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comparison all stuff/Difference finderMADE 7 TO 7 fastversion 2-14-2019.R @ 4:74ada21ceb70 draft

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author jfb
date Fri, 19 Apr 2019 14:00:46 -0400
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3:dff99bed3f56 4:74ada21ceb70
1 #I should make an SOP for this. Problems we encountered: no x in the xY motif, and the kilodemon
2 #the output files have both Y and xY, they shouldn't why is that happening? make it not happen
3 #make sure that accession numbers stay locked to each motif, somehow
4 #output should look just like the KALIP input
5 #S2 is negatives
6 #ff you want ONLY FULL MOTIFS, put "YES" here, please use all caps
7 FullMotifsOnly_questionmark<-"NO"
8 #If you want ONLY TRUNCATED MOTIFS, put "YES" here, please use all caps
9 TruncatedMotifsOnly_questionmark<-"NO"
10 #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)
11 Are_You_Looking_For_Commonality<-"NO"
12
13
14 #put the names of your input files here
15 FirstSubstrateSet<- read.csv("Substrates 1A TiO2 and FeNTA no duplicates.csv", stringsAsFactors=FALSE)
16 Firstsubbackfreq<- read.csv("SBF 1A TiO2 and FeNTA no duplicates.csv", header=FALSE, stringsAsFactors=FALSE)
17
18 SecondSubstrateSet<- read.csv("Substrates 1B TiO2 and FeNTA no duplicates.csv", stringsAsFactors=FALSE)
19 Secondsubbackfreq<- read.csv("SBF 1B TiO2 and FeNTA no duplicates.csv", header=FALSE, stringsAsFactors=FALSE)
20
21 # ThirdSubstrateSet<- read.csv("Galaxy69-BTK_PLUS_R3_Substrates.csv", stringsAsFactors=FALSE)
22 # Thirdsubbackfreq<- read.csv("Galaxy70-BTK_PLUS_R3_SubstrateBackgroundFrequency.csv", header=FALSE, stringsAsFactors=FALSE)
23
24 #then put the names of your output files here
25 # Shared_motifs_table<-"180719_GALAXY-BTK-plus-rep-OVLP-7to7-substrates.csv"
26 # Shared_subbackfreq_table<-"180719_GALAXY-BTK-plus-rep-OVLP-7to7-SubBackFreq.csv"
27
28 # Shared_motifs_table<-"Shared motifs 7-27-17.csv"
29 # Shared_subbackfreq_table<-"SubstrateBackgrounFrequency-for-shared-motifs 4 7-27-17.csv"
30
31 First_unshared_motifs_table<-"pka_minus_wo-plus_wo_vector_subs.csv"
32 First_unshared_subbackfreq<-"pka_minus_wo-plus_wo_vector_sbf.csv"
33
34 Second_unshared_motifs_table<-"pka_plus_wo-minus_wo_vector_subs.csv"
35 Second_unshared_subbackfreq<-"pka_plus_wo-minus_wo_vector_sbf.csv"
36
37 # Third_unshared_motifs_table<-"R3 subs.csv"
38 # Third_unshared_subbackfreq<-"R3 SBF.csv"
39
40 #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
41 #other languages to see if any of them can do it.
42 ####################################################################################################################################
43
44
45
46
47
48 # grepl(pattern = "S", x=asdf, ignore.case = TRUE)
49
50 FirstCentralLetters<-FirstSubstrateSet[,11]
51 SecondCentralLetters<-SecondSubstrateSet[,11]
52
53 FirstEsses<-sapply(FirstCentralLetters, grepl, pattern="S", ignore.case=TRUE)
54 FirstTees<-sapply(FirstCentralLetters, grepl, pattern="T", ignore.case=TRUE)
55 FirstWys<-sapply(FirstCentralLetters, grepl, pattern="Y", ignore.case=TRUE)
56
57 SecondEsses<-sapply(SecondCentralLetters, grepl, pattern="S", ignore.case=TRUE)
58 SecondTees<-sapply(SecondCentralLetters, grepl, pattern="T", ignore.case=TRUE)
59 SecondWys<-sapply(SecondCentralLetters, grepl, pattern="Y", ignore.case=TRUE)
60
61 FirstCentralLetters<-replace(FirstCentralLetters,FirstEsses,"xS")
62 FirstCentralLetters<-replace(FirstCentralLetters,FirstTees,"xT")
63 FirstCentralLetters<-replace(FirstCentralLetters,FirstWys,"xY")
64
65 SecondCentralLetters<-replace(SecondCentralLetters,SecondEsses,"xS")
66 SecondCentralLetters<-replace(SecondCentralLetters,SecondTees,"xT")
67 SecondCentralLetters<-replace(SecondCentralLetters,SecondWys,"xY")
68
69 FirstCentralLetters->FirstSubstrateSet[,11]
70 SecondCentralLetters->SecondSubstrateSet[,11]
71
72 ####################################################################################################################################
73 ####################################################################################################################################
74 # better version of this code written in C: what happens when two kinases share a motif, but they found that motif in two
75 # separate proteins thus two separate accession numbers?
76 # It should actually output the shared motif and BOTH accession numbers. Right now it does not, it only maps out the second
77 # accession number. So that needs to be fixed BUT you need to keep the commonality between a motif and its accession number
78 ####################################################################################################################################
79 ####################################################################################################################################
80 ####################################################################################################################################
81 ####################################################################################################################################
82
83 #Create the motif sets, deciding wether or not you're looking for truncated or full here
84 #full only
85
86
87 if (Are_You_Looking_For_Commonality=="NO"){
88
89 ###############################################
90 #ALL motifs, full and truncated
91
92 if (FullMotifsOnly_questionmark!="YES"&&TruncatedMotifsOnly_questionmark!="YES"){
93 # FTLwtmotifs=matrix(,nrow = nrow(FirstSubstrateSet),ncol=1)
94 # FTLwtAccessionNumbers=matrix(,nrow = nrow(FirstSubstrateSet),ncol=1)
95
96 #so what this does is
97 #find the central phospho position and add spaces to either side of it
98 #create a pasted together motif which will be used for difference finding
99 #keep motifs and accession numbers in the same index position of two vectors
100
101 #so instead just take the FLTwt[i,4:18], and replace "" with "O"
102 #then perform paste function
103 #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
104
105 FTLwtmotifs<-FirstSubstrateSet[,4:18]
106 # FTLwtmotifs<-sapply(FTLwtmotifs, gsub, pattern=" ", replacement="O",ignore.case=TRUE)
107 FTLwtmotifs<-replace(FTLwtmotifs, FTLwtmotifs=="", "O")
108 FTLwtmotifs<-apply(FTLwtmotifs, 1, paste, sep="", collapse="")
109 FTLwtAccessionNumbers<-FirstSubstrateSet[,3]
110
111 # D835Ymotifs=matrix(,nrow = nrow(SecondSubstrateSet),ncol=1)
112 # D835YAccessionNumbers<-matrix(,nrow = nrow(SecondSubstrateSet),ncol = 1)
113
114 D835Ymotifs<-SecondSubstrateSet[,4:18]
115 # D835Ymotifs<-sapply(D835Ymotifs, gsub, patter="", replacement="O",ignore.case=TRUE)
116 D835Ymotifs<-replace(D835Ymotifs, D835Ymotifs=="", "O")
117 D835Ymotifs<-replace(D835Ymotifs, D835Ymotifs=="", "O")
118 D835Ymotifs<-apply(D835Ymotifs, 1, paste, sep="", collapse="")
119 D835YAccessionNumbers<-SecondSubstrateSet[,3]
120
121 names(FTLwtmotifs)<-FTLwtAccessionNumbers
122 names(D835Ymotifs)<-D835YAccessionNumbers
123
124 }
125
126
127 FTLwtmotifsFINAL<-FTLwtmotifs[!FTLwtmotifs %in% D835Ymotifs]
128 FTLwtmotifsFINAL<-FTLwtmotifsFINAL[!duplicated(FTLwtmotifsFINAL)]
129
130 D835YmotifsFINAL<-D835Ymotifs[!D835Ymotifs %in% FTLwtmotifs]
131 D835YmotifsFINAL<-D835YmotifsFINAL[!duplicated(D835YmotifsFINAL)]
132
133
134
135 # columnalheader<-c(rep(NA,36))
136 # FTLFinalMatrix<-matrix(data =columnalheader,nrow = 1)
137 #
138 #how to make this an apply
139 #actual first turn names(motifsFINAL) into a vector, then gsub to replace all "|" pipe characters with "*" star characters
140 #first take the accession numbers as Firstsubbackfreq[1,], then gsub to replace all "|" pipe characters with "*" star characters
141 #then use AccessionNumbers as a vector and use
142 #matches <- unique (grep(paste(toMatch,collapse="|"), names(motifsFINAL), value=TRUE))
143
144 FLTwtNames<-names(FTLwtmotifsFINAL)
145 FLTwtNames<-FLTwtNames[!duplicated(FLTwtNames)]
146 #the problem is the names includes a lot of things that are multi names separated by ;
147 #I need to do soem paper writing and poster writing
148
149 FLTwtNames<-gsub(pattern = '\\|', replacement = "*", x=FLTwtNames)
150 FLTwtNames<-paste(FLTwtNames,collapse = "|")
151
152 AccNums<-as.character(Firstsubbackfreq[1,])
153 AccNums<-gsub(pattern = "\\|", replacement = "*", x=AccNums)
154
155
156 firstthree123<-gsub(pattern = "\\|", replacement = "", x=FLTwtNames)
157 lastthree123<-gsub(pattern = "\\|", replacement = "", x=AccNums)
158
159 pasty<-paste(lastthree123,collapse = "|")
160
161 my_matches<-unique(grep(pattern = FLTwtNames, x=AccNums, value = TRUE))
162 # matches <- unique (grep(paste(FLTwtNames,collapse="|"), AccNums, value=TRUE))
163 My_matches<- AccNums %in% FLTwtNames #use apply grep function
164 My_matches<-grep(pattern = pasty, x=firstthree123, ignore.case = TRUE)
165 sensation<-firstthree123[My_matches]
166 what<-firstthree123[!firstthree123 %in% sensation]
167
168 #my matches are which columns in the SBF file still have a motif with them
169 FirstFINALSBF<-Firstsubbackfreq[My_matches]
170 FTLFinalMatrix<-FirstFINALSBF
171 duped<-FTLFinalMatrix[1,]
172 duped<-duped[!duplicated(duped)]
173 names(duped)<-NULL
174 duped<-unlist(duped)
175 unduped<-FTLFinalMatrix[,!duplicated(duped)]
176 FTLFinalMatrix<-unduped
177 # FTLFinalMatrix<-FTLFinalMatrix[2:nrow(FTLFinalMatrix),]
178
179 # columnalheader<-c(rep(NA,36))
180 # D835YFinalMatrix<-matrix(data =columnalheader,nrow = 1)
181
182 D835names<-names(D835YmotifsFINAL)
183 D835names<-D835names[!duplicated(D835names)]
184 AccNums<-as.character(Secondsubbackfreq[1,])
185 My_matches<-AccNums %in% D835names
186 SecondFINALSBF<-Secondsubbackfreq[My_matches]
187 D835YFinalMatrix<-SecondFINALSBF
188 duped<-D835YFinalMatrix[1,]
189 duped<-duped[!duplicated(duped)]
190 names(duped)<-NULL
191 duped<-unlist(duped)
192 unduped<-D835YFinalMatrix[,!duplicated(duped)]
193 D835YFinalMatrix<-unduped
194 #there's a problem, accession numbers are duplicated
195
196 # FTLoutputmatrix<-matrix(data=c(FTLwtmotifsFINAL,names(FTLwtmotifsFINAL)),ncol = 2)
197
198 FTLwtmotifsFINAL<-gsub(pattern = "O", replacement = " ", x=FTLwtmotifsFINAL)
199 FTLwtmotifsFINAL<-gsub(pattern = "x", replacement = "", x=FTLwtmotifsFINAL)
200 FTLoutputmatrix<-matrix(data = c(FTLwtmotifsFINAL,names(FTLwtmotifsFINAL)), ncol=2)
201
202 # FTLwtmotifsFINAL<-gsub(pattern = "O", replacement = " ", x=FTLwtmotifsFINAL)
203 # FTLwtmotifsFINAL<-gsub(pattern = "x", replacement = "", x=FTLwtmotifsFINAL)
204 # FTLoutputmatrix<-matrix(data = c(FTLwtmotifsFINAL,names(FTLwtmotifsFINAL)), ncol=2)
205
206 FLTheader<-c("Substrate","Species","Reference","-7","-6","-5","-4","-3","-2","-1","0","1","2","3","4","5","6","7","Phosphite")
207 # FLTheader<-unlist(FLTheader)
208 lefthandFLT<-matrix(data = rep(NA,times=2*nrow(FTLoutputmatrix)),nrow=nrow(FTLoutputmatrix))
209 righthandFLT<-matrix(data = rep(NA,times=1*nrow(FTLoutputmatrix)),nrow=nrow(FTLoutputmatrix))
210 FLTaccessionset<-FTLoutputmatrix[,2]
211 FTLmeat<-sapply(FTLoutputmatrix[,1], strsplit, "")
212 FTLmeat<-sapply(FTLmeat, unlist)
213 colnames(FTLmeat)<-NULL
214 FTLmeat<-t(FTLmeat)
215
216 FTLoutputmatrix2<-cbind(lefthandFLT,FLTaccessionset,FTLmeat,righthandFLT)
217 colnames(FTLoutputmatrix2)<-NULL
218 rownames(FTLoutputmatrix2)<-NULL
219 colnames(FLTheader)<-NULL
220 rownames(FLTheader)<-NULL
221
222
223 FirstCentralLettersAGAIN<-FTLoutputmatrix2[,11]
224
225 FirstEsses<-sapply(FirstCentralLettersAGAIN, grepl, pattern="S", ignore.case=TRUE)
226 FirstTees<-sapply(FirstCentralLettersAGAIN, grepl, pattern="T", ignore.case=TRUE)
227 FirstWys<-sapply(FirstCentralLettersAGAIN, grepl, pattern="Y", ignore.case=TRUE)
228
229 FirstCentralLettersAGAIN<-replace(FirstCentralLettersAGAIN,FirstEsses,"xS")
230 FirstCentralLettersAGAIN<-replace(FirstCentralLettersAGAIN,FirstTees,"xT")
231 FirstCentralLettersAGAIN<-replace(FirstCentralLettersAGAIN,FirstWys,"xY")
232
233 FirstCentralLettersAGAIN->FTLoutputmatrix2[,11]
234
235 FTLoutputmatrix2<-rbind(FLTheader,FTLoutputmatrix2)
236
237 write.table(x=FTLoutputmatrix2,
238 file=First_unshared_motifs_table,
239 quote=FALSE, sep=",",
240 row.names=FALSE,col.names = FALSE, na="", append=TRUE)
241
242 columnalheader<-c("Accession Numbers",as.character(Firstsubbackfreq[1:35,1]))
243 columnalheader<-matrix(columnalheader,ncol = 1)
244 # write.table(x=columnalheader,
245 # file=First_unshared_subbackfreq,
246 # quote=FALSE, sep=",",
247 # row.names=FALSE,col.names = FALSE, na="", append=TRUE)
248
249 FTLFinalMatrix<-cbind(columnalheader,FTLFinalMatrix)
250
251 write.table(x=FTLFinalMatrix,
252 file=First_unshared_subbackfreq,
253 quote=FALSE, sep=",",
254 row.names=FALSE,col.names = FALSE, na="", append=TRUE)
255
256 ############################################################################################################
257
258 D835YmotifsFINAL<-gsub(pattern = "O", replacement = " ", x=D835YmotifsFINAL)
259 D835YmotifsFINAL<-gsub(pattern = "x", replacement = "", x=D835YmotifsFINAL)
260 D835Youtputmatrix<-matrix(data = c(D835YmotifsFINAL,names(D835YmotifsFINAL)), ncol=2)
261
262 # D835YmotifsFINAL<-gsub(pattern = "O", replacement = " ", x=D835YoutputmatrixL)
263 # D835YmotifsFINAL<-gsub(pattern = "x", replacement = "", x=D835Youtputmatrix)
264 # D835Youtputmatrix<-matrix(data = c(D835Youtputmatrix,names(D835Youtputmatrix)), ncol=2)
265 #
266
267 # D835Youtputmatrix<-matrix(data=c(D835YmotifsFINAL,names(D835YmotifsFINAL)),ncol = 2)
268
269 D835Yheader<-c("Substrate","Species","Reference","-7","-6","-5","-4","-3","-2","-1","0","1","2","3","4","5","6","7","Phosphite")
270 # D835Yheader<-unlist(D835Yheader)
271 lefthandD835<-matrix(data = rep(NA,times=2*nrow(D835Youtputmatrix)),nrow=nrow(D835Youtputmatrix))
272 righthandD835<-matrix(data = rep(NA,times=1*nrow(D835Youtputmatrix)),nrow=nrow(D835Youtputmatrix))
273 D835Yaset<-D835Youtputmatrix[,2]
274 D835meat<-sapply(D835Youtputmatrix[,1], strsplit, "")
275 D835meat<-sapply(D835meat, unlist)
276 colnames(D835meat)<-NULL
277 D835meat<-t(D835meat)
278
279 # FTLmeat<-sapply(FTLoutputmatrix[,1], strsplit, "")
280 # FTLmeat<-sapply(FTLmeat, unlist)
281 # colnames(FTLmeat)<-NULL
282 # FTLmeat<-t(FTLmeat)
283
284
285 D835Youtputmatrix2<-cbind(lefthandD835,D835Yaset,D835meat,righthandD835)
286 colnames(D835Youtputmatrix2)<-NULL
287 rownames(D835Youtputmatrix2)<-NULL
288 colnames(D835Yheader)<-NULL
289 rownames(D835Yheader)<-NULL
290
291
292 SecondCentralLettersAGAIN<-D835Youtputmatrix2[,11]
293
294 SecondEsses<-sapply(SecondCentralLettersAGAIN, grepl, pattern="S", ignore.case=TRUE)
295 SecondTees<-sapply(SecondCentralLettersAGAIN, grepl, pattern="T", ignore.case=TRUE)
296 SecondWys<-sapply(SecondCentralLettersAGAIN, grepl, pattern="Y", ignore.case=TRUE)
297
298 SecondCentralLettersAGAIN<-replace(SecondCentralLettersAGAIN,SecondEsses,"xS")
299 SecondCentralLettersAGAIN<-replace(SecondCentralLettersAGAIN,SecondTees,"xT")
300 SecondCentralLettersAGAIN<-replace(SecondCentralLettersAGAIN,SecondWys,"xY")
301
302 SecondCentralLettersAGAIN->D835Youtputmatrix2[,11]
303
304 D835Youtputmatrix2<-rbind(D835Yheader,D835Youtputmatrix2)
305
306 write.table(x=D835Youtputmatrix2,
307 file=Second_unshared_motifs_table,
308 quote=FALSE, sep=",",
309 row.names=FALSE,col.names = FALSE, na="", append=TRUE)
310
311 columnalheader<-c("Accession Numbers",as.character(Firstsubbackfreq[1:35,1]))
312 columnalheader<-matrix(columnalheader,ncol = 1)
313 # write.table(x=columnalheader,
314 # file=Second_unshared_subbackfreq,
315 # quote=FALSE, sep=",",
316 # row.names=FALSE,col.names = FALSE, na="", append=TRUE)
317
318 D835YFinalMatrix<-cbind(columnalheader,D835YFinalMatrix)
319
320 write.table(x=D835YFinalMatrix,
321 file=Second_unshared_subbackfreq,
322 quote=FALSE, sep=",",
323 row.names=FALSE,col.names = FALSE, na="", append=TRUE)
324 }
325
326
327
328 # for (i in 1:nrow(FirstSubstrateSet)){
329 # FTLwtletters<-FirstSubstrateSet[i,4:18]
330 # FTLwtletters<-FTLwtletters[FTLwtletters !="XXXXX"]
331 # FTLwtletters<-paste(FTLwtletters, sep="", collapse="")
332 # leftspaces<-c()
333 # rightspaces<-c()
334 #
335 # YYYmotif <- unlist(strsplit(FTLwtletters, split = ""))
336 # YYYposition <- match(x = "x", table = YYYmotif)
337 # #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
338 # #just 3 letters to the left of x
339 #
340 # YYYLettersToTheLeft <- YYYposition - 1
341 # #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
342 # #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1
343 # YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1
344 # #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
345 # #variable the user puts in is
346 #
347 #
348 # if (YYYLettersToTheLeft < 7 | YYYLettersToTheRight < 7) {
349 # leftspaces<-rep(" ",times=(7-YYYLettersToTheLeft))
350 # rightspaces<-rep(" ",times=7-(YYYLettersToTheRight))
351 # #add blank spaces if the motif has less than 4 letters to the left/right
352 # motif<-c(leftspaces,YYYmotif,rightspaces)
353 # #save that motif, which is the Y and +/- 4 amino acids, including truncation
354 # motif<-motif[!motif %in% "x"]
355 # motif<-paste(motif, sep="", collapse="")
356 # FTLwtletters<-motif
357 # FTLwtmotifs[i,1]<-FTLwtletters
358 # FTLwtAccessionNumbers[i,1]<-FirstSubstrateSet[i,3]
359 # }
360 #
361 # if(YYYLettersToTheLeft>6 && YYYLettersToTheRight>6){
362 # motif<-YYYmotif
363 # #add blank spaces if the motif has less than 4 letters to the left/right
364 # motif<-c(leftspaces,YYYmotif,rightspaces)
365 # #save that motif, which is the Y and +/- 4 amino acids, including truncation
366 # motif<-motif[!motif %in% "x"]
367 # motif<-paste(motif, sep="", collapse="")
368 # FTLwtletters<-motif
369 # FTLwtmotifs[i,1]<-FTLwtletters
370 # FTLwtAccessionNumbers[i,1]<-FirstSubstrateSet[i,3]
371 #
372 #
373 # }
374 #
375 # }
376
377
378
379 # for (i in 1:nrow(SecondSubstrateSet)){
380 # D835letters<-SecondSubstrateSet[i,4:18]
381 # D835letters<-D835letters[D835letters !="XXXXX"]
382 # D835letters<-paste(D835letters, sep="", collapse="")
383 # leftspaces<-c()
384 # rightspaces<-c()
385 #
386 # YYYmotif <- unlist(strsplit(D835letters, split = ""))
387 # YYYposition <- match(x = "x", table = YYYmotif)
388 # #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
389 # #just 3 letters to the left of x
390 #
391 # YYYLettersToTheLeft <- YYYposition - 1
392 # #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
393 # #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1
394 # YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1
395 # #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
396 # #variable the user puts in is
397 # if (YYYLettersToTheLeft < 7 | YYYLettersToTheRight < 7) {
398 # leftspaces<-rep(" ",times=(7-YYYLettersToTheLeft))
399 # rightspaces<-rep(" ",times=7-(YYYLettersToTheRight))
400 # #add blank spaces if the motif has less than 4 letters to the left/right
401 # motif<-c(leftspaces,YYYmotif,rightspaces)
402 # #save that motif, which is the Y and +/- 4 amino acids, including truncation
403 # motif<-motif[!motif %in% "x"]
404 # motif<-paste(motif, sep="", collapse="")
405 # D835letters<-motif
406 # D835Ymotifs[i,1]<-D835letters
407 # D835YAccessionNumbers[i,1]<-FirstSubstrateSet[i,3]
408 # }
409 #
410 # if(YYYLettersToTheLeft>6 && YYYLettersToTheRight>6){
411 # motif<-YYYmotif
412 # #add blank spaces if the motif has less than 4 letters to the left/right
413 # motif<-c(leftspaces,YYYmotif,rightspaces)
414 # #save that motif, which is the Y and +/- 4 amino acids, including truncation
415 # motif<-motif[!motif %in% "x"]
416 # motif<-paste(motif, sep="", collapse="")
417 # D835letters<-motif
418 # D835Ymotifs[i,1]<-D835letters
419 # D835YAccessionNumbers[i,1]<-FirstSubstrateSet[i,3]
420 # }
421 # }
422
423 # for (k in 1:length(FTLwtmotifsFINAL)) {
424 # AN<-00000
425 # #I don't remember why, but I felt it necessary to destroy the accession number multiple times to ensure it is
426 # #destroyed immediately after use
427 # for (m in 1:ncol(Firstsubbackfreq)) {
428 # AN <- as.character(Firstsubbackfreq[1, m])
429 # if (grepl(pattern = AN,
430 # x = names(FTLwtmotifsFINAL[k]),
431 # fixed = TRUE) == TRUE) {
432 # outputmatrix <- as.character(Firstsubbackfreq[, m])
433 # outputmatrix <- matrix(outputmatrix, nrow = 1)
434 # #with that accession number, find a match in the subbackfreq file and save it here
435 # FTLFinalMatrix<-rbind(FTLFinalMatrix,outputmatrix)
436 # }
437 # }
438 # }
439 # for (k in 1:length(D835YmotifsFINAL)) {
440 # #I don't remember why, but I felt it necessary to destroy the accession number multiple times to ensure it is
441 # #destroyed immediately after use
442 # for (m in 1:ncol(Secondsubbackfreq)) {
443 # AN <- as.character(Secondsubbackfreq[1, m])
444 # if (grepl(pattern = AN,
445 # x = names(D835YmotifsFINAL[k]),
446 # fixed = TRUE) == TRUE) {
447 # outputmatrix <- as.character(Secondsubbackfreq[, m])
448 # outputmatrix <- matrix(outputmatrix, nrow = 1)
449 # #with that accession number, find a match in the subbackfreq file and save it here
450 # D835YFinalMatrix<-rbind(D835YFinalMatrix,outputmatrix)
451 # }
452 # }
453 # }