FTLwtmotifsFINAL %in% ITDmotifs] - FTLwtmotifsFINAL<-FTLwtmotifsFINAL[!duplicated(FTLwtmotifsFINAL)] - - - ITDmotifsFINAL<-ITDmotifs[!ITDmotifs %in% D835Ymotifs] - ITDmotifsFINAL<-ITDmotifsFINAL[!ITDmotifsFINAL %in% FTLwtmotifs] - ITDmotifsFINAL<-ITDmotifsFINAL[!duplicated(ITDmotifsFINAL)] - - - D835YmotifsFINAL<-D835Ymotifs[!D835Ymotifs %in% FTLwtmotifs] - D835YmotifsFINAL<-D835YmotifsFINAL[!D835YmotifsFINAL %in% ITDmotifs] - D835YmotifsFINAL<-D835YmotifsFINAL[!duplicated(D835YmotifsFINAL)] - - - columnalheader<-c(rep(NA,35)) - FTLFinalMatrix<-matrix(data =columnalheader,nrow = 1) - - for (k in 1:length(FTLwtmotifsFINAL)) { - AN<-00000 - #I don't remember why, but I felt it necessary to destroy the accession number multiple times to ensure it is - #destroyed immediately after use - for (m in 1:ncol(Firstsubbackfreq)) { - AN <- as.character(Firstsubbackfreq[1, m]) - if (grepl(pattern = AN, - x = names(FTLwtmotifsFINAL[k]), - fixed = TRUE) == TRUE) { - outputmatrix <- as.character(Firstsubbackfreq[, m]) - outputmatrix <- matrix(outputmatrix, nrow = 1) - #with that accession number, find a match in the subbackfreq file and save it here - FTLFinalMatrix<-rbind(FTLFinalMatrix,outputmatrix) - } - } - } - FTLFinalMatrix<-FTLFinalMatrix[!duplicated(FTLFinalMatrix),] - - columnalheader<-c(rep(NA,35)) - ITDFinalMatrix<-matrix(data =columnalheader,nrow = 1) - - for (k in 1:length(ITDmotifsFINAL)) { - AN<-00000 - #I don't remember why, but I felt it necessary to destroy the accession number multiple times to ensure it is - #destroyed immediately after use - for (m in 1:ncol(Thirdsubbackfreq)) { - AN <- as.character(Thirdsubbackfreq[1, m]) - if (grepl(pattern = AN, - x = names(ITDmotifsFINAL[k]), - fixed = TRUE) == TRUE) { - outputmatrix <- as.character(Thirdsubbackfreq[, m]) - outputmatrix <- matrix(outputmatrix, nrow = 1) - #with that accession number, find a match in the subbackfreq file and save it here - ITDFinalMatrix<-rbind(ITDFinalMatrix,outputmatrix) - } - } - } - ITDFinalMatrix<-ITDFinalMatrix[!duplicated(ITDFinalMatrix),] - - columnalheader<-c(rep(NA,35)) - D835YFinalMatrix<-matrix(data =columnalheader,nrow = 1) - - for (k in 1:length(D835YmotifsFINAL)) { - #I don't remember why, but I felt it necessary to destroy the accession number multiple times to ensure it is - #destroyed immediately after use - for (m in 1:ncol(Secondsubbackfreq)) { - AN <- as.character(Secondsubbackfreq[1, m]) - if (grepl(pattern = AN, - x = names(D835YmotifsFINAL[k]), - fixed = TRUE) == TRUE) { - outputmatrix <- as.character(Secondsubbackfreq[, m]) - outputmatrix <- matrix(outputmatrix, nrow = 1) - #with that accession number, find a match in the subbackfreq file and save it here - D835YFinalMatrix<-rbind(D835YFinalMatrix,outputmatrix) - } - } - } - D835YFinalMatrix<-D835YFinalMatrix[!duplicated(D835YFinalMatrix),] - - FTLoutputmatrix<-matrix(data=c(FTLwtmotifsFINAL,names(FTLwtmotifsFINAL)),ncol = 2) - - - write.table(x=FTLoutputmatrix, - file=First_unshared_motifs_table, - quote=FALSE, sep=",", - row.names=FALSE,col.names = FALSE, na="", append=TRUE) - - columnalheader<-c("Accession Numbers",as.character(Thirdsubbackfreq[1:35,1])) - columnalheader<-matrix(columnalheader,nrow = 1) - write.table(x=columnalheader, - file=First_unshared_subbackfreq, - quote=FALSE, sep=",", - row.names=FALSE,col.names = FALSE, na="", append=TRUE) - - write.table(x=FTLFinalMatrix, - file=First_unshared_subbackfreq, - quote=FALSE, sep=",", - row.names=FALSE,col.names = FALSE, na="", append=TRUE) - - ############################################################################################################ - - D835Youtputmatrix<-matrix(data=c(D835YmotifsFINAL,names(D835YmotifsFINAL)),ncol = 2) - - write.table(x=D835Youtputmatrix, - file=Second_unshared_motifs_table, - quote=FALSE, sep=",", - row.names=FALSE,col.names = FALSE, na="", append=TRUE) - - columnalheader<-c("Accession Numbers",as.character(Thirdsubbackfreq[1:35,1])) - columnalheader<-matrix(columnalheader,nrow = 1) - write.table(x=columnalheader, - file=Second_unshared_subbackfreq, - quote=FALSE, sep=",", - row.names=FALSE,col.names = FALSE, na="", append=TRUE) - - write.table(x=D835YFinalMatrix, - file=Second_unshared_subbackfreq, - quote=FALSE, sep=",", - row.names=FALSE,col.names = FALSE, na="", append=TRUE) - - ############################################################################################################ - - ITDoutputmatrix<-matrix(data = c(ITDmotifsFINAL,names(ITDmotifsFINAL)),ncol = 2) - - write.table(x=ITDoutputmatrix, - file=Third_unshared_motifs_table, - quote=FALSE, sep=",", - row.names=FALSE,col.names = FALSE, na="", append=TRUE) - - columnalheader<-c("Accession Numbers",as.character(Thirdsubbackfreq[1:35,1])) - columnalheader<-matrix(columnalheader,nrow = 1) - write.table(x=columnalheader, - file=Third_unshared_subbackfreq, - quote=FALSE, sep=",", - row.names=FALSE,col.names = FALSE, na="", append=TRUE) - - write.table(x=ITDFinalMatrix, - file=Third_unshared_subbackfreq, - quote=FALSE, sep=",", - row.names=FALSE,col.names = FALSE, na="", append=TRUE) - -} - -# if (Are_You_Looking_For_Commonality=="NO"){ -# -# -# FTLwtmotifsFULLMATRIX<-cbind(FTLwtmotifs,FTLwtAccessionNumbers) -# ITDmotifsFULLMATRIX<-cbind(ITDmotifs,ITDAccessionNumbers) -# D835YmotifsFULLMATRIX<-cbind(D835Ymotifs,D835YAccessionNumbers) -# # ?duplicated -# -# FTLwtmotifsFINAL<-FTLwtmotifs[!FTLwtmotifs %in% D835Ymotifs] -# FTLwtmotifsFINAL<-FTLwtmotifsFINAL[!FTLwtmotifsFINAL %in% ITDmotifs] -# FTLwtmotifsFINAL<-matrix(data=FTLwtmotifsFINAL, ncol = 1) -# -# ITDmotifsFINAL<-ITDmotifs[!ITDmotifs %in% D835Ymotifs] -# ITDmotifsFINAL<-ITDmotifsFINAL[!ITDmotifsFINAL %in% FTLwtmotifs] -# ITDmotifsFINAL<-matrix(data=ITDmotifsFINAL, ncol = 1) -# -# D835YmotifsFINAL<-D835Ymotifs[!D835Ymotifs %in% FTLwtmotifs] -# D835YmotifsFINAL<-D835YmotifsFINAL[!D835YmotifsFINAL %in% ITDmotifs] -# D835YmotifsFINAL<-matrix(data=D835YmotifsFINAL, ncol = 1) -# -# FTLnondupeAccessionNumbers<-c() -# -# for (z in 1:nrow(FTLwtmotifsFINAL)) { -# for (w in 1:nrow(FTLwtmotifsFULLMATRIX)) { -# if (is.na(FTLwtmotifsFULLMATRIX[w,1])!=TRUE) -# if (FTLwtmotifsFINAL[z]==FTLwtmotifsFULLMATRIX[w,1]){ -# FTLnondupeAccessionNumbers<-c(FTLnondupeAccessionNumbers,FTLwtmotifsFULLMATRIX[w,2]) -# } -# } -# } -# -# -# #find accession numbers here, put a matrix of those things, amino acid %, but only after I've unduped them -# FTLnondupeAccessionNumbers<-FTLnondupeAccessionNumbers[!duplicated(FTLnondupeAccessionNumbers)] -# -# columnalheader<-c(rep(NA,35)) -# FTLFinalMatrix<-matrix(data =columnalheader,nrow = 1) -# -# for (k in 1:length(FTLnondupeAccessionNumbers)) { -# #I don't remember why, but I felt it necessary to destroy the accession number multiple times to ensure it is -# #destroyed immediately after use -# for (m in 1:ncol(Firstsubbackfreq)) { -# AN <- as.character(Firstsubbackfreq[1, m]) -# if (grepl(pattern = AN, -# x = FTLnondupeAccessionNumbers[k], -# fixed = TRUE) == TRUE) { -# outputmatrix <- as.character(Firstsubbackfreq[, m]) -# outputmatrix <- matrix(outputmatrix, nrow = 1) -# #with that accession number, find a match in the subbackfreq file and save it here -# FTLFinalMatrix<-rbind(FTLFinalMatrix,outputmatrix) -# } -# } -# } -# ITDnondupeAccessionNumbers<-c() -# -# for (z in 1:nrow(ITDmotifsFINAL)) { -# for (w in 1:nrow(ITDmotifsFULLMATRIX)) { -# if (is.na(ITDmotifsFULLMATRIX[w,1])!=TRUE) -# if (ITDmotifsFINAL[z]==ITDmotifsFULLMATRIX[w,1]){ -# ITDnondupeAccessionNumbers<-c(ITDnondupeAccessionNumbers,ITDmotifsFULLMATRIX[w,2]) -# } -# } -# } -# -# -# #find accession numbers here, put a matrix of those things, amino acid %, but only after I've unduped them -# ITDnondupeAccessionNumbers<-ITDnondupeAccessionNumbers[!duplicated(ITDnondupeAccessionNumbers)] -# -# columnalheader<-c(rep(NA,35)) -# ITDFinalMatrix<-matrix(data =columnalheader,nrow = 1) -# -# for (k in 1:length(ITDnondupeAccessionNumbers)) { -# #I don't remember why, but I felt it necessary to destroy the accession number multiple times to ensure it is -# #destroyed immediately after use -# for (m in 1:ncol(Thirdsubbackfreq)) { -# AN <- as.character(Thirdsubbackfreq[1, m]) -# if (grepl(pattern = AN, -# x = ITDnondupeAccessionNumbers[k], -# fixed = TRUE) == TRUE) { -# outputmatrix <- as.character(Thirdsubbackfreq[, m]) -# outputmatrix <- matrix(outputmatrix, nrow = 1) -# #with that accession number, find a match in the subbackfreq file and save it here -# ITDFinalMatrix<-rbind(ITDFinalMatrix,outputmatrix) -# } -# } -# } -# -# -# D835YnondupeAccessionNumbers<-c() -# -# for (z in 1:nrow(D835YmotifsFINAL)) { -# for (w in 1:nrow(D835YmotifsFULLMATRIX)) { -# if (is.na(D835YmotifsFULLMATRIX[w,1])!=TRUE) -# if (D835YmotifsFINAL[z]==D835YmotifsFULLMATRIX[w,1]){ -# D835YnondupeAccessionNumbers<-c(D835YnondupeAccessionNumbers,D835YmotifsFULLMATRIX[w,2]) -# } -# } -# } -# -# -# #find accession numbers here, put a matrix of those things, amino acid %, but only after I've unduped them -# D835YnondupeAccessionNumbers<-D835YnondupeAccessionNumbers[!duplicated(D835YnondupeAccessionNumbers)] -# -# columnalheader<-c(rep(NA,35)) -# D835YFinalMatrix<-matrix(data =columnalheader,nrow = 1) -# -# for (k in 1:length(D835YnondupeAccessionNumbers)) { -# #I don't remember why, but I felt it necessary to destroy the accession number multiple times to ensure it is -# #destroyed immediately after use -# for (m in 1:ncol(Secondsubbackfreq)) { -# AN <- as.character(Secondsubbackfreq[1, m]) -# if (grepl(pattern = AN, -# x = D835YnondupeAccessionNumbers[k], -# fixed = TRUE) == TRUE) { -# outputmatrix <- as.character(Secondsubbackfreq[, m]) -# outputmatrix <- matrix(outputmatrix, nrow = 1) -# #with that accession number, find a match in the subbackfreq file and save it here -# D835YFinalMatrix<-rbind(D835YFinalMatrix,outputmatrix) -# } -# } -# } -# -# -# -# # FinalFTLmotifs<-FTLwtmotifsFINAL[!duplicated(FTLwtmotifsFINAL)] -# # FinalFTLAccessionNumbers<-FTLnondupeAccessionNumbers[!duplicated(FTLnondupeAccessionNumbers)] -# # necessaryNAs<-rep(NA,times=(length(FinalFTLmotifs)-length(FinalFTLAccessionNumbers))) -# # FinalFTLAccessionNumbers<-c(FinalFTLAccessionNumbers,necessaryNAs) -# # TRUEFTLoutputmatrix<-cbind(FinalFTLmotifs,FinalFTLAccessionNumbers) -# # TRUEFTLoutputmatrix -# -# write.table(x=FTLwtmotifsFINAL, -# file=First_unshared_motifs_table, -# quote=FALSE, sep=",", -# row.names=FALSE,col.names = FALSE, na="", append=TRUE) -# -# columnalheader<-c("Accession Numbers",as.character(Thirdsubbackfreq[1:35,1])) -# columnalheader<-matrix(columnalheader,nrow = 1) -# write.table(x=columnalheader, -# file=First_unshared_subbackfreq, -# quote=FALSE, sep=",", -# row.names=FALSE,col.names = FALSE, na="", append=TRUE) -# -# write.table(x=FTLFinalMatrix, -# file=First_unshared_subbackfreq, -# quote=FALSE, sep=",", -# row.names=FALSE,col.names = FALSE, na="", append=TRUE) -# -# -# -# -# -# -# -# -# -# -# -# -# write.table(x=D835YmotifsFINAL, -# file=Second_unshared_motifs_table, -# quote=FALSE, sep=",", -# row.names=FALSE,col.names = FALSE, na="", append=TRUE) -# -# columnalheader<-c("Accession Numbers",as.character(Thirdsubbackfreq[1:35,1])) -# columnalheader<-matrix(columnalheader,nrow = 1) -# write.table(x=columnalheader, -# file=Second_unshared_subbackfreq, -# quote=FALSE, sep=",", -# row.names=FALSE,col.names = FALSE, na="", append=TRUE) -# -# write.table(x=D835YFinalMatrix, -# file=Second_unshared_subbackfreq, -# quote=FALSE, sep=",", -# row.names=FALSE,col.names = FALSE, na="", append=TRUE) -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# write.table(x=ITDmotifsFINAL, -# file=Third_unshared_motifs_table, -# quote=FALSE, sep=",", -# row.names=FALSE,col.names = FALSE, na="", append=TRUE) -# -# columnalheader<-c("Accession Numbers",as.character(Thirdsubbackfreq[1:35,1])) -# columnalheader<-matrix(columnalheader,nrow = 1) -# write.table(x=columnalheader, -# file=Third_unshared_subbackfreq, -# quote=FALSE, sep=",", -# row.names=FALSE,col.names = FALSE, na="", append=TRUE) -# -# write.table(x=ITDFinalMatrix, -# file=Third_unshared_subbackfreq, -# quote=FALSE, sep=",", -# row.names=FALSE,col.names = FALSE, na="", append=TRUE) -# -# -# -# -# -# -# }
--- a/all stuff/Difference finder MADE 7 TO 7 4-18-2019.R Fri Apr 19 16:55:29 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,351 +0,0 @@ -#I should make an SOP for this. Problems we encountered: no x in the xY motif, and the kilodemon -#the output files have both Y and xY, they shouldn't why is that happening? make it not happen -#make sure that accession numbers stay locked to each motif, somehow -#output should look just like the KALIP input - -#ff you want ONLY FULL MOTIFS, put "YES" here, please use all caps -FullMotifsOnly_questionmark<-"NO" -#If you want ONLY TRUNCATED MOTIFS, put "YES" here, please use all caps -TruncatedMotifsOnly_questionmark<-"NO" -#if you want to find the overlap, put a "YES" here (all caps), if you want to find the non-overlap, put "NO" (all caps) -Are_You_Looking_For_Commonality<-"NO" - - -#put the names of your input files here -FirstSubstrateSet<- read.csv("Galaxy1071-(17A_TiO2_Substrates.csv).csv", stringsAsFactors=FALSE) -Firstsubbackfreq<- read.csv("Galaxy1072-(17A_TiO2_SubstrateBackgroundFrequency.csv).csv", header=FALSE, stringsAsFactors=FALSE) - -SecondSubstrateSet<- read.csv("Galaxy1073-(17A_FeNTA_Substrates.csv) (1).csv", stringsAsFactors=FALSE) -Secondsubbackfreq<- read.csv("Galaxy1074-(17A_FeNTA_SubstrateBackgroundFrequency.csv).csv", header=FALSE, stringsAsFactors=FALSE) - -# ThirdSubstrateSet<- read.csv("Galaxy69-BTK_PLUS_R3_Substrates.csv", stringsAsFactors=FALSE) -# Thirdsubbackfreq<- read.csv("Galaxy70-BTK_PLUS_R3_SubstrateBackgroundFrequency.csv", header=FALSE, stringsAsFactors=FALSE) - -#then put the names of your output files here -# Shared_motifs_table<-"180719_GALAXY-BTK-plus-rep-OVLP-7to7-substrates.csv" -# Shared_subbackfreq_table<-"180719_GALAXY-BTK-plus-rep-OVLP-7to7-SubBackFreq.csv" - -# Shared_motifs_table<-"Shared motifs 7-27-17.csv" -# Shared_subbackfreq_table<-"SubstrateBackgrounFrequency-for-shared-motifs 4 7-27-17.csv" - -First_unshared_motifs_table<-"17A TIo2 without FeNTA.csv" -First_unshared_subbackfreq<-"17A TIo2 without FeNTA sbf.csv" - -Second_unshared_motifs_table<-"17A FeNTA without TIo2.csv" -Second_unshared_subbackfreq<-"17A FeNTA without TIo2 sbf.csv" - -# Third_unshared_motifs_table<-"R3 subs.csv" -# Third_unshared_subbackfreq<-"R3 SBF.csv" - -#final note, this code is going to be unworkable if you want to make a Venn diagram of more than 3 circles. I think I'll poke around -#other languages to see if any of them can do it. -#################################################################################################################################### - - - - - -# grepl(pattern = "S", x=asdf, ignore.case = TRUE) - -FirstCentralLetters<-FirstSubstrateSet[,11] -SecondCentralLetters<-SecondSubstrateSet[,11] - -FirstEsses<-sapply(FirstCentralLetters, grepl, pattern="S", ignore.case=TRUE) -FirstTees<-sapply(FirstCentralLetters, grepl, pattern="T", ignore.case=TRUE) -FirstWys<-sapply(FirstCentralLetters, grepl, pattern="Y", ignore.case=TRUE) - -SecondEsses<-sapply(SecondCentralLetters, grepl, pattern="S", ignore.case=TRUE) -SecondTees<-sapply(SecondCentralLetters, grepl, pattern="T", ignore.case=TRUE) -SecondWys<-sapply(SecondCentralLetters, grepl, pattern="Y", ignore.case=TRUE) - -FirstCentralLetters<-replace(FirstCentralLetters,FirstEsses,"xS") -FirstCentralLetters<-replace(FirstCentralLetters,FirstTees,"xT") -FirstCentralLetters<-replace(FirstCentralLetters,FirstWys,"xY") - -SecondCentralLetters<-replace(SecondCentralLetters,SecondEsses,"xS") -SecondCentralLetters<-replace(SecondCentralLetters,SecondTees,"xT") -SecondCentralLetters<-replace(SecondCentralLetters,SecondWys,"xY") - -FirstCentralLetters->FirstSubstrateSet[,11] -SecondCentralLetters->SecondSubstrateSet[,11] - -#################################################################################################################################### -#################################################################################################################################### -# better version of this code written in C: what happens when two kinases share a motif, but they found that motif in two -# separate proteins thus two separate accession numbers? -# It should actually output the shared motif and BOTH accession numbers. Right now it does not, it only maps out the second -# accession number. So that needs to be fixed BUT you need to keep the commonality between a motif and its accession number -#################################################################################################################################### -#################################################################################################################################### -#################################################################################################################################### -#################################################################################################################################### - -#Create the motif sets, deciding wether or not you're looking for truncated or full here -#full only - - -if (Are_You_Looking_For_Commonality=="NO"){ - - ############################################### - #ALL motifs, full and truncated - - if (FullMotifsOnly_questionmark!="YES"&&TruncatedMotifsOnly_questionmark!="YES"){ - FTLwtmotifs=matrix(,nrow = nrow(FirstSubstrateSet),ncol=1) - FTLwtAccessionNumbers=matrix(,nrow = nrow(FirstSubstrateSet),ncol=1) - - for (i in 1:nrow(FirstSubstrateSet)){ - FTLwtletters<-FirstSubstrateSet[i,4:18] - FTLwtletters<-FTLwtletters[FTLwtletters !="XXXXX"] - FTLwtletters<-paste(FTLwtletters, sep="", collapse="") - leftspaces<-c() - rightspaces<-c() - - YYYmotif <- unlist(strsplit(FTLwtletters, split = "")) - YYYposition <- match(x = "x", table = YYYmotif) - #position itself tells me how much is to the left of that X by what it's number is. x at position 4 tells me that there are - #just 3 letters to the left of x - - YYYLettersToTheLeft <- YYYposition - 1 - #how many letters to the right SHOULD just be length(motif)-position-1 if it's 5 long and x is at 3 then Y is at 4 and there is - #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1 - YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1 - #then sanity check, we're currently looking only at +/-4, but this spot allows for up to +/- 7 as well, just depends on what the - #variable the user puts in is - - - if (YYYLettersToTheLeft < 7 | YYYLettersToTheRight < 7) { - leftspaces<-rep(" ",times=(7-YYYLettersToTheLeft)) - rightspaces<-rep(" ",times=7-(YYYLettersToTheRight)) - #add blank spaces if the motif has less than 4 letters to the left/right - motif<-c(leftspaces,YYYmotif,rightspaces) - #save that motif, which is the Y and +/- 4 amino acids, including truncation - motif<-motif[!motif %in% "x"] - motif<-paste(motif, sep="", collapse="") - FTLwtletters<-motif - FTLwtmotifs[i,1]<-FTLwtletters - FTLwtAccessionNumbers[i,1]<-FirstSubstrateSet[i,3] - } - - if(YYYLettersToTheLeft>6 && YYYLettersToTheRight>6){ - motif<-YYYmotif - #add blank spaces if the motif has less than 4 letters to the left/right - motif<-c(leftspaces,YYYmotif,rightspaces) - #save that motif, which is the Y and +/- 4 amino acids, including truncation - motif<-motif[!motif %in% "x"] - motif<-paste(motif, sep="", collapse="") - FTLwtletters<-motif - FTLwtmotifs[i,1]<-FTLwtletters - FTLwtAccessionNumbers[i,1]<-FirstSubstrateSet[i,3] - - - } - - } - - D835Ymotifs=matrix(,nrow = nrow(SecondSubstrateSet),ncol=1) - D835YAccessionNumbers<-matrix(,nrow = nrow(SecondSubstrateSet),ncol = 1) - - for (i in 1:nrow(SecondSubstrateSet)){ - D835letters<-SecondSubstrateSet[i,4:18] - D835letters<-D835letters[D835letters !="XXXXX"] - D835letters<-paste(D835letters, sep="", collapse="") - leftspaces<-c() - rightspaces<-c() - - YYYmotif <- unlist(strsplit(D835letters, split = "")) - YYYposition <- match(x = "x", table = YYYmotif) - #position itself tells me how much is to the left of that X by what it's number is. x at position 4 tells me that there are - #just 3 letters to the left of x - - YYYLettersToTheLeft <- YYYposition - 1 - #how many letters to the right SHOULD just be length(motif)-position-1 if it's 5 long and x is at 3 then Y is at 4 and there is - #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1 - YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1 - #then sanity check, we're currently looking only at +/-4, but this spot allows for up to +/- 7 as well, just depends on what the - #variable the user puts in is - if (YYYLettersToTheLeft < 7 | YYYLettersToTheRight < 7) { - leftspaces<-rep(" ",times=(7-YYYLettersToTheLeft)) - rightspaces<-rep(" ",times=7-(YYYLettersToTheRight)) - #add blank spaces if the motif has less than 4 letters to the left/right - motif<-c(leftspaces,YYYmotif,rightspaces) - #save that motif, which is the Y and +/- 4 amino acids, including truncation - motif<-motif[!motif %in% "x"] - motif<-paste(motif, sep="", collapse="") - D835letters<-motif - D835Ymotifs[i,1]<-D835letters - D835YAccessionNumbers[i,1]<-SecondSubstrateSet[i,3] - } - - if(YYYLettersToTheLeft>6 && YYYLettersToTheRight>6){ - motif<-YYYmotif - #add blank spaces if the motif has less than 4 letters to the left/right - motif<-c(leftspaces,YYYmotif,rightspaces) - #save that motif, which is the Y and +/- 4 amino acids, including truncation - motif<-motif[!motif %in% "x"] - motif<-paste(motif, sep="", collapse="") - D835letters<-motif - D835Ymotifs[i,1]<-D835letters - D835YAccessionNumbers[i,1]<-SecondSubstrateSet[i,3] - } - } - - names(FTLwtmotifs)<-FTLwtAccessionNumbers - names(D835Ymotifs)<-D835YAccessionNumbers - - } - - - FTLwtmotifsFINAL<-FTLwtmotifs[!FTLwtmotifs %in% D835Ymotifs] - FTLwtmotifsFINAL<-FTLwtmotifsFINAL[!duplicated(FTLwtmotifsFINAL)] - - D835YmotifsFINAL<-D835Ymotifs[!D835Ymotifs %in% FTLwtmotifs] - D835YmotifsFINAL<-D835YmotifsFINAL[!duplicated(D835YmotifsFINAL)] - - - columnalheader<-c(rep(NA,36)) - FTLFinalMatrix<-matrix(data =columnalheader,nrow = 1) - - for (k in 1:length(FTLwtmotifsFINAL)) { - AN<-00000 - #I don't remember why, but I felt it necessary to destroy the accession number multiple times to ensure it is - #destroyed immediately after use - for (m in 1:ncol(Firstsubbackfreq)) { - AN <- as.character(Firstsubbackfreq[1, m]) - if (grepl(pattern = AN, - x = names(FTLwtmotifsFINAL[k]), - fixed = TRUE) == TRUE) { - outputmatrix <- as.character(Firstsubbackfreq[, m]) - outputmatrix <- matrix(outputmatrix, nrow = 1) - #with that accession number, find a match in the subbackfreq file and save it here - FTLFinalMatrix<-rbind(FTLFinalMatrix,outputmatrix) - } - } - } - FTLFinalMatrix<-FTLFinalMatrix[!duplicated(FTLFinalMatrix),] - FTLFinalMatrix<-FTLFinalMatrix[2:nrow(FTLFinalMatrix),] - - columnalheader<-c(rep(NA,36)) - D835YFinalMatrix<-matrix(data =columnalheader,nrow = 1) - - for (k in 1:length(D835YmotifsFINAL)) { - #I don't remember why, but I felt it necessary to destroy the accession number multiple times to ensure it is - #destroyed immediately after use - for (m in 1:ncol(Secondsubbackfreq)) { - AN <- as.character(Secondsubbackfreq[1, m]) - if (grepl(pattern = AN, - x = names(D835YmotifsFINAL[k]), - fixed = TRUE) == TRUE) { - outputmatrix <- as.character(Secondsubbackfreq[, m]) - outputmatrix <- matrix(outputmatrix, nrow = 1) - #with that accession number, find a match in the subbackfreq file and save it here - D835YFinalMatrix<-rbind(D835YFinalMatrix,outputmatrix) - } - } - } - D835YFinalMatrix<-D835YFinalMatrix[!duplicated(D835YFinalMatrix),] - D835YFinalMatrix<-D835YFinalMatrix[2:nrow(D835YFinalMatrix),] - - FTLoutputmatrix<-matrix(data=c(FTLwtmotifsFINAL,names(FTLwtmotifsFINAL)),ncol = 2) - - - FLTheader<-c("Substrate","Species","Reference","-7","-6","-5","-4","-3","-2","-1","0","1","2","3","4","5","6","7","Phosphite") - # FLTheader<-unlist(FLTheader) - lefthandFLT<-matrix(data = rep(NA,times=2*nrow(FTLoutputmatrix)),nrow=nrow(FTLoutputmatrix)) - righthandFLT<-matrix(data = rep(NA,times=1*nrow(FTLoutputmatrix)),nrow=nrow(FTLoutputmatrix)) - FLTaccessionset<-FTLoutputmatrix[,2] - FTLmeat<-sapply(FTLoutputmatrix[,1], strsplit, "") - FTLmeat<-sapply(FTLmeat, unlist) - colnames(FTLmeat)<-NULL - FTLmeat<-t(FTLmeat) - - FTLoutputmatrix2<-cbind(lefthandFLT,FLTaccessionset,FTLmeat,righthandFLT) - colnames(FTLoutputmatrix2)<-NULL - rownames(FTLoutputmatrix2)<-NULL - colnames(FLTheader)<-NULL - rownames(FLTheader)<-NULL - - - FirstCentralLettersAGAIN<-FTLoutputmatrix2[,11] - - FirstEsses<-sapply(FirstCentralLettersAGAIN, grepl, pattern="S", ignore.case=TRUE) - FirstTees<-sapply(FirstCentralLettersAGAIN, grepl, pattern="T", ignore.case=TRUE) - FirstWys<-sapply(FirstCentralLettersAGAIN, grepl, pattern="Y", ignore.case=TRUE) - - FirstCentralLettersAGAIN<-replace(FirstCentralLettersAGAIN,FirstEsses,"xS") - FirstCentralLettersAGAIN<-replace(FirstCentralLettersAGAIN,FirstTees,"xT") - FirstCentralLettersAGAIN<-replace(FirstCentralLettersAGAIN,FirstWys,"xY") - - FirstCentralLettersAGAIN->FTLoutputmatrix2[,11] - - FTLoutputmatrix2<-rbind(FLTheader,FTLoutputmatrix2) - - write.table(x=FTLoutputmatrix2, - file=First_unshared_motifs_table, - quote=FALSE, sep=",", - row.names=FALSE,col.names = FALSE, na="", append=TRUE) - - columnalheader<-c("Accession Numbers",as.character(Firstsubbackfreq[1:35,1])) - columnalheader<-matrix(columnalheader,nrow = 1) - write.table(x=columnalheader, - file=First_unshared_subbackfreq, - quote=FALSE, sep=",", - row.names=FALSE,col.names = FALSE, na="", append=TRUE) - - write.table(x=FTLFinalMatrix, - file=First_unshared_subbackfreq, - quote=FALSE, sep=",", - row.names=FALSE,col.names = FALSE, na="", append=TRUE) - - ############################################################################################################ - - D835Youtputmatrix<-matrix(data=c(D835YmotifsFINAL,names(D835YmotifsFINAL)),ncol = 2) - - D835Yheader<-c("Substrate","Species","Reference","-7","-6","-5","-4","-3","-2","-1","0","1","2","3","4","5","6","7","Phosphite") - # D835Yheader<-unlist(D835Yheader) - lefthandD835<-matrix(data = rep(NA,times=2*nrow(D835Youtputmatrix)),nrow=nrow(D835Youtputmatrix)) - righthandD835<-matrix(data = rep(NA,times=1*nrow(D835Youtputmatrix)),nrow=nrow(D835Youtputmatrix)) - D835Yaset<-D835Youtputmatrix[,2] - D835meat<-sapply(D835Youtputmatrix[,1], strsplit, "") - D835meat<-sapply(D835meat, unlist) - colnames(D835meat)<-NULL - D835meat<-t(D835meat) - - D835Youtputmatrix2<-cbind(lefthandD835,D835Yaset,D835meat,righthandD835) - colnames(D835Youtputmatrix2)<-NULL - rownames(D835Youtputmatrix2)<-NULL - colnames(D835Yheader)<-NULL - rownames(D835Yheader)<-NULL - - - SecondCentralLettersAGAIN<-D835Youtputmatrix2[,11] - - SecondEsses<-sapply(SecondCentralLettersAGAIN, grepl, pattern="S", ignore.case=TRUE) - SecondTees<-sapply(SecondCentralLettersAGAIN, grepl, pattern="T", ignore.case=TRUE) - SecondWys<-sapply(SecondCentralLettersAGAIN, grepl, pattern="Y", ignore.case=TRUE) - - SecondCentralLettersAGAIN<-replace(SecondCentralLettersAGAIN,SecondEsses,"xS") - SecondCentralLettersAGAIN<-replace(SecondCentralLettersAGAIN,SecondTees,"xT") - SecondCentralLettersAGAIN<-replace(SecondCentralLettersAGAIN,SecondWys,"xY") - - SecondCentralLettersAGAIN->D835Youtputmatrix2[,11] - - D835Youtputmatrix2<-rbind(D835Yheader,D835Youtputmatrix2) - - write.table(x=D835Youtputmatrix2, - file=Second_unshared_motifs_table, - quote=FALSE, sep=",", - row.names=FALSE,col.names = FALSE, na="", append=TRUE) - - columnalheader<-c("Accession Numbers",as.character(Firstsubbackfreq[1:35,1])) - columnalheader<-matrix(columnalheader,nrow = 1) - write.table(x=columnalheader, - file=Second_unshared_subbackfreq, - quote=FALSE, sep=",", - row.names=FALSE,col.names = FALSE, na="", append=TRUE) - - write.table(x=D835YFinalMatrix, - file=Second_unshared_subbackfreq, - quote=FALSE, sep=",", - row.names=FALSE,col.names = FALSE, na="", append=TRUE) -} -
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/all stuff/Difference finder for GalaxyP 2-21-20.R Fri Feb 21 13:07:45 2020 -0500 @@ -0,0 +1,358 @@ +#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
--- a/all stuff/Difference finder for GalaxyP 4-18-2019.R Fri Apr 19 16:55:29 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,351 +0,0 @@ -#I should make an SOP for this. Problems we encountered: no x in the xY motif, and the kilodemon -#the output files have both Y and xY, they shouldn't why is that happening? make it not happen -#make sure that accession numbers stay locked to each motif, somehow -#output should look just like the KALIP input - -#ff you want ONLY FULL MOTIFS, put "YES" here, please use all caps -FullMotifsOnly_questionmark<-"NO" -#If you want ONLY TRUNCATED MOTIFS, put "YES" here, please use all caps -TruncatedMotifsOnly_questionmark<-"NO" -#if you want to find the overlap, put a "YES" here (all caps), if you want to find the non-overlap, put "NO" (all caps) -Are_You_Looking_For_Commonality<-"NO" - - -#put the names of your input files here -FirstSubstrateSet<- read.csv("S1.csv", stringsAsFactors=FALSE) -Firstsubbackfreq<- read.csv("SBF1.csv", header=FALSE, stringsAsFactors=FALSE) - -SecondSubstrateSet<- read.csv("S2.csv", stringsAsFactors=FALSE) -Secondsubbackfreq<- read.csv("SBF2.csv", header=FALSE, stringsAsFactors=FALSE) - -# ThirdSubstrateSet<- read.csv("Galaxy69-BTK_PLUS_R3_Substrates.csv", stringsAsFactors=FALSE) -# Thirdsubbackfreq<- read.csv("Galaxy70-BTK_PLUS_R3_SubstrateBackgroundFrequency.csv", header=FALSE, stringsAsFactors=FALSE) - -#then put the names of your output files here -# Shared_motifs_table<-"180719_GALAXY-BTK-plus-rep-OVLP-7to7-substrates.csv" -# Shared_subbackfreq_table<-"180719_GALAXY-BTK-plus-rep-OVLP-7to7-SubBackFreq.csv" - -# Shared_motifs_table<-"Shared motifs 7-27-17.csv" -# Shared_subbackfreq_table<-"SubstrateBackgrounFrequency-for-shared-motifs 4 7-27-17.csv" - -First_unshared_motifs_table<-"1RS.csv" -First_unshared_subbackfreq<-"1RSBF.csv" - -Second_unshared_motifs_table<-"2RS.csv" -Second_unshared_subbackfreq<-"2RSBF.csv" - -# Third_unshared_motifs_table<-"R3 subs.csv" -# Third_unshared_subbackfreq<-"R3 SBF.csv" - -#final note, this code is going to be unworkable if you want to make a Venn diagram of more than 3 circles. I think I'll poke around -#other languages to see if any of them can do it. -#################################################################################################################################### - - - - - -# grepl(pattern = "S", x=asdf, ignore.case = TRUE) - -FirstCentralLetters<-FirstSubstrateSet[,11] -SecondCentralLetters<-SecondSubstrateSet[,11] - -FirstEsses<-sapply(FirstCentralLetters, grepl, pattern="S", ignore.case=TRUE) -FirstTees<-sapply(FirstCentralLetters, grepl, pattern="T", ignore.case=TRUE) -FirstWys<-sapply(FirstCentralLetters, grepl, pattern="Y", ignore.case=TRUE) - -SecondEsses<-sapply(SecondCentralLetters, grepl, pattern="S", ignore.case=TRUE) -SecondTees<-sapply(SecondCentralLetters, grepl, pattern="T", ignore.case=TRUE) -SecondWys<-sapply(SecondCentralLetters, grepl, pattern="Y", ignore.case=TRUE) - -FirstCentralLetters<-replace(FirstCentralLetters,FirstEsses,"xS") -FirstCentralLetters<-replace(FirstCentralLetters,FirstTees,"xT") -FirstCentralLetters<-replace(FirstCentralLetters,FirstWys,"xY") - -SecondCentralLetters<-replace(SecondCentralLetters,SecondEsses,"xS") -SecondCentralLetters<-replace(SecondCentralLetters,SecondTees,"xT") -SecondCentralLetters<-replace(SecondCentralLetters,SecondWys,"xY") - -FirstCentralLetters->FirstSubstrateSet[,11] -SecondCentralLetters->SecondSubstrateSet[,11] - -#################################################################################################################################### -#################################################################################################################################### -# better version of this code written in C: what happens when two kinases share a motif, but they found that motif in two -# separate proteins thus two separate accession numbers? -# It should actually output the shared motif and BOTH accession numbers. Right now it does not, it only maps out the second -# accession number. So that needs to be fixed BUT you need to keep the commonality between a motif and its accession number -#################################################################################################################################### -#################################################################################################################################### -#################################################################################################################################### -#################################################################################################################################### - -#Create the motif sets, deciding wether or not you're looking for truncated or full here -#full only - - -if (Are_You_Looking_For_Commonality=="NO"){ - - ############################################### - #ALL motifs, full and truncated - - if (FullMotifsOnly_questionmark!="YES"&&TruncatedMotifsOnly_questionmark!="YES"){ - FTLwtmotifs=matrix(,nrow = nrow(FirstSubstrateSet),ncol=1) - FTLwtAccessionNumbers=matrix(,nrow = nrow(FirstSubstrateSet),ncol=1) - - for (i in 1:nrow(FirstSubstrateSet)){ - FTLwtletters<-FirstSubstrateSet[i,4:18] - FTLwtletters<-FTLwtletters[FTLwtletters !="XXXXX"] - FTLwtletters<-paste(FTLwtletters, sep="", collapse="") - leftspaces<-c() - rightspaces<-c() - - YYYmotif <- unlist(strsplit(FTLwtletters, split = "")) - YYYposition <- match(x = "x", table = YYYmotif) - #position itself tells me how much is to the left of that X by what it's number is. x at position 4 tells me that there are - #just 3 letters to the left of x - - YYYLettersToTheLeft <- YYYposition - 1 - #how many letters to the right SHOULD just be length(motif)-position-1 if it's 5 long and x is at 3 then Y is at 4 and there is - #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1 - YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1 - #then sanity check, we're currently looking only at +/-4, but this spot allows for up to +/- 7 as well, just depends on what the - #variable the user puts in is - - - if (YYYLettersToTheLeft < 7 | YYYLettersToTheRight < 7) { - leftspaces<-rep(" ",times=(7-YYYLettersToTheLeft)) - rightspaces<-rep(" ",times=7-(YYYLettersToTheRight)) - #add blank spaces if the motif has less than 4 letters to the left/right - motif<-c(leftspaces,YYYmotif,rightspaces) - #save that motif, which is the Y and +/- 4 amino acids, including truncation - motif<-motif[!motif %in% "x"] - motif<-paste(motif, sep="", collapse="") - FTLwtletters<-motif - FTLwtmotifs[i,1]<-FTLwtletters - FTLwtAccessionNumbers[i,1]<-FirstSubstrateSet[i,3] - } - - if(YYYLettersToTheLeft>6 && YYYLettersToTheRight>6){ - motif<-YYYmotif - #add blank spaces if the motif has less than 4 letters to the left/right - motif<-c(leftspaces,YYYmotif,rightspaces) - #save that motif, which is the Y and +/- 4 amino acids, including truncation - motif<-motif[!motif %in% "x"] - motif<-paste(motif, sep="", collapse="") - FTLwtletters<-motif - FTLwtmotifs[i,1]<-FTLwtletters - FTLwtAccessionNumbers[i,1]<-FirstSubstrateSet[i,3] - - - } - - } - - D835Ymotifs=matrix(,nrow = nrow(SecondSubstrateSet),ncol=1) - D835YAccessionNumbers<-matrix(,nrow = nrow(SecondSubstrateSet),ncol = 1) - - for (i in 1:nrow(SecondSubstrateSet)){ - D835letters<-SecondSubstrateSet[i,4:18] - D835letters<-D835letters[D835letters !="XXXXX"] - D835letters<-paste(D835letters, sep="", collapse="") - leftspaces<-c() - rightspaces<-c() - - YYYmotif <- unlist(strsplit(D835letters, split = "")) - YYYposition <- match(x = "x", table = YYYmotif) - #position itself tells me how much is to the left of that X by what it's number is. x at position 4 tells me that there are - #just 3 letters to the left of x - - YYYLettersToTheLeft <- YYYposition - 1 - #how many letters to the right SHOULD just be length(motif)-position-1 if it's 5 long and x is at 3 then Y is at 4 and there is - #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1 - YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1 - #then sanity check, we're currently looking only at +/-4, but this spot allows for up to +/- 7 as well, just depends on what the - #variable the user puts in is - if (YYYLettersToTheLeft < 7 | YYYLettersToTheRight < 7) { - leftspaces<-rep(" ",times=(7-YYYLettersToTheLeft)) - rightspaces<-rep(" ",times=7-(YYYLettersToTheRight)) - #add blank spaces if the motif has less than 4 letters to the left/right - motif<-c(leftspaces,YYYmotif,rightspaces) - #save that motif, which is the Y and +/- 4 amino acids, including truncation - motif<-motif[!motif %in% "x"] - motif<-paste(motif, sep="", collapse="") - D835letters<-motif - D835Ymotifs[i,1]<-D835letters - D835YAccessionNumbers[i,1]<-SecondSubstrateSet[i,3] - } - - if(YYYLettersToTheLeft>6 && YYYLettersToTheRight>6){ - motif<-YYYmotif - #add blank spaces if the motif has less than 4 letters to the left/right - motif<-c(leftspaces,YYYmotif,rightspaces) - #save that motif, which is the Y and +/- 4 amino acids, including truncation - motif<-motif[!motif %in% "x"] - motif<-paste(motif, sep="", collapse="") - D835letters<-motif - D835Ymotifs[i,1]<-D835letters - D835YAccessionNumbers[i,1]<-SecondSubstrateSet[i,3] - } - } - - names(FTLwtmotifs)<-FTLwtAccessionNumbers - names(D835Ymotifs)<-D835YAccessionNumbers - - } - - - FTLwtmotifsFINAL<-FTLwtmotifs[!FTLwtmotifs %in% D835Ymotifs] - FTLwtmotifsFINAL<-FTLwtmotifsFINAL[!duplicated(FTLwtmotifsFINAL)] - - D835YmotifsFINAL<-D835Ymotifs[!D835Ymotifs %in% FTLwtmotifs] - D835YmotifsFINAL<-D835YmotifsFINAL[!duplicated(D835YmotifsFINAL)] - - - columnalheader<-c(rep(NA,36)) - FTLFinalMatrix<-matrix(data =columnalheader,nrow = 1) - - for (k in 1:length(FTLwtmotifsFINAL)) { - AN<-00000 - #I don't remember why, but I felt it necessary to destroy the accession number multiple times to ensure it is - #destroyed immediately after use - for (m in 1:ncol(Firstsubbackfreq)) { - AN <- as.character(Firstsubbackfreq[1, m]) - if (grepl(pattern = AN, - x = names(FTLwtmotifsFINAL[k]), - fixed = TRUE) == TRUE) { - outputmatrix <- as.character(Firstsubbackfreq[, m]) - outputmatrix <- matrix(outputmatrix, nrow = 1) - #with that accession number, find a match in the subbackfreq file and save it here - FTLFinalMatrix<-rbind(FTLFinalMatrix,outputmatrix) - } - } - } - FTLFinalMatrix<-FTLFinalMatrix[!duplicated(FTLFinalMatrix),] - FTLFinalMatrix<-FTLFinalMatrix[2:nrow(FTLFinalMatrix),] - - columnalheader<-c(rep(NA,36)) - D835YFinalMatrix<-matrix(data =columnalheader,nrow = 1) - - for (k in 1:length(D835YmotifsFINAL)) { - #I don't remember why, but I felt it necessary to destroy the accession number multiple times to ensure it is - #destroyed immediately after use - for (m in 1:ncol(Secondsubbackfreq)) { - AN <- as.character(Secondsubbackfreq[1, m]) - if (grepl(pattern = AN, - x = names(D835YmotifsFINAL[k]), - fixed = TRUE) == TRUE) { - outputmatrix <- as.character(Secondsubbackfreq[, m]) - outputmatrix <- matrix(outputmatrix, nrow = 1) - #with that accession number, find a match in the subbackfreq file and save it here - D835YFinalMatrix<-rbind(D835YFinalMatrix,outputmatrix) - } - } - } - D835YFinalMatrix<-D835YFinalMatrix[!duplicated(D835YFinalMatrix),] - D835YFinalMatrix<-D835YFinalMatrix[2:nrow(D835YFinalMatrix),] - - FTLoutputmatrix<-matrix(data=c(FTLwtmotifsFINAL,names(FTLwtmotifsFINAL)),ncol = 2) - - - FLTheader<-c("Substrate","Species","Reference","-7","-6","-5","-4","-3","-2","-1","0","1","2","3","4","5","6","7","Phosphite") - # FLTheader<-unlist(FLTheader) - lefthandFLT<-matrix(data = rep(NA,times=2*nrow(FTLoutputmatrix)),nrow=nrow(FTLoutputmatrix)) - righthandFLT<-matrix(data = rep(NA,times=1*nrow(FTLoutputmatrix)),nrow=nrow(FTLoutputmatrix)) - FLTaccessionset<-FTLoutputmatrix[,2] - FTLmeat<-sapply(FTLoutputmatrix[,1], strsplit, "") - FTLmeat<-sapply(FTLmeat, unlist) - colnames(FTLmeat)<-NULL - FTLmeat<-t(FTLmeat) - - FTLoutputmatrix2<-cbind(lefthandFLT,FLTaccessionset,FTLmeat,righthandFLT) - colnames(FTLoutputmatrix2)<-NULL - rownames(FTLoutputmatrix2)<-NULL - colnames(FLTheader)<-NULL - rownames(FLTheader)<-NULL - - - FirstCentralLettersAGAIN<-FTLoutputmatrix2[,11] - - FirstEsses<-sapply(FirstCentralLettersAGAIN, grepl, pattern="S", ignore.case=TRUE) - FirstTees<-sapply(FirstCentralLettersAGAIN, grepl, pattern="T", ignore.case=TRUE) - FirstWys<-sapply(FirstCentralLettersAGAIN, grepl, pattern="Y", ignore.case=TRUE) - - FirstCentralLettersAGAIN<-replace(FirstCentralLettersAGAIN,FirstEsses,"xS") - FirstCentralLettersAGAIN<-replace(FirstCentralLettersAGAIN,FirstTees,"xT") - FirstCentralLettersAGAIN<-replace(FirstCentralLettersAGAIN,FirstWys,"xY") - - FirstCentralLettersAGAIN->FTLoutputmatrix2[,11] - - FTLoutputmatrix2<-rbind(FLTheader,FTLoutputmatrix2) - - write.table(x=FTLoutputmatrix2, - file=First_unshared_motifs_table, - quote=FALSE, sep=",", - row.names=FALSE,col.names = FALSE, na="", append=TRUE) - - columnalheader<-c("Accession Numbers",as.character(Firstsubbackfreq[1:35,1])) - columnalheader<-matrix(columnalheader,nrow = 1) - write.table(x=columnalheader, - file=First_unshared_subbackfreq, - quote=FALSE, sep=",", - row.names=FALSE,col.names = FALSE, na="", append=TRUE) - - write.table(x=FTLFinalMatrix, - file=First_unshared_subbackfreq, - quote=FALSE, sep=",", - row.names=FALSE,col.names = FALSE, na="", append=TRUE) - - ############################################################################################################ - - D835Youtputmatrix<-matrix(data=c(D835YmotifsFINAL,names(D835YmotifsFINAL)),ncol = 2) - - D835Yheader<-c("Substrate","Species","Reference","-7","-6","-5","-4","-3","-2","-1","0","1","2","3","4","5","6","7","Phosphite") - # D835Yheader<-unlist(D835Yheader) - lefthandD835<-matrix(data = rep(NA,times=2*nrow(D835Youtputmatrix)),nrow=nrow(D835Youtputmatrix)) - righthandD835<-matrix(data = rep(NA,times=1*nrow(D835Youtputmatrix)),nrow=nrow(D835Youtputmatrix)) - D835Yaset<-D835Youtputmatrix[,2] - D835meat<-sapply(D835Youtputmatrix[,1], strsplit, "") - D835meat<-sapply(D835meat, unlist) - colnames(D835meat)<-NULL - D835meat<-t(D835meat) - - D835Youtputmatrix2<-cbind(lefthandD835,D835Yaset,D835meat,righthandD835) - colnames(D835Youtputmatrix2)<-NULL - rownames(D835Youtputmatrix2)<-NULL - colnames(D835Yheader)<-NULL - rownames(D835Yheader)<-NULL - - - SecondCentralLettersAGAIN<-D835Youtputmatrix2[,11] - - SecondEsses<-sapply(SecondCentralLettersAGAIN, grepl, pattern="S", ignore.case=TRUE) - SecondTees<-sapply(SecondCentralLettersAGAIN, grepl, pattern="T", ignore.case=TRUE) - SecondWys<-sapply(SecondCentralLettersAGAIN, grepl, pattern="Y", ignore.case=TRUE) - - SecondCentralLettersAGAIN<-replace(SecondCentralLettersAGAIN,SecondEsses,"xS") - SecondCentralLettersAGAIN<-replace(SecondCentralLettersAGAIN,SecondTees,"xT") - SecondCentralLettersAGAIN<-replace(SecondCentralLettersAGAIN,SecondWys,"xY") - - SecondCentralLettersAGAIN->D835Youtputmatrix2[,11] - - D835Youtputmatrix2<-rbind(D835Yheader,D835Youtputmatrix2) - - write.table(x=D835Youtputmatrix2, - file=Second_unshared_motifs_table, - quote=FALSE, sep=",", - row.names=FALSE,col.names = FALSE, na="", append=TRUE) - - columnalheader<-c("Accession Numbers",as.character(Firstsubbackfreq[1:35,1])) - columnalheader<-matrix(columnalheader,nrow = 1) - write.table(x=columnalheader, - file=Second_unshared_subbackfreq, - quote=FALSE, sep=",", - row.names=FALSE,col.names = FALSE, na="", append=TRUE) - - write.table(x=D835YFinalMatrix, - file=Second_unshared_subbackfreq, - quote=FALSE, sep=",", - row.names=FALSE,col.names = FALSE, na="", append=TRUE) -} -
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/all stuff/Difference finder for GalaxyP working.R Fri Feb 21 13:07:45 2020 -0500 @@ -0,0 +1,358 @@ +#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
--- a/all stuff/Difference finderMADE 7 TO 7 1-15-2019.R Fri Apr 19 16:55:29 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,351 +0,0 @@ -#I should make an SOP for this. Problems we encountered: no x in the xY motif, and the kilodemon -#the output files have both Y and xY, they shouldn't why is that happening? make it not happen -#make sure that accession numbers stay locked to each motif, somehow -#output should look just like the KALIP input - -#ff you want ONLY FULL MOTIFS, put "YES" here, please use all caps -FullMotifsOnly_questionmark<-"NO" -#If you want ONLY TRUNCATED MOTIFS, put "YES" here, please use all caps -TruncatedMotifsOnly_questionmark<-"NO" -#if you want to find the overlap, put a "YES" here (all caps), if you want to find the non-overlap, put "NO" (all caps) -Are_You_Looking_For_Commonality<-"NO" - - -#put the names of your input files here -FirstSubstrateSet<- read.csv("S1.csv", stringsAsFactors=FALSE) -Firstsubbackfreq<- read.csv("SBF1.csv", header=FALSE, stringsAsFactors=FALSE) - -SecondSubstrateSet<- read.csv("S2.csv", stringsAsFactors=FALSE) -Secondsubbackfreq<- read.csv("SBF2.csv", header=FALSE, stringsAsFactors=FALSE) - -# ThirdSubstrateSet<- read.csv("Galaxy69-BTK_PLUS_R3_Substrates.csv", stringsAsFactors=FALSE) -# Thirdsubbackfreq<- read.csv("Galaxy70-BTK_PLUS_R3_SubstrateBackgroundFrequency.csv", header=FALSE, stringsAsFactors=FALSE) - -#then put the names of your output files here -# Shared_motifs_table<-"180719_GALAXY-BTK-plus-rep-OVLP-7to7-substrates.csv" -# Shared_subbackfreq_table<-"180719_GALAXY-BTK-plus-rep-OVLP-7to7-SubBackFreq.csv" - -# Shared_motifs_table<-"Shared motifs 7-27-17.csv" -# Shared_subbackfreq_table<-"SubstrateBackgrounFrequency-for-shared-motifs 4 7-27-17.csv" - -First_unshared_motifs_table<-"1RS.csv" -First_unshared_subbackfreq<-"1RSBF.csv" - -Second_unshared_motifs_table<-"2RS.csv" -Second_unshared_subbackfreq<-"2RSBF.csv" - -# Third_unshared_motifs_table<-"R3 subs.csv" -# Third_unshared_subbackfreq<-"R3 SBF.csv" - -#final note, this code is going to be unworkable if you want to make a Venn diagram of more than 3 circles. I think I'll poke around -#other languages to see if any of them can do it. -#################################################################################################################################### - - - - - -# grepl(pattern = "S", x=asdf, ignore.case = TRUE) - -FirstCentralLetters<-FirstSubstrateSet[,11] -SecondCentralLetters<-SecondSubstrateSet[,11] - -FirstEsses<-sapply(FirstCentralLetters, grepl, pattern="S", ignore.case=TRUE) -FirstTees<-sapply(FirstCentralLetters, grepl, pattern="T", ignore.case=TRUE) -FirstWys<-sapply(FirstCentralLetters, grepl, pattern="Y", ignore.case=TRUE) - -SecondEsses<-sapply(SecondCentralLetters, grepl, pattern="S", ignore.case=TRUE) -SecondTees<-sapply(SecondCentralLetters, grepl, pattern="T", ignore.case=TRUE) -SecondWys<-sapply(SecondCentralLetters, grepl, pattern="Y", ignore.case=TRUE) - -FirstCentralLetters<-replace(FirstCentralLetters,FirstEsses,"xS") -FirstCentralLetters<-replace(FirstCentralLetters,FirstTees,"xT") -FirstCentralLetters<-replace(FirstCentralLetters,FirstWys,"xY") - -SecondCentralLetters<-replace(SecondCentralLetters,SecondEsses,"xS") -SecondCentralLetters<-replace(SecondCentralLetters,SecondTees,"xT") -SecondCentralLetters<-replace(SecondCentralLetters,SecondWys,"xY") - -FirstCentralLetters->FirstSubstrateSet[,11] -SecondCentralLetters->SecondSubstrateSet[,11] - -#################################################################################################################################### -#################################################################################################################################### -# better version of this code written in C: what happens when two kinases share a motif, but they found that motif in two -# separate proteins thus two separate accession numbers? -# It should actually output the shared motif and BOTH accession numbers. Right now it does not, it only maps out the second -# accession number. So that needs to be fixed BUT you need to keep the commonality between a motif and its accession number -#################################################################################################################################### -#################################################################################################################################### -#################################################################################################################################### -#################################################################################################################################### - -#Create the motif sets, deciding wether or not you're looking for truncated or full here -#full only - - -if (Are_You_Looking_For_Commonality=="NO"){ - - ############################################### - #ALL motifs, full and truncated - - if (FullMotifsOnly_questionmark!="YES"&&TruncatedMotifsOnly_questionmark!="YES"){ - FTLwtmotifs=matrix(,nrow = nrow(FirstSubstrateSet),ncol=1) - FTLwtAccessionNumbers=matrix(,nrow = nrow(FirstSubstrateSet),ncol=1) - - for (i in 1:nrow(FirstSubstrateSet)){ - FTLwtletters<-FirstSubstrateSet[i,4:18] - FTLwtletters<-FTLwtletters[FTLwtletters !="XXXXX"] - FTLwtletters<-paste(FTLwtletters, sep="", collapse="") - leftspaces<-c() - rightspaces<-c() - - YYYmotif <- unlist(strsplit(FTLwtletters, split = "")) - YYYposition <- match(x = "x", table = YYYmotif) - #position itself tells me how much is to the left of that X by what it's number is. x at position 4 tells me that there are - #just 3 letters to the left of x - - YYYLettersToTheLeft <- YYYposition - 1 - #how many letters to the right SHOULD just be length(motif)-position-1 if it's 5 long and x is at 3 then Y is at 4 and there is - #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1 - YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1 - #then sanity check, we're currently looking only at +/-4, but this spot allows for up to +/- 7 as well, just depends on what the - #variable the user puts in is - - - if (YYYLettersToTheLeft < 7 | YYYLettersToTheRight < 7) { - leftspaces<-rep(" ",times=(7-YYYLettersToTheLeft)) - rightspaces<-rep(" ",times=7-(YYYLettersToTheRight)) - #add blank spaces if the motif has less than 4 letters to the left/right - motif<-c(leftspaces,YYYmotif,rightspaces) - #save that motif, which is the Y and +/- 4 amino acids, including truncation - motif<-motif[!motif %in% "x"] - motif<-paste(motif, sep="", collapse="") - FTLwtletters<-motif - FTLwtmotifs[i,1]<-FTLwtletters - FTLwtAccessionNumbers[i,1]<-FirstSubstrateSet[i,3] - } - - if(YYYLettersToTheLeft>6 && YYYLettersToTheRight>6){ - motif<-YYYmotif - #add blank spaces if the motif has less than 4 letters to the left/right - motif<-c(leftspaces,YYYmotif,rightspaces) - #save that motif, which is the Y and +/- 4 amino acids, including truncation - motif<-motif[!motif %in% "x"] - motif<-paste(motif, sep="", collapse="") - FTLwtletters<-motif - FTLwtmotifs[i,1]<-FTLwtletters - FTLwtAccessionNumbers[i,1]<-FirstSubstrateSet[i,3] - - - } - - } - - D835Ymotifs=matrix(,nrow = nrow(SecondSubstrateSet),ncol=1) - D835YAccessionNumbers<-matrix(,nrow = nrow(SecondSubstrateSet),ncol = 1) - - for (i in 1:nrow(SecondSubstrateSet)){ - D835letters<-SecondSubstrateSet[i,4:18] - D835letters<-D835letters[D835letters !="XXXXX"] - D835letters<-paste(D835letters, sep="", collapse="") - leftspaces<-c() - rightspaces<-c() - - YYYmotif <- unlist(strsplit(D835letters, split = "")) - YYYposition <- match(x = "x", table = YYYmotif) - #position itself tells me how much is to the left of that X by what it's number is. x at position 4 tells me that there are - #just 3 letters to the left of x - - YYYLettersToTheLeft <- YYYposition - 1 - #how many letters to the right SHOULD just be length(motif)-position-1 if it's 5 long and x is at 3 then Y is at 4 and there is - #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1 - YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1 - #then sanity check, we're currently looking only at +/-4, but this spot allows for up to +/- 7 as well, just depends on what the - #variable the user puts in is - if (YYYLettersToTheLeft < 7 | YYYLettersToTheRight < 7) { - leftspaces<-rep(" ",times=(7-YYYLettersToTheLeft)) - rightspaces<-rep(" ",times=7-(YYYLettersToTheRight)) - #add blank spaces if the motif has less than 4 letters to the left/right - motif<-c(leftspaces,YYYmotif,rightspaces) - #save that motif, which is the Y and +/- 4 amino acids, including truncation - motif<-motif[!motif %in% "x"] - motif<-paste(motif, sep="", collapse="") - D835letters<-motif - D835Ymotifs[i,1]<-D835letters - D835YAccessionNumbers[i,1]<-FirstSubstrateSet[i,3] - } - - if(YYYLettersToTheLeft>6 && YYYLettersToTheRight>6){ - motif<-YYYmotif - #add blank spaces if the motif has less than 4 letters to the left/right - motif<-c(leftspaces,YYYmotif,rightspaces) - #save that motif, which is the Y and +/- 4 amino acids, including truncation - motif<-motif[!motif %in% "x"] - motif<-paste(motif, sep="", collapse="") - D835letters<-motif - D835Ymotifs[i,1]<-D835letters - D835YAccessionNumbers[i,1]<-FirstSubstrateSet[i,3] - } - } - - names(FTLwtmotifs)<-FTLwtAccessionNumbers - names(D835Ymotifs)<-D835YAccessionNumbers - - } - - - FTLwtmotifsFINAL<-FTLwtmotifs[!FTLwtmotifs %in% D835Ymotifs] - FTLwtmotifsFINAL<-FTLwtmotifsFINAL[!duplicated(FTLwtmotifsFINAL)] - - D835YmotifsFINAL<-D835Ymotifs[!D835Ymotifs %in% FTLwtmotifs] - D835YmotifsFINAL<-D835YmotifsFINAL[!duplicated(D835YmotifsFINAL)] - - - columnalheader<-c(rep(NA,36)) - FTLFinalMatrix<-matrix(data =columnalheader,nrow = 1) - - for (k in 1:length(FTLwtmotifsFINAL)) { - AN<-00000 - #I don't remember why, but I felt it necessary to destroy the accession number multiple times to ensure it is - #destroyed immediately after use - for (m in 1:ncol(Firstsubbackfreq)) { - AN <- as.character(Firstsubbackfreq[1, m]) - if (grepl(pattern = AN, - x = names(FTLwtmotifsFINAL[k]), - fixed = TRUE) == TRUE) { - outputmatrix <- as.character(Firstsubbackfreq[, m]) - outputmatrix <- matrix(outputmatrix, nrow = 1) - #with that accession number, find a match in the subbackfreq file and save it here - FTLFinalMatrix<-rbind(FTLFinalMatrix,outputmatrix) - } - } - } - FTLFinalMatrix<-FTLFinalMatrix[!duplicated(FTLFinalMatrix),] - FTLFinalMatrix<-FTLFinalMatrix[2:nrow(FTLFinalMatrix),] - - columnalheader<-c(rep(NA,36)) - D835YFinalMatrix<-matrix(data =columnalheader,nrow = 1) - - for (k in 1:length(D835YmotifsFINAL)) { - #I don't remember why, but I felt it necessary to destroy the accession number multiple times to ensure it is - #destroyed immediately after use - for (m in 1:ncol(Secondsubbackfreq)) { - AN <- as.character(Secondsubbackfreq[1, m]) - if (grepl(pattern = AN, - x = names(D835YmotifsFINAL[k]), - fixed = TRUE) == TRUE) { - outputmatrix <- as.character(Secondsubbackfreq[, m]) - outputmatrix <- matrix(outputmatrix, nrow = 1) - #with that accession number, find a match in the subbackfreq file and save it here - D835YFinalMatrix<-rbind(D835YFinalMatrix,outputmatrix) - } - } - } - D835YFinalMatrix<-D835YFinalMatrix[!duplicated(D835YFinalMatrix),] - D835YFinalMatrix<-D835YFinalMatrix[2:nrow(D835YFinalMatrix),] - - FTLoutputmatrix<-matrix(data=c(FTLwtmotifsFINAL,names(FTLwtmotifsFINAL)),ncol = 2) - - - FLTheader<-c("Substrate","Species","Reference","-7","-6","-5","-4","-3","-2","-1","0","1","2","3","4","5","6","7","Phosphite") - # FLTheader<-unlist(FLTheader) - lefthandFLT<-matrix(data = rep(NA,times=2*nrow(FTLoutputmatrix)),nrow=nrow(FTLoutputmatrix)) - righthandFLT<-matrix(data = rep(NA,times=1*nrow(FTLoutputmatrix)),nrow=nrow(FTLoutputmatrix)) - FLTaccessionset<-FTLoutputmatrix[,2] - FTLmeat<-sapply(FTLoutputmatrix[,1], strsplit, "") - FTLmeat<-sapply(FTLmeat, unlist) - colnames(FTLmeat)<-NULL - FTLmeat<-t(FTLmeat) - - FTLoutputmatrix2<-cbind(lefthandFLT,FLTaccessionset,FTLmeat,righthandFLT) - colnames(FTLoutputmatrix2)<-NULL - rownames(FTLoutputmatrix2)<-NULL - colnames(FLTheader)<-NULL - rownames(FLTheader)<-NULL - - - FirstCentralLettersAGAIN<-FTLoutputmatrix2[,11] - - FirstEsses<-sapply(FirstCentralLettersAGAIN, grepl, pattern="S", ignore.case=TRUE) - FirstTees<-sapply(FirstCentralLettersAGAIN, grepl, pattern="T", ignore.case=TRUE) - FirstWys<-sapply(FirstCentralLettersAGAIN, grepl, pattern="Y", ignore.case=TRUE) - - FirstCentralLettersAGAIN<-replace(FirstCentralLettersAGAIN,FirstEsses,"xS") - FirstCentralLettersAGAIN<-replace(FirstCentralLettersAGAIN,FirstTees,"xT") - FirstCentralLettersAGAIN<-replace(FirstCentralLettersAGAIN,FirstWys,"xY") - - FirstCentralLettersAGAIN->FTLoutputmatrix2[,11] - - FTLoutputmatrix2<-rbind(FLTheader,FTLoutputmatrix2) - - write.table(x=FTLoutputmatrix2, - file=First_unshared_motifs_table, - quote=FALSE, sep=",", - row.names=FALSE,col.names = FALSE, na="", append=TRUE) - - columnalheader<-c("Accession Numbers",as.character(Firstsubbackfreq[1:35,1])) - columnalheader<-matrix(columnalheader,nrow = 1) - write.table(x=columnalheader, - file=First_unshared_subbackfreq, - quote=FALSE, sep=",", - row.names=FALSE,col.names = FALSE, na="", append=TRUE) - - write.table(x=FTLFinalMatrix, - file=First_unshared_subbackfreq, - quote=FALSE, sep=",", - row.names=FALSE,col.names = FALSE, na="", append=TRUE) - - ############################################################################################################ - - D835Youtputmatrix<-matrix(data=c(D835YmotifsFINAL,names(D835YmotifsFINAL)),ncol = 2) - - D835Yheader<-c("Substrate","Species","Reference","-7","-6","-5","-4","-3","-2","-1","0","1","2","3","4","5","6","7","Phosphite") - # D835Yheader<-unlist(D835Yheader) - lefthandD835<-matrix(data = rep(NA,times=2*nrow(D835Youtputmatrix)),nrow=nrow(D835Youtputmatrix)) - righthandD835<-matrix(data = rep(NA,times=1*nrow(D835Youtputmatrix)),nrow=nrow(D835Youtputmatrix)) - D835Yaset<-D835Youtputmatrix[,2] - D835meat<-sapply(D835Youtputmatrix[,1], strsplit, "") - D835meat<-sapply(D835meat, unlist) - colnames(D835meat)<-NULL - D835meat<-t(D835meat) - - D835Youtputmatrix2<-cbind(lefthandD835,D835Yaset,D835meat,righthandD835) - colnames(D835Youtputmatrix2)<-NULL - rownames(D835Youtputmatrix2)<-NULL - colnames(D835Yheader)<-NULL - rownames(D835Yheader)<-NULL - - - SecondCentralLettersAGAIN<-D835Youtputmatrix2[,11] - - SecondEsses<-sapply(SecondCentralLettersAGAIN, grepl, pattern="S", ignore.case=TRUE) - SecondTees<-sapply(SecondCentralLettersAGAIN, grepl, pattern="T", ignore.case=TRUE) - SecondWys<-sapply(SecondCentralLettersAGAIN, grepl, pattern="Y", ignore.case=TRUE) - - SecondCentralLettersAGAIN<-replace(SecondCentralLettersAGAIN,SecondEsses,"xS") - SecondCentralLettersAGAIN<-replace(SecondCentralLettersAGAIN,SecondTees,"xT") - SecondCentralLettersAGAIN<-replace(SecondCentralLettersAGAIN,SecondWys,"xY") - - SecondCentralLettersAGAIN->D835Youtputmatrix2[,11] - - D835Youtputmatrix2<-rbind(D835Yheader,D835Youtputmatrix2) - - write.table(x=D835Youtputmatrix2, - file=Second_unshared_motifs_table, - quote=FALSE, sep=",", - row.names=FALSE,col.names = FALSE, na="", append=TRUE) - - columnalheader<-c("Accession Numbers",as.character(Firstsubbackfreq[1:35,1])) - columnalheader<-matrix(columnalheader,nrow = 1) - write.table(x=columnalheader, - file=Second_unshared_subbackfreq, - quote=FALSE, sep=",", - row.names=FALSE,col.names = FALSE, na="", append=TRUE) - - write.table(x=D835YFinalMatrix, - file=Second_unshared_subbackfreq, - quote=FALSE, sep=",", - row.names=FALSE,col.names = FALSE, na="", append=TRUE) -} -
--- a/all stuff/Difference finderMADE 7 TO 7 fastversion 2-14-2019.R Fri Apr 19 16:55:29 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,453 +0,0 @@ -#I should make an SOP for this. Problems we encountered: no x in the xY motif, and the kilodemon -#the output files have both Y and xY, they shouldn't why is that happening? make it not happen -#make sure that accession numbers stay locked to each motif, somehow -#output should look just like the KALIP input -#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) -# } -# } -# } \ No newline at end of file
--- a/all stuff/Difference finderMADE 7 TO 7 fastversion.R Fri Apr 19 16:55:29 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,451 +0,0 @@ -#I should make an SOP for this. Problems we encountered: no x in the xY motif, and the kilodemon -#the output files have both Y and xY, they shouldn't why is that happening? make it not happen -#make sure that accession numbers stay locked to each motif, somehow -#output should look just like the KALIP input -#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("pka_minus_wo_vector_subs.csv", stringsAsFactors=FALSE) -Firstsubbackfreq<- read.csv("pka_minus_wo_vector_sbf.csv", header=FALSE, stringsAsFactors=FALSE) - -SecondSubstrateSet<- read.csv("pka_plus_wo_vector_substrates.csv", stringsAsFactors=FALSE) -Secondsubbackfreq<- read.csv("pka_plus_wo_vector_sbf.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=lastthree123, ignore.case = TRUE) - - #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) -# } -# } -# } \ No newline at end of file
--- a/all stuff/difference finder for 2 overlaps proper names 7-7_1-15-2019.R Fri Apr 19 16:55:29 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,547 +0,0 @@ -#Difference finder for only 2 - -#ff you want ONLY FULL MOTIFS, put "YES" here, please use all caps -FullMotifsOnly_questionmark<-"NO" -#If you want ONLY TRUNCATED MOTIFS, put "YES" here, please use all caps -TruncatedMotifsOnly_questionmark<-"NO" - -FirstSubstrateSet<- read.csv("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) - -First_unshared_motifs_table<-"Substrates 1A no duplicates no negatives.csv" -First_unshared_subbackfreq<-"SBF 1A no duplicates no negatives.csv" - -Second_unshared_motifs_table<-"Substrates 1B no duplicates no negatives.csv" -Second_unshared_subbackfreq<-"SBF 1B no duplicates no negatives.csv" - - -LeftOfYLetters<-7 -RightOfYLetters<-7 - -if (FullMotifsOnly_questionmark=="YES"){ - FirstMotifs=rep(NA,times=nrow(FirstSubstrateSet)) - FirstAccessionNumbers=rep(NA,times=nrow(FirstSubstrateSet)) - leftspaces<-c() - rightspaces<-c() - for (i in 1:nrow(FirstSubstrateSet)){ - FirstLetters<-FirstSubstrateSet[i,7:15] - FirstLetters<-FirstLetters[FirstLetters !="XXXXX"] - FirstLetters<-paste(FirstLetters, sep="", collapse="") - - - YYYmotif <- unlist(strsplit(FirstLetters, split = "")) - YYYposition <- match(x = "x", table = YYYmotif) - #position itself tells me how much is to the left of that X by what it's number is. x at position 4 tells me that there are - #just 3 letters to the left of x - - YYYLettersToTheLeft <- YYYposition - 1 - #how many letters to the right SHOULD just be length(motif)-position-1 if it's 5 long and x is at 3 then Y is at 4 and there is - #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1 - YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1 - #then sanity check, we're currently looking only at +/-4, but this spot allows for up to +/- 7 as well, just depends on what the - #variable the user puts in is - - if (YYYLettersToTheLeft > 3 && YYYLettersToTheRight > 3) { - motif<-YYYmotif - #save that motif, which is the Y and +/- 4 amino acids, including truncation - motif<-motif[!motif %in% "x"] - motif<-paste(motif, sep="", collapse="") - FirstLetters<-motif - FirstMotifs[i]<-FirstLetters - FirstAccessionNumbers[i]<-FirstSubstrateSet[i,3] - } - - } - # FirstMotifs <- FirstMotifs[!is.na(FirstMotifs)] - # FirstMotifs<-matrix(FirstMotifs,ncol = 1) - # - - SecondMotifs=rep(NA,times=nrow(FirstSubstrateSet)) - SecondAccessionNumbers=rep(NA,times=nrow(FirstSubstrateSet)) - - for (i in 1:nrow(SecondSubstrateSet)){ - SecondLetters<-SecondSubstrateSet[i,7:15] - SecondLetters<-SecondLetters[SecondLetters !="XXXXX"] - SecondLetters<-paste(SecondLetters, sep="", collapse="") - - - YYYmotif <- unlist(strsplit(SecondLetters, split = "")) - YYYposition <- match(x = "x", table = YYYmotif) - #position itself tells me how much is to the left of that X by what it's number is. x at position 4 tells me that there are - #just 3 letters to the left of x - - YYYLettersToTheLeft <- YYYposition - 1 - #how many letters to the right SHOULD just be length(motif)-position-1 if it's 5 long and x is at 3 then Y is at 4 and there is - #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1 - YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1 - #then sanity check, we're currently looking only at +/-4, but this spot allows for up to +/- 7 as well, just depends on what the - #variable the user puts in is - - if (YYYLettersToTheLeft > 3 && YYYLettersToTheRight > 3) { - motif<-YYYmotif - #add blank spaces if the motif has less than 4 letters to the left/right - motif<-c(leftspaces,YYYmotif,rightspaces) - #save that motif, which is the Y and +/- 4 amino acids, including truncation - motif<-motif[!motif %in% "x"] - motif<-paste(motif, sep="", collapse="") - SecondLetters<-motif - SecondMotifs[i]<-SecondLetters - SecondAccessionNumbers[i]<-SecondSubstrateSet[i,3] - } - } - names(FirstMotifs)<-FirstAccessionNumbers - names(SecondMotifs)<-SecondAccessionNumbers - - -# ITDmotifs=rep(NA,times=nrow(FirstSubstrateSet)) -# ITDAccessionNumbers=rep(NA,times=nrow(FirstSubstrateSet)) - if(1==0){ - for (i in 1:nrow(ThirdSubstrateSet)){ - ITDletters<-ThirdSubstrateSet[i,7:15] - ITDletters<-ITDletters[ITDletters !="XXXXX"] - ITDletters<-paste(ITDletters, sep="", collapse="") - YYYmotif <- unlist(strsplit(ITDletters, split = "")) - YYYposition <- match(x = "x", table = YYYmotif) - #position itself tells me how much is to the left of that X by what it's number is. x at position 4 tells me that there are - #just 3 letters to the left of x - - YYYLettersToTheLeft <- YYYposition - 1 - #how many letters to the right SHOULD just be length(motif)-position-1 if it's 5 long and x is at 3 then Y is at 4 and there is - #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1 - YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1 - #then sanity check, we're currently looking only at +/-4, but this spot allows for up to +/- 7 as well, just depends on what the - #variable the user puts in is - - if (YYYLettersToTheLeft > 3 && YYYLettersToTheRight > 3) { - motif<-YYYmotif - #add blank spaces if the motif has less than 4 letters to the left/right - motif<-c(leftspaces,YYYmotif,rightspaces) - #save that motif, which is the Y and +/- 4 amino acids, including truncation - motif<-motif[!motif %in% "x"] - motif<-paste(motif, sep="", collapse="") - ITDletters<-motif - ITDmotifs[i]<-ITDletters - ITDAccessionNumbers[i]<-ThirdSubstrateSet[i,3] - - } - } - } - #names(ITDmotifs)<-ITDAccessionNumbers - names(SecondMotifs)<-SecondAccessionNumbers - names(FirstMotifs)<-FirstAccessionNumbers -} - - -##############################################3 -#Truncated only -if (TruncatedMotifsOnly_questionmark=="YES"){ - FirstMotifs=matrix(,nrow = nrow(FirstSubstrateSet),ncol=1) - FirstAccessionNumbers=matrix(,nrow = nrow(FirstSubstrateSet),ncol=1) - - for (i in 1:nrow(FirstSubstrateSet)){ - FirstLetters<-FirstSubstrateSet[i,7:15] - FirstLetters<-FirstLetters[FirstLetters !="XXXXX"] - FirstLetters<-paste(FirstLetters, sep="", collapse="") - - - YYYmotif <- unlist(strsplit(FirstLetters, split = "")) - YYYposition <- match(x = "x", table = YYYmotif) - #position itself tells me how much is to the left of that X by what it's number is. x at position 4 tells me that there are - #just 3 letters to the left of x - - YYYLettersToTheLeft <- YYYposition - 1 - #how many letters to the right SHOULD just be length(motif)-position-1 if it's 5 long and x is at 3 then Y is at 4 and there is - #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1 - YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1 - #then sanity check, we're currently looking only at +/-4, but this spot allows for up to +/- 7 as well, just depends on what the - #variable the user puts in is - - if (YYYLettersToTheLeft < 4 | YYYLettersToTheRight < 4) { - leftspaces<-rep(" ",times=(4-YYYLettersToTheLeft)) - rightspaces<-rep(" ",times=4-(YYYLettersToTheRight)) - #add blank spaces if the motif has less than 4 letters to the left/right - motif<-c(leftspaces,YYYmotif,rightspaces) - #save that motif, which is the Y and +/- 4 amino acids, including truncation - motif<-motif[!motif %in% "x"] - motif<-paste(motif, sep="", collapse="") - FirstLetters<-motif - FirstMotifs[i,1]<-FirstLetters - FirstAccessionNumbers[i,1]<-FirstSubstrateSet[i,3] - } - - } - - SecondMotifs=matrix(,nrow = nrow(SecondSubstrateSet),ncol=1) - SecondAccessionNumbers<-matrix(,nrow = nrow(SecondSubstrateSet),ncol = 1) - i=2 - for (i in 1:nrow(SecondSubstrateSet)){ - SecondLetters<-SecondSubstrateSet[i,7:15] - SecondLetters<-SecondLetters[SecondLetters !="XXXXX"] - SecondLetters<-paste(SecondLetters, sep="", collapse="") - - - YYYmotif <- unlist(strsplit(SecondLetters, split = "")) - YYYposition <- match(x = "x", table = YYYmotif) - #position itself tells me how much is to the left of that X by what it's number is. x at position 4 tells me that there are - #just 3 letters to the left of x - - YYYLettersToTheLeft <- YYYposition - 1 - #how many letters to the right SHOULD just be length(motif)-position-1 if it's 5 long and x is at 3 then Y is at 4 and there is - #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1 - YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1 - #then sanity check, we're currently looking only at +/-4, but this spot allows for up to +/- 7 as well, just depends on what the - #variable the user puts in is - - if (YYYLettersToTheLeft < 4 | YYYLettersToTheRight < 4) { - leftspaces<-rep(" ",times=(4-YYYLettersToTheLeft)) - rightspaces<-rep(" ",times=4-(YYYLettersToTheRight)) - #add blank spaces if the motif has less than 4 letters to the left/right - motif<-c(leftspaces,YYYmotif,rightspaces) - #save that motif, which is the Y and +/- 4 amino acids, including truncation - motif<-motif[!motif %in% "x"] - motif<-paste(motif, sep="", collapse="") - SecondLetters<-motif - SecondAccessionNumbers[i,1]<-SecondSubstrateSet[i,3] - SecondMotifs[i,1]<-SecondLetters - } - } - -# ITDmotifs=matrix(,nrow = nrow(ThirdSubstrateSet),ncol=1) -# ITDAccessionNumbers<-matrix(,nrow = nrow(ThirdSubstrateSet)) - if(1==0){ - for (i in 1:nrow(ThirdSubstrateSet)){ - ITDletters<-ThirdSubstrateSet[i,7:15] - ITDletters<-ITDletters[ITDletters !="XXXXX"] - ITDletters<-paste(ITDletters, sep="", collapse="") - YYYmotif <- unlist(strsplit(ITDletters, split = "")) - YYYposition <- match(x = "x", table = YYYmotif) - #position itself tells me how much is to the left of that X by what it's number is. x at position 4 tells me that there are - #just 3 letters to the left of x - - YYYLettersToTheLeft <- YYYposition - 1 - #how many letters to the right SHOULD just be length(motif)-position-1 if it's 5 long and x is at 3 then Y is at 4 and there is - #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1 - YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1 - #then sanity check, we're currently looking only at +/-4, but this spot allows for up to +/- 7 as well, just depends on what the - #variable the user puts in is - - if (YYYLettersToTheLeft < 4 | YYYLettersToTheRight < 4) { - leftspaces<-rep(" ",times=(4-YYYLettersToTheLeft)) - rightspaces<-rep(" ",times=4-(YYYLettersToTheRight)) - #add blank spaces if the motif has less than 4 letters to the left/right - motif<-c(leftspaces,YYYmotif,rightspaces) - #save that motif, which is the Y and +/- 4 amino acids, including truncation - motif<-motif[!motif %in% "x"] - motif<-paste(motif, sep="", collapse="") - ITDletters<-motif - ITDAccessionNumbers[i,1]<-ThirdSubstrateSet[i,3] - ITDmotifs[i,1]<-ITDletters - } - } - } - names(FirstMotifs)<-FirstAccessionNumbers - names(SecondMotifs)<-SecondAccessionNumbers - #names(ITDmotifs)<-ITDAccessionNumbers -} - -############################################### -#ALL motifs, full and truncated - -if (FullMotifsOnly_questionmark!="YES"&&TruncatedMotifsOnly_questionmark!="YES"){ - #print("!")} - FirstMotifs=matrix(,nrow = nrow(FirstSubstrateSet),ncol=1) - FirstAccessionNumbers=matrix(,nrow = nrow(FirstSubstrateSet),ncol=1) - - for (i in 1:nrow(FirstSubstrateSet)){ - FirstLetters<-FirstSubstrateSet[i,7:15] - FirstLetters<-FirstLetters[FirstLetters !="XXXXX"] - FirstLetters<-paste(FirstLetters, sep="", collapse="") - leftspaces<-c() - rightspaces<-c() - - YYYmotif <- unlist(strsplit(FirstLetters, split = "")) - YYYposition <- match(x = "x", table = YYYmotif) - #position itself tells me how much is to the left of that X by what it's number is. x at position 4 tells me that there are - #just 3 letters to the left of x - - YYYLettersToTheLeft <- YYYposition - 1 - #how many letters to the right SHOULD just be length(motif)-position-1 if it's 5 long and x is at 3 then Y is at 4 and there is - #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1 - YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1 - #then sanity check, we're currently looking only at +/-4, but this spot allows for up to +/- 7 as well, just depends on what the - #variable the user puts in is - - - if (YYYLettersToTheLeft < 4 | YYYLettersToTheRight < 4) { - leftspaces<-rep(" ",times=(4-YYYLettersToTheLeft)) - rightspaces<-rep(" ",times=4-(YYYLettersToTheRight)) - #add blank spaces if the motif has less than 4 letters to the left/right - motif<-c(leftspaces,YYYmotif,rightspaces) - #save that motif, which is the Y and +/- 4 amino acids, including truncation - motif<-motif[!motif %in% "x"] - motif<-paste(motif, sep="", collapse="") - FirstLetters<-motif - FirstMotifs[i,1]<-FirstLetters - FirstAccessionNumbers[i,1]<-FirstSubstrateSet[i,3] - } - - if(YYYLettersToTheLeft>3 && YYYLettersToTheRight>3){ - motif<-YYYmotif - #add blank spaces if the motif has less than 4 letters to the left/right - motif<-c(leftspaces,YYYmotif,rightspaces) - #save that motif, which is the Y and +/- 4 amino acids, including truncation - motif<-motif[!motif %in% "x"] - motif<-paste(motif, sep="", collapse="") - FirstLetters<-motif - FirstMotifs[i,1]<-FirstLetters - FirstAccessionNumbers[i,1]<-FirstSubstrateSet[i,3] - - - } - - } - - SecondMotifs=matrix(,nrow = nrow(SecondSubstrateSet),ncol=1) - SecondAccessionNumbers<-matrix(,nrow = nrow(SecondSubstrateSet),ncol = 1) - - for (i in 1:nrow(SecondSubstrateSet)){ - SecondLetters<-SecondSubstrateSet[i,7:15] - SecondLetters<-SecondLetters[SecondLetters !="XXXXX"] - SecondLetters<-paste(SecondLetters, sep="", collapse="") - leftspaces<-c() - rightspaces<-c() - - YYYmotif <- unlist(strsplit(SecondLetters, split = "")) - YYYposition <- match(x = "x", table = YYYmotif) - #position itself tells me how much is to the left of that X by what it's number is. x at position 4 tells me that there are - #just 3 letters to the left of x - - YYYLettersToTheLeft <- YYYposition - 1 - #how many letters to the right SHOULD just be length(motif)-position-1 if it's 5 long and x is at 3 then Y is at 4 and there is - #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1 - YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1 - #then sanity check, we're currently looking only at +/-4, but this spot allows for up to +/- 7 as well, just depends on what the - #variable the user puts in is - if (YYYLettersToTheLeft < 4 | YYYLettersToTheRight < 4) { - leftspaces<-rep(" ",times=(4-YYYLettersToTheLeft)) - rightspaces<-rep(" ",times=4-(YYYLettersToTheRight)) - #add blank spaces if the motif has less than 4 letters to the left/right - motif<-c(leftspaces,YYYmotif,rightspaces) - #save that motif, which is the Y and +/- 4 amino acids, including truncation - motif<-motif[!motif %in% "x"] - motif<-paste(motif, sep="", collapse="") - SecondLetters<-motif - SecondMotifs[i,1]<-SecondLetters - SecondAccessionNumbers[i,1]<-SecondSubstrateSet[i,3] - } - - if(YYYLettersToTheLeft>3 && YYYLettersToTheRight>3){ - motif<-YYYmotif - #add blank spaces if the motif has less than 4 letters to the left/right - motif<-c(leftspaces,YYYmotif,rightspaces) - #save that motif, which is the Y and +/- 4 amino acids, including truncation - motif<-motif[!motif %in% "x"] - motif<-paste(motif, sep="", collapse="") - SecondLetters<-motif - SecondMotifs[i,1]<-SecondLetters - SecondAccessionNumbers[i,1]<-SecondSubstrateSet[i,3] - } - } - - - #ITDmotifs=matrix(,nrow = nrow(ThirdSubstrateSet),ncol=1) - #ITDAccessionNumbers<-matrix(,nrow = nrow(ThirdSubstrateSet)) - if(1==0){ - for (i in 1:nrow(ThirdSubstrateSet)){ - ITDletters<-ThirdSubstrateSet[i,7:15] - ITDletters<-ITDletters[ITDletters !="XXXXX"] - ITDletters<-paste(ITDletters, sep="", collapse="") - YYYmotif <- unlist(strsplit(ITDletters, split = "")) - leftspaces<-c() - rightspaces<-c() - YYYposition <- match(x = "x", table = YYYmotif) - #position itself tells me how much is to the left of that X by what it's number is. x at position 4 tells me that there are - #just 3 letters to the left of x - - YYYLettersToTheLeft <- YYYposition - 1 - #how many letters to the right SHOULD just be length(motif)-position-1 if it's 5 long and x is at 3 then Y is at 4 and there is - #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1 - YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1 - #then sanity check, we're currently looking only at +/-4, but this spot allows for up to +/- 7 as well, just depends on what the - #variable the user puts in is - if (YYYLettersToTheLeft < 4 | YYYLettersToTheRight < 4) { - leftspaces<-rep(" ",times=(4-YYYLettersToTheLeft)) - rightspaces<-rep(" ",times=4-(YYYLettersToTheRight)) - #add blank spaces if the motif has less than 4 letters to the left/right - motif<-c(leftspaces,YYYmotif,rightspaces) - #save that motif, which is the Y and +/- 4 amino acids, including truncation - motif<-motif[!motif %in% "x"] - motif<-paste(motif, sep="", collapse="") - ITDletters<-motif - ITDmotifs[i,1]<-ITDletters - ITDAccessionNumbers[i,1]<-FirstSubstrateSet[i,3] - } - - if(YYYLettersToTheLeft>3 && YYYLettersToTheRight>3){ - motif<-YYYmotif - #add blank spaces if the motif has less than 4 letters to the left/right - motif<-c(leftspaces,YYYmotif,rightspaces) - #save that motif, which is the Y and +/- 4 amino acids, including truncation - motif<-motif[!motif %in% "x"] - motif<-paste(motif, sep="", collapse="") - ITDletters<-motif - ITDmotifs[i,1]<-ITDletters - ITDAccessionNumbers[i,1]<-FirstSubstrateSet[i,3] - } - } - } - names(FirstMotifs)<-FirstAccessionNumbers - names(SecondMotifs)<-SecondAccessionNumbers - #names(ITDmotifs)<-ITDAccessionNumbers -} - - -FirstMotifsFINAL<-FirstMotifs[!FirstMotifs %in% SecondMotifs] -#FirstMotifsFINAL<-FirstMotifsFINAL[!FirstMotifsFINAL %in% ITDmotifs] -FirstMotifsFINAL<-FirstMotifsFINAL[!duplicated(FirstMotifsFINAL)] - - -# ITDmotifsFINAL<-ITDmotifs[!ITDmotifs %in% SecondMotifs] -# ITDmotifsFINAL<-ITDmotifsFINAL[!ITDmotifsFINAL %in% FirstMotifs] -# ITDmotifsFINAL<-ITDmotifsFINAL[!duplicated(ITDmotifsFINAL)] - - -SecondMotifsFINAL<-SecondMotifs[!SecondMotifs %in% FirstMotifs] -#SecondMotifsFINAL<-SecondMotifsFINAL[!SecondMotifsFINAL %in% ITDmotifs] -SecondMotifsFINAL<-SecondMotifsFINAL[!duplicated(SecondMotifsFINAL)] - - -columnalheader<-c(rep(NA,36)) -FirstFinalMatrix<-matrix(data =columnalheader,nrow = 1) - -for (k in 1:length(FirstMotifsFINAL)) { - AN<-00000 - #I don't remember why, but I felt it necessary to destroy the accession number multiple times to ensure it is - #destroyed immediately after use - for (m in 2:ncol(Firstsubbackfreq)) { - AN <- as.character(Firstsubbackfreq[2, m]) - #print(AN)} - if (grepl(pattern = AN, - x = names(FirstMotifsFINAL[k]), - fixed = TRUE) == TRUE) { - outputmatrix <- as.character(Firstsubbackfreq[, m]) - outputmatrix <- matrix(outputmatrix, nrow = 1) - #with that accession number, find a match in the subbackfreq file and save it here - FirstFinalMatrix<-rbind(FirstFinalMatrix,outputmatrix) - # print(AN,outputmatrix)} - } - } -} -FirstFinalMatrix<-FirstFinalMatrix[!duplicated(FirstFinalMatrix),] - -#columnalheader<-c(rep(NA,36)) -#ITDFinalMatrix<-matrix(data =columnalheader,nrow = 1) - -if(1==0){ - for (k in 1:length(ITDmotifsFINAL)) { - AN<-00000 - #I don't remember why, but I felt it necessary to destroy the accession number multiple times to ensure it is - #destroyed immediately after use - for (m in 1:ncol(Thirdsubbackfreq)) { - AN <- as.character(Thirdsubbackfreq[1, m]) - if (grepl(pattern = AN, - x = names(ITDmotifsFINAL[k]), - fixed = TRUE) == TRUE) { - outputmatrix <- as.character(Thirdsubbackfreq[, m]) - outputmatrix <- matrix(outputmatrix, nrow = 1) - #with that accession number, find a match in the subbackfreq file and save it here - ITDFinalMatrix<-rbind(ITDFinalMatrix,outputmatrix) - } - } - } - ITDFinalMatrix<-ITDFinalMatrix[!duplicated(ITDFinalMatrix),] -} - -columnalheader<-c(rep(NA,36)) -SecondFinalMatrix<-matrix(data =columnalheader,nrow = 1) - -for (k in 1:length(SecondMotifsFINAL)) { - #I don't remember why, but I felt it necessary to destroy the accession number multiple times to ensure it is - #destroyed immediately after use - for (m in 1:ncol(Secondsubbackfreq)) { - AN <- as.character(Secondsubbackfreq[1, m]) - if (grepl(pattern = AN, - x = names(SecondMotifsFINAL[k]), - fixed = TRUE) == TRUE) { - outputmatrix <- as.character(Secondsubbackfreq[, m]) - outputmatrix <- matrix(outputmatrix, nrow = 1) - #with that accession number, find a match in the subbackfreq file and save it here - SecondFinalMatrix<-rbind(SecondFinalMatrix,outputmatrix) - } - } -} -SecondFinalMatrix<-SecondFinalMatrix[!duplicated(SecondFinalMatrix),] -FTLoutputmatrix<-matrix(data=c(FirstMotifsFINAL,names(FirstMotifsFINAL)),ncol = 2) - - -write.table(x=FTLoutputmatrix, - file=First_unshared_motifs_table, - quote=FALSE, sep=",", - row.names=FALSE,col.names = FALSE, na="", append=TRUE) - -columnalheader<-c(as.character(Firstsubbackfreq[1:36,1])) -columnalheader<-matrix(columnalheader,nrow = 1) -write.table(x=columnalheader, - file=First_unshared_subbackfreq, - quote=FALSE, sep=",", - row.names=FALSE,col.names = FALSE, na="", append=TRUE) -FirstFinalMatrix<-FirstFinalMatrix[2:nrow(FirstFinalMatrix),] -write.table(x=FirstFinalMatrix, - file=First_unshared_subbackfreq, - quote=FALSE, sep=",", - row.names=FALSE,col.names = FALSE, na="", append=TRUE) - -############################################################################################################ - -D835Youtputmatrix<-matrix(data=c(SecondMotifsFINAL,names(SecondMotifsFINAL)),ncol = 2) - -write.table(x=D835Youtputmatrix, - file=Second_unshared_motifs_table, - quote=FALSE, sep=",", - row.names=FALSE,col.names = FALSE, na="", append=TRUE) - -columnalheader<-c(as.character(Firstsubbackfreq[1:36,1])) -columnalheader<-matrix(columnalheader,nrow = 1) -write.table(x=columnalheader, - file=Second_unshared_subbackfreq, - quote=FALSE, sep=",", - row.names=FALSE,col.names = FALSE, na="", append=TRUE) -SecondFinalMatrix<-SecondFinalMatrix[2:nrow(SecondFinalMatrix),] -write.table(x=SecondFinalMatrix, - file=Second_unshared_subbackfreq, - quote=FALSE, sep=",", - row.names=FALSE,col.names = FALSE, na="", append=TRUE) - -############################################################################################################ - -# ITDoutputmatrix<-matrix(data = c(ITDmotifsFINAL,names(ITDmotifsFINAL)),ncol = 2) -# -# write.table(x=ITDoutputmatrix, -# file=Third_unshared_motifs_table, -# quote=FALSE, sep=",", -# row.names=FALSE,col.names = FALSE, na="", append=TRUE) -# -# columnalheader<-c(as.character(Thirdsubbackfreq[1:36,1])) -# columnalheader<-matrix(columnalheader,nrow = 1) -# write.table(x=columnalheader, -# file=Third_unshared_subbackfreq, -# quote=FALSE, sep=",", -# row.names=FALSE,col.names = FALSE, na="", append=TRUE) -# ITDFinalMatrix<-ITDFinalMatrix[2:nrow(ITDFinalMatrix),] -# write.table(x=ITDFinalMatrix, -# file=Third_unshared_subbackfreq, -# quote=FALSE, sep=",", -# row.names=FALSE,col.names = FALSE, na="", append=TRUE) \ No newline at end of file
--- a/all stuff/differenceFinder.xml Fri Apr 19 16:55:29 2019 -0400 +++ b/all stuff/differenceFinder.xml Fri Feb 21 13:07:45 2020 -0500 @@ -9,7 +9,7 @@ ln -s '$input3' S2.csv && ln -s '$input4' SBF2.csv && - Rscript '$__tool_directory__/Difference finder for GalaxyP 4-18-2019.R' + Rscript '$__tool_directory__/Difference finder for GalaxyP 2-21-20.R' ]]></command> <inputs> <param format="csv" name="input1" type="data" label="First Substrate Set"/>