Mercurial > repos > jfb > difference_finder

comparison all stuff/difference finder for 2 overlaps proper names 7-7_1-15-2019.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 #Difference finder for only 2
2
3 #ff you want ONLY FULL MOTIFS, put "YES" here, please use all caps
4 FullMotifsOnly_questionmark<-"NO"
5 #If you want ONLY TRUNCATED MOTIFS, put "YES" here, please use all caps
6 TruncatedMotifsOnly_questionmark<-"NO"
7
8 FirstSubstrateSet<- read.csv("Substrates 1A TiO2 and FeNTA no duplicates.csv", stringsAsFactors=FALSE)
9 Firstsubbackfreq<- read.csv("SBF 1A TiO2 and FeNTA no duplicates.csv", header=FALSE, stringsAsFactors=FALSE)
10
11 SecondSubstrateSet<- read.csv("Substrates 1B TiO2 and FeNTA no duplicates.csv", stringsAsFactors=FALSE)
12 Secondsubbackfreq<- read.csv("SBF 1B TiO2 and FeNTA no duplicates.csv", header=FALSE, stringsAsFactors=FALSE)
13
14 First_unshared_motifs_table<-"Substrates 1A no duplicates no negatives.csv"
15 First_unshared_subbackfreq<-"SBF 1A no duplicates no negatives.csv"
16
17 Second_unshared_motifs_table<-"Substrates 1B no duplicates no negatives.csv"
18 Second_unshared_subbackfreq<-"SBF 1B no duplicates no negatives.csv"
19
20
21 LeftOfYLetters<-7
22 RightOfYLetters<-7
23
24 if (FullMotifsOnly_questionmark=="YES"){
25 FirstMotifs=rep(NA,times=nrow(FirstSubstrateSet))
26 FirstAccessionNumbers=rep(NA,times=nrow(FirstSubstrateSet))
27 leftspaces<-c()
28 rightspaces<-c()
29 for (i in 1:nrow(FirstSubstrateSet)){
30 FirstLetters<-FirstSubstrateSet[i,7:15]
31 FirstLetters<-FirstLetters[FirstLetters !="XXXXX"]
32 FirstLetters<-paste(FirstLetters, sep="", collapse="")
33
34
35 YYYmotif <- unlist(strsplit(FirstLetters, split = ""))
36 YYYposition <- match(x = "x", table = YYYmotif)
37 #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
38 #just 3 letters to the left of x
39
40 YYYLettersToTheLeft <- YYYposition - 1
41 #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
42 #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1
43 YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1
44 #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
45 #variable the user puts in is
46
47 if (YYYLettersToTheLeft > 3 && YYYLettersToTheRight > 3) {
48 motif<-YYYmotif
49 #save that motif, which is the Y and +/- 4 amino acids, including truncation
50 motif<-motif[!motif %in% "x"]
51 motif<-paste(motif, sep="", collapse="")
52 FirstLetters<-motif
53 FirstMotifs[i]<-FirstLetters
54 FirstAccessionNumbers[i]<-FirstSubstrateSet[i,3]
55 }
56
57 }
58 # FirstMotifs <- FirstMotifs[!is.na(FirstMotifs)]
59 # FirstMotifs<-matrix(FirstMotifs,ncol = 1)
60 #
61
62 SecondMotifs=rep(NA,times=nrow(FirstSubstrateSet))
63 SecondAccessionNumbers=rep(NA,times=nrow(FirstSubstrateSet))
64
65 for (i in 1:nrow(SecondSubstrateSet)){
66 SecondLetters<-SecondSubstrateSet[i,7:15]
67 SecondLetters<-SecondLetters[SecondLetters !="XXXXX"]
68 SecondLetters<-paste(SecondLetters, sep="", collapse="")
69
70
71 YYYmotif <- unlist(strsplit(SecondLetters, split = ""))
72 YYYposition <- match(x = "x", table = YYYmotif)
73 #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
74 #just 3 letters to the left of x
75
76 YYYLettersToTheLeft <- YYYposition - 1
77 #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
78 #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1
79 YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1
80 #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
81 #variable the user puts in is
82
83 if (YYYLettersToTheLeft > 3 && YYYLettersToTheRight > 3) {
84 motif<-YYYmotif
85 #add blank spaces if the motif has less than 4 letters to the left/right
86 motif<-c(leftspaces,YYYmotif,rightspaces)
87 #save that motif, which is the Y and +/- 4 amino acids, including truncation
88 motif<-motif[!motif %in% "x"]
89 motif<-paste(motif, sep="", collapse="")
90 SecondLetters<-motif
91 SecondMotifs[i]<-SecondLetters
92 SecondAccessionNumbers[i]<-SecondSubstrateSet[i,3]
93 }
94 }
95 names(FirstMotifs)<-FirstAccessionNumbers
96 names(SecondMotifs)<-SecondAccessionNumbers
97
98
99 # ITDmotifs=rep(NA,times=nrow(FirstSubstrateSet))
100 # ITDAccessionNumbers=rep(NA,times=nrow(FirstSubstrateSet))
101 if(1==0){
102 for (i in 1:nrow(ThirdSubstrateSet)){
103 ITDletters<-ThirdSubstrateSet[i,7:15]
104 ITDletters<-ITDletters[ITDletters !="XXXXX"]
105 ITDletters<-paste(ITDletters, sep="", collapse="")
106 YYYmotif <- unlist(strsplit(ITDletters, split = ""))
107 YYYposition <- match(x = "x", table = YYYmotif)
108 #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
109 #just 3 letters to the left of x
110
111 YYYLettersToTheLeft <- YYYposition - 1
112 #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
113 #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1
114 YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1
115 #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
116 #variable the user puts in is
117
118 if (YYYLettersToTheLeft > 3 && YYYLettersToTheRight > 3) {
119 motif<-YYYmotif
120 #add blank spaces if the motif has less than 4 letters to the left/right
121 motif<-c(leftspaces,YYYmotif,rightspaces)
122 #save that motif, which is the Y and +/- 4 amino acids, including truncation
123 motif<-motif[!motif %in% "x"]
124 motif<-paste(motif, sep="", collapse="")
125 ITDletters<-motif
126 ITDmotifs[i]<-ITDletters
127 ITDAccessionNumbers[i]<-ThirdSubstrateSet[i,3]
128
129 }
130 }
131 }
132 #names(ITDmotifs)<-ITDAccessionNumbers
133 names(SecondMotifs)<-SecondAccessionNumbers
134 names(FirstMotifs)<-FirstAccessionNumbers
135 }
136
137
138 ##############################################3
139 #Truncated only
140 if (TruncatedMotifsOnly_questionmark=="YES"){
141 FirstMotifs=matrix(,nrow = nrow(FirstSubstrateSet),ncol=1)
142 FirstAccessionNumbers=matrix(,nrow = nrow(FirstSubstrateSet),ncol=1)
143
144 for (i in 1:nrow(FirstSubstrateSet)){
145 FirstLetters<-FirstSubstrateSet[i,7:15]
146 FirstLetters<-FirstLetters[FirstLetters !="XXXXX"]
147 FirstLetters<-paste(FirstLetters, sep="", collapse="")
148
149
150 YYYmotif <- unlist(strsplit(FirstLetters, split = ""))
151 YYYposition <- match(x = "x", table = YYYmotif)
152 #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
153 #just 3 letters to the left of x
154
155 YYYLettersToTheLeft <- YYYposition - 1
156 #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
157 #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1
158 YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1
159 #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
160 #variable the user puts in is
161
162 if (YYYLettersToTheLeft < 4 | YYYLettersToTheRight < 4) {
163 leftspaces<-rep(" ",times=(4-YYYLettersToTheLeft))
164 rightspaces<-rep(" ",times=4-(YYYLettersToTheRight))
165 #add blank spaces if the motif has less than 4 letters to the left/right
166 motif<-c(leftspaces,YYYmotif,rightspaces)
167 #save that motif, which is the Y and +/- 4 amino acids, including truncation
168 motif<-motif[!motif %in% "x"]
169 motif<-paste(motif, sep="", collapse="")
170 FirstLetters<-motif
171 FirstMotifs[i,1]<-FirstLetters
172 FirstAccessionNumbers[i,1]<-FirstSubstrateSet[i,3]
173 }
174
175 }
176
177 SecondMotifs=matrix(,nrow = nrow(SecondSubstrateSet),ncol=1)
178 SecondAccessionNumbers<-matrix(,nrow = nrow(SecondSubstrateSet),ncol = 1)
179 i=2
180 for (i in 1:nrow(SecondSubstrateSet)){
181 SecondLetters<-SecondSubstrateSet[i,7:15]
182 SecondLetters<-SecondLetters[SecondLetters !="XXXXX"]
183 SecondLetters<-paste(SecondLetters, sep="", collapse="")
184
185
186 YYYmotif <- unlist(strsplit(SecondLetters, split = ""))
187 YYYposition <- match(x = "x", table = YYYmotif)
188 #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
189 #just 3 letters to the left of x
190
191 YYYLettersToTheLeft <- YYYposition - 1
192 #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
193 #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1
194 YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1
195 #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
196 #variable the user puts in is
197
198 if (YYYLettersToTheLeft < 4 | YYYLettersToTheRight < 4) {
199 leftspaces<-rep(" ",times=(4-YYYLettersToTheLeft))
200 rightspaces<-rep(" ",times=4-(YYYLettersToTheRight))
201 #add blank spaces if the motif has less than 4 letters to the left/right
202 motif<-c(leftspaces,YYYmotif,rightspaces)
203 #save that motif, which is the Y and +/- 4 amino acids, including truncation
204 motif<-motif[!motif %in% "x"]
205 motif<-paste(motif, sep="", collapse="")
206 SecondLetters<-motif
207 SecondAccessionNumbers[i,1]<-SecondSubstrateSet[i,3]
208 SecondMotifs[i,1]<-SecondLetters
209 }
210 }
211
212 # ITDmotifs=matrix(,nrow = nrow(ThirdSubstrateSet),ncol=1)
213 # ITDAccessionNumbers<-matrix(,nrow = nrow(ThirdSubstrateSet))
214 if(1==0){
215 for (i in 1:nrow(ThirdSubstrateSet)){
216 ITDletters<-ThirdSubstrateSet[i,7:15]
217 ITDletters<-ITDletters[ITDletters !="XXXXX"]
218 ITDletters<-paste(ITDletters, sep="", collapse="")
219 YYYmotif <- unlist(strsplit(ITDletters, split = ""))
220 YYYposition <- match(x = "x", table = YYYmotif)
221 #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
222 #just 3 letters to the left of x
223
224 YYYLettersToTheLeft <- YYYposition - 1
225 #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
226 #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1
227 YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1
228 #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
229 #variable the user puts in is
230
231 if (YYYLettersToTheLeft < 4 | YYYLettersToTheRight < 4) {
232 leftspaces<-rep(" ",times=(4-YYYLettersToTheLeft))
233 rightspaces<-rep(" ",times=4-(YYYLettersToTheRight))
234 #add blank spaces if the motif has less than 4 letters to the left/right
235 motif<-c(leftspaces,YYYmotif,rightspaces)
236 #save that motif, which is the Y and +/- 4 amino acids, including truncation
237 motif<-motif[!motif %in% "x"]
238 motif<-paste(motif, sep="", collapse="")
239 ITDletters<-motif
240 ITDAccessionNumbers[i,1]<-ThirdSubstrateSet[i,3]
241 ITDmotifs[i,1]<-ITDletters
242 }
243 }
244 }
245 names(FirstMotifs)<-FirstAccessionNumbers
246 names(SecondMotifs)<-SecondAccessionNumbers
247 #names(ITDmotifs)<-ITDAccessionNumbers
248 }
249
250 ###############################################
251 #ALL motifs, full and truncated
252
253 if (FullMotifsOnly_questionmark!="YES"&&TruncatedMotifsOnly_questionmark!="YES"){
254 #print("!")}
255 FirstMotifs=matrix(,nrow = nrow(FirstSubstrateSet),ncol=1)
256 FirstAccessionNumbers=matrix(,nrow = nrow(FirstSubstrateSet),ncol=1)
257
258 for (i in 1:nrow(FirstSubstrateSet)){
259 FirstLetters<-FirstSubstrateSet[i,7:15]
260 FirstLetters<-FirstLetters[FirstLetters !="XXXXX"]
261 FirstLetters<-paste(FirstLetters, sep="", collapse="")
262 leftspaces<-c()
263 rightspaces<-c()
264
265 YYYmotif <- unlist(strsplit(FirstLetters, split = ""))
266 YYYposition <- match(x = "x", table = YYYmotif)
267 #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
268 #just 3 letters to the left of x
269
270 YYYLettersToTheLeft <- YYYposition - 1
271 #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
272 #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1
273 YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1
274 #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
275 #variable the user puts in is
276
277
278 if (YYYLettersToTheLeft < 4 | YYYLettersToTheRight < 4) {
279 leftspaces<-rep(" ",times=(4-YYYLettersToTheLeft))
280 rightspaces<-rep(" ",times=4-(YYYLettersToTheRight))
281 #add blank spaces if the motif has less than 4 letters to the left/right
282 motif<-c(leftspaces,YYYmotif,rightspaces)
283 #save that motif, which is the Y and +/- 4 amino acids, including truncation
284 motif<-motif[!motif %in% "x"]
285 motif<-paste(motif, sep="", collapse="")
286 FirstLetters<-motif
287 FirstMotifs[i,1]<-FirstLetters
288 FirstAccessionNumbers[i,1]<-FirstSubstrateSet[i,3]
289 }
290
291 if(YYYLettersToTheLeft>3 && YYYLettersToTheRight>3){
292 motif<-YYYmotif
293 #add blank spaces if the motif has less than 4 letters to the left/right
294 motif<-c(leftspaces,YYYmotif,rightspaces)
295 #save that motif, which is the Y and +/- 4 amino acids, including truncation
296 motif<-motif[!motif %in% "x"]
297 motif<-paste(motif, sep="", collapse="")
298 FirstLetters<-motif
299 FirstMotifs[i,1]<-FirstLetters
300 FirstAccessionNumbers[i,1]<-FirstSubstrateSet[i,3]
301
302
303 }
304
305 }
306
307 SecondMotifs=matrix(,nrow = nrow(SecondSubstrateSet),ncol=1)
308 SecondAccessionNumbers<-matrix(,nrow = nrow(SecondSubstrateSet),ncol = 1)
309
310 for (i in 1:nrow(SecondSubstrateSet)){
311 SecondLetters<-SecondSubstrateSet[i,7:15]
312 SecondLetters<-SecondLetters[SecondLetters !="XXXXX"]
313 SecondLetters<-paste(SecondLetters, sep="", collapse="")
314 leftspaces<-c()
315 rightspaces<-c()
316
317 YYYmotif <- unlist(strsplit(SecondLetters, split = ""))
318 YYYposition <- match(x = "x", table = YYYmotif)
319 #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
320 #just 3 letters to the left of x
321
322 YYYLettersToTheLeft <- YYYposition - 1
323 #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
324 #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1
325 YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1
326 #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
327 #variable the user puts in is
328 if (YYYLettersToTheLeft < 4 | YYYLettersToTheRight < 4) {
329 leftspaces<-rep(" ",times=(4-YYYLettersToTheLeft))
330 rightspaces<-rep(" ",times=4-(YYYLettersToTheRight))
331 #add blank spaces if the motif has less than 4 letters to the left/right
332 motif<-c(leftspaces,YYYmotif,rightspaces)
333 #save that motif, which is the Y and +/- 4 amino acids, including truncation
334 motif<-motif[!motif %in% "x"]
335 motif<-paste(motif, sep="", collapse="")
336 SecondLetters<-motif
337 SecondMotifs[i,1]<-SecondLetters
338 SecondAccessionNumbers[i,1]<-SecondSubstrateSet[i,3]
339 }
340
341 if(YYYLettersToTheLeft>3 && YYYLettersToTheRight>3){
342 motif<-YYYmotif
343 #add blank spaces if the motif has less than 4 letters to the left/right
344 motif<-c(leftspaces,YYYmotif,rightspaces)
345 #save that motif, which is the Y and +/- 4 amino acids, including truncation
346 motif<-motif[!motif %in% "x"]
347 motif<-paste(motif, sep="", collapse="")
348 SecondLetters<-motif
349 SecondMotifs[i,1]<-SecondLetters
350 SecondAccessionNumbers[i,1]<-SecondSubstrateSet[i,3]
351 }
352 }
353
354
355 #ITDmotifs=matrix(,nrow = nrow(ThirdSubstrateSet),ncol=1)
356 #ITDAccessionNumbers<-matrix(,nrow = nrow(ThirdSubstrateSet))
357 if(1==0){
358 for (i in 1:nrow(ThirdSubstrateSet)){
359 ITDletters<-ThirdSubstrateSet[i,7:15]
360 ITDletters<-ITDletters[ITDletters !="XXXXX"]
361 ITDletters<-paste(ITDletters, sep="", collapse="")
362 YYYmotif <- unlist(strsplit(ITDletters, split = ""))
363 leftspaces<-c()
364 rightspaces<-c()
365 YYYposition <- match(x = "x", table = YYYmotif)
366 #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
367 #just 3 letters to the left of x
368
369 YYYLettersToTheLeft <- YYYposition - 1
370 #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
371 #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1
372 YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1
373 #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
374 #variable the user puts in is
375 if (YYYLettersToTheLeft < 4 | YYYLettersToTheRight < 4) {
376 leftspaces<-rep(" ",times=(4-YYYLettersToTheLeft))
377 rightspaces<-rep(" ",times=4-(YYYLettersToTheRight))
378 #add blank spaces if the motif has less than 4 letters to the left/right
379 motif<-c(leftspaces,YYYmotif,rightspaces)
380 #save that motif, which is the Y and +/- 4 amino acids, including truncation
381 motif<-motif[!motif %in% "x"]
382 motif<-paste(motif, sep="", collapse="")
383 ITDletters<-motif
384 ITDmotifs[i,1]<-ITDletters
385 ITDAccessionNumbers[i,1]<-FirstSubstrateSet[i,3]
386 }
387
388 if(YYYLettersToTheLeft>3 && YYYLettersToTheRight>3){
389 motif<-YYYmotif
390 #add blank spaces if the motif has less than 4 letters to the left/right
391 motif<-c(leftspaces,YYYmotif,rightspaces)
392 #save that motif, which is the Y and +/- 4 amino acids, including truncation
393 motif<-motif[!motif %in% "x"]
394 motif<-paste(motif, sep="", collapse="")
395 ITDletters<-motif
396 ITDmotifs[i,1]<-ITDletters
397 ITDAccessionNumbers[i,1]<-FirstSubstrateSet[i,3]
398 }
399 }
400 }
401 names(FirstMotifs)<-FirstAccessionNumbers
402 names(SecondMotifs)<-SecondAccessionNumbers
403 #names(ITDmotifs)<-ITDAccessionNumbers
404 }
405
406
407 FirstMotifsFINAL<-FirstMotifs[!FirstMotifs %in% SecondMotifs]
408 #FirstMotifsFINAL<-FirstMotifsFINAL[!FirstMotifsFINAL %in% ITDmotifs]
409 FirstMotifsFINAL<-FirstMotifsFINAL[!duplicated(FirstMotifsFINAL)]
410
411
412 # ITDmotifsFINAL<-ITDmotifs[!ITDmotifs %in% SecondMotifs]
413 # ITDmotifsFINAL<-ITDmotifsFINAL[!ITDmotifsFINAL %in% FirstMotifs]
414 # ITDmotifsFINAL<-ITDmotifsFINAL[!duplicated(ITDmotifsFINAL)]
415
416
417 SecondMotifsFINAL<-SecondMotifs[!SecondMotifs %in% FirstMotifs]
418 #SecondMotifsFINAL<-SecondMotifsFINAL[!SecondMotifsFINAL %in% ITDmotifs]
419 SecondMotifsFINAL<-SecondMotifsFINAL[!duplicated(SecondMotifsFINAL)]
420
421
422 columnalheader<-c(rep(NA,36))
423 FirstFinalMatrix<-matrix(data =columnalheader,nrow = 1)
424
425 for (k in 1:length(FirstMotifsFINAL)) {
426 AN<-00000
427 #I don't remember why, but I felt it necessary to destroy the accession number multiple times to ensure it is
428 #destroyed immediately after use
429 for (m in 2:ncol(Firstsubbackfreq)) {
430 AN <- as.character(Firstsubbackfreq[2, m])
431 #print(AN)}
432 if (grepl(pattern = AN,
433 x = names(FirstMotifsFINAL[k]),
434 fixed = TRUE) == TRUE) {
435 outputmatrix <- as.character(Firstsubbackfreq[, m])
436 outputmatrix <- matrix(outputmatrix, nrow = 1)
437 #with that accession number, find a match in the subbackfreq file and save it here
438 FirstFinalMatrix<-rbind(FirstFinalMatrix,outputmatrix)
439 # print(AN,outputmatrix)}
440 }
441 }
442 }
443 FirstFinalMatrix<-FirstFinalMatrix[!duplicated(FirstFinalMatrix),]
444
445 #columnalheader<-c(rep(NA,36))
446 #ITDFinalMatrix<-matrix(data =columnalheader,nrow = 1)
447
448 if(1==0){
449 for (k in 1:length(ITDmotifsFINAL)) {
450 AN<-00000
451 #I don't remember why, but I felt it necessary to destroy the accession number multiple times to ensure it is
452 #destroyed immediately after use
453 for (m in 1:ncol(Thirdsubbackfreq)) {
454 AN <- as.character(Thirdsubbackfreq[1, m])
455 if (grepl(pattern = AN,
456 x = names(ITDmotifsFINAL[k]),
457 fixed = TRUE) == TRUE) {
458 outputmatrix <- as.character(Thirdsubbackfreq[, m])
459 outputmatrix <- matrix(outputmatrix, nrow = 1)
460 #with that accession number, find a match in the subbackfreq file and save it here
461 ITDFinalMatrix<-rbind(ITDFinalMatrix,outputmatrix)
462 }
463 }
464 }
465 ITDFinalMatrix<-ITDFinalMatrix[!duplicated(ITDFinalMatrix),]
466 }
467
468 columnalheader<-c(rep(NA,36))
469 SecondFinalMatrix<-matrix(data =columnalheader,nrow = 1)
470
471 for (k in 1:length(SecondMotifsFINAL)) {
472 #I don't remember why, but I felt it necessary to destroy the accession number multiple times to ensure it is
473 #destroyed immediately after use
474 for (m in 1:ncol(Secondsubbackfreq)) {
475 AN <- as.character(Secondsubbackfreq[1, m])
476 if (grepl(pattern = AN,
477 x = names(SecondMotifsFINAL[k]),
478 fixed = TRUE) == TRUE) {
479 outputmatrix <- as.character(Secondsubbackfreq[, m])
480 outputmatrix <- matrix(outputmatrix, nrow = 1)
481 #with that accession number, find a match in the subbackfreq file and save it here
482 SecondFinalMatrix<-rbind(SecondFinalMatrix,outputmatrix)
483 }
484 }
485 }
486 SecondFinalMatrix<-SecondFinalMatrix[!duplicated(SecondFinalMatrix),]
487 FTLoutputmatrix<-matrix(data=c(FirstMotifsFINAL,names(FirstMotifsFINAL)),ncol = 2)
488
489
490 write.table(x=FTLoutputmatrix,
491 file=First_unshared_motifs_table,
492 quote=FALSE, sep=",",
493 row.names=FALSE,col.names = FALSE, na="", append=TRUE)
494
495 columnalheader<-c(as.character(Firstsubbackfreq[1:36,1]))
496 columnalheader<-matrix(columnalheader,nrow = 1)
497 write.table(x=columnalheader,
498 file=First_unshared_subbackfreq,
499 quote=FALSE, sep=",",
500 row.names=FALSE,col.names = FALSE, na="", append=TRUE)
501 FirstFinalMatrix<-FirstFinalMatrix[2:nrow(FirstFinalMatrix),]
502 write.table(x=FirstFinalMatrix,
503 file=First_unshared_subbackfreq,
504 quote=FALSE, sep=",",
505 row.names=FALSE,col.names = FALSE, na="", append=TRUE)
506
507 ############################################################################################################
508
509 D835Youtputmatrix<-matrix(data=c(SecondMotifsFINAL,names(SecondMotifsFINAL)),ncol = 2)
510
511 write.table(x=D835Youtputmatrix,
512 file=Second_unshared_motifs_table,
513 quote=FALSE, sep=",",
514 row.names=FALSE,col.names = FALSE, na="", append=TRUE)
515
516 columnalheader<-c(as.character(Firstsubbackfreq[1:36,1]))
517 columnalheader<-matrix(columnalheader,nrow = 1)
518 write.table(x=columnalheader,
519 file=Second_unshared_subbackfreq,
520 quote=FALSE, sep=",",
521 row.names=FALSE,col.names = FALSE, na="", append=TRUE)
522 SecondFinalMatrix<-SecondFinalMatrix[2:nrow(SecondFinalMatrix),]
523 write.table(x=SecondFinalMatrix,
524 file=Second_unshared_subbackfreq,
525 quote=FALSE, sep=",",
526 row.names=FALSE,col.names = FALSE, na="", append=TRUE)
527
528 ############################################################################################################
529
530 # ITDoutputmatrix<-matrix(data = c(ITDmotifsFINAL,names(ITDmotifsFINAL)),ncol = 2)
531 #
532 # write.table(x=ITDoutputmatrix,
533 # file=Third_unshared_motifs_table,
534 # quote=FALSE, sep=",",
535 # row.names=FALSE,col.names = FALSE, na="", append=TRUE)
536 #
537 # columnalheader<-c(as.character(Thirdsubbackfreq[1:36,1]))
538 # columnalheader<-matrix(columnalheader,nrow = 1)
539 # write.table(x=columnalheader,
540 # file=Third_unshared_subbackfreq,
541 # quote=FALSE, sep=",",
542 # row.names=FALSE,col.names = FALSE, na="", append=TRUE)
543 # ITDFinalMatrix<-ITDFinalMatrix[2:nrow(ITDFinalMatrix),]
544 # write.table(x=ITDFinalMatrix,
545 # file=Third_unshared_subbackfreq,
546 # quote=FALSE, sep=",",
547 # row.names=FALSE,col.names = FALSE, na="", append=TRUE)