Mercurial > repos > galaxyp > psm_to_sam
comparison tool-data/.Rhistory @ 2:e1bb35f6ca28 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
author | galaxyp |
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date | Thu, 14 Jan 2016 18:13:18 -0500 |
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1:34f9e847dd4e | 2:e1bb35f6ca28 |
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1 } | |
2 channel = sub("\\S+?\\.(iTRAQ\\.\\d+)", "\\1", mergedSampleName, perl=T) | |
3 return(paste0(sample, "-", channel)) | |
4 } | |
5 coreSampleNames = list() | |
6 for(i in seq(2, length(multiplexData), 4)) | |
7 { | |
8 firstGroupNum = 0.75 * i | |
9 print(getMultiplexSampleName(sampleNames[i-1], 1, coreSampleNames)) | |
10 sampleNames[i-1] = sub("(\\S+?)_(\\S+?)_(\\S+?)(\\.iTRAQ.\\d+)", "\\1\\4", sampleNames[i-1], perl=T) | |
11 sampleNames[i] = sub("(\\S+?)_(\\S+?)_(\\S+?)(\\.iTRAQ.\\d+)", "\\2\\4", sampleNames[i], perl=T) | |
12 sampleNames[i+1] = sub("(\\S+?)_(\\S+?)_(\\S+?)(\\.iTRAQ.\\d+)", "\\3\\4", sampleNames[i+1], perl=T) | |
13 print(sampleNames[i-1]) | |
14 print(sampleNames[i]) | |
15 print(sampleNames[i+1]) | |
16 #ratios[,firstGroupNum] = ZeroSafeDivide(multiplexData[,i], multiplexData[,i+3]) | |
17 #ratios[,firstGroupNum+1] = ZeroSafeDivide(multiplexData[,i+1], multiplexData[,i+3]) | |
18 #ratios[,firstGroupNum+2] = ZeroSafeDivide(multiplexData[,i+2], multiplexData[,i+3]) | |
19 } | |
20 getMultiplexSampleName = function(mergedSampleName, tokenIndex, coreSampleNames) | |
21 { | |
22 sample = sub("(\\S+?)_(\\S+?)_(\\S+?)\\.iTRAQ\\.\\d+", paste0("\\", tokenIndex), mergedSampleName, perl=T) | |
23 if(is.null(coreSampleNames[[sample]])) | |
24 { | |
25 coreSampleNames[[sample]] = 1 | |
26 } | |
27 else | |
28 { | |
29 sample = paste0(sample, incrementChar("A", coreSampleNames[[sample]])) | |
30 coreSampleNames[[sample]] = coreSampleNames[[sample]] + 1 | |
31 } | |
32 channel = sub("\\S+?\\.(iTRAQ\\.\\d+)", "\\1", mergedSampleName, perl=T) | |
33 coreSampleNames <<- coreSampleNames | |
34 return(paste0(sample, "-", channel)) | |
35 } | |
36 coreSampleNames = list() | |
37 for(i in seq(2, length(multiplexData), 4)) | |
38 { | |
39 firstGroupNum = 0.75 * i | |
40 print(getMultiplexSampleName(sampleNames[i-1], 1, coreSampleNames)) | |
41 sampleNames[i-1] = sub("(\\S+?)_(\\S+?)_(\\S+?)(\\.iTRAQ.\\d+)", "\\1\\4", sampleNames[i-1], perl=T) | |
42 sampleNames[i] = sub("(\\S+?)_(\\S+?)_(\\S+?)(\\.iTRAQ.\\d+)", "\\2\\4", sampleNames[i], perl=T) | |
43 sampleNames[i+1] = sub("(\\S+?)_(\\S+?)_(\\S+?)(\\.iTRAQ.\\d+)", "\\3\\4", sampleNames[i+1], perl=T) | |
44 #print(sampleNames[i-1]) | |
45 #print(sampleNames[i]) | |
46 #print(sampleNames[i+1]) | |
47 #ratios[,firstGroupNum] = ZeroSafeDivide(multiplexData[,i], multiplexData[,i+3]) | |
48 #ratios[,firstGroupNum+1] = ZeroSafeDivide(multiplexData[,i+1], multiplexData[,i+3]) | |
49 #ratios[,firstGroupNum+2] = ZeroSafeDivide(multiplexData[,i+2], multiplexData[,i+3]) | |
50 } | |
51 sampleNames = colnames(multiplexData)[-1]#[c(F, rep(c(T,T,T,F), numSamples/3))] | |
52 incrementChar = function(c, step=1) { return(rawToChar(as.raw(as.integer(charToRaw(c))+step))); } | |
53 getMultiplexSampleName = function(mergedSampleName, tokenIndex, coreSampleNames) | |
54 { | |
55 sample = sub("(\\S+?)_(\\S+?)_(\\S+?)\\.iTRAQ\\.\\d+", paste0("\\", tokenIndex), mergedSampleName, perl=T) | |
56 if(is.null(coreSampleNames[[sample]])) | |
57 { | |
58 coreSampleNames[[sample]] = 1 | |
59 } | |
60 else | |
61 { | |
62 sample = paste0(sample, incrementChar("A", coreSampleNames[[sample]])) | |
63 coreSampleNames[[sample]] = coreSampleNames[[sample]] + 1 | |
64 } | |
65 channel = sub("\\S+?\\.(iTRAQ\\.\\d+)", "\\1", mergedSampleName, perl=T) | |
66 coreSampleNames <<- coreSampleNames | |
67 return(paste0(sample, "-", channel)) | |
68 } | |
69 coreSampleNames = list() | |
70 for(i in seq(2, length(multiplexData), 4)) | |
71 { | |
72 firstGroupNum = 0.75 * i | |
73 sampleNames[i-1] = getMultiplexSampleName(sampleNames[i-1], 1, coreSampleNames) | |
74 sampleNames[i] = getMultiplexSampleName(sampleNames[i], 2, coreSampleNames) | |
75 sampleNames[i+1] = getMultiplexSampleName(sampleNames[i+1], 3, coreSampleNames) | |
76 print(sampleNames[i-1]) | |
77 print(sampleNames[i]) | |
78 print(sampleNames[i+1]) | |
79 #ratios[,firstGroupNum] = ZeroSafeDivide(multiplexData[,i], multiplexData[,i+3]) | |
80 #ratios[,firstGroupNum+1] = ZeroSafeDivide(multiplexData[,i+1], multiplexData[,i+3]) | |
81 #ratios[,firstGroupNum+2] = ZeroSafeDivide(multiplexData[,i+2], multiplexData[,i+3]) | |
82 } | |
83 sampleNames = colnames(multiplexData)[-1]#[c(F, rep(c(T,T,T,F), numSamples/3))] | |
84 incrementChar = function(c, step=1) { return(rawToChar(as.raw(as.integer(charToRaw(c))+step))); } | |
85 getMultiplexSampleName = function(mergedSampleName, tokenIndex, coreSampleNames) | |
86 { | |
87 sample = sub("(\\S+?)_(\\S+?)_(\\S+?)\\.iTRAQ\\.\\d+", paste0("\\", tokenIndex), mergedSampleName, perl=T) | |
88 if(is.null(coreSampleNames[[sample]])) | |
89 { | |
90 coreSampleNames[[sample]] = 1 | |
91 } | |
92 else | |
93 { | |
94 sample = paste0(sample, "-", incrementChar("A", coreSampleNames[[sample]])) | |
95 coreSampleNames[[sample]] = coreSampleNames[[sample]] + 1 | |
96 } | |
97 channel = sub("\\S+?\\.(iTRAQ\\.\\d+)", "\\1", mergedSampleName, perl=T) | |
98 coreSampleNames <<- coreSampleNames | |
99 return(paste0(sample, "-", channel)) | |
100 } | |
101 coreSampleNames = list() | |
102 for(i in seq(2, length(multiplexData), 4)) | |
103 { | |
104 firstGroupNum = 0.75 * i | |
105 sampleNames[i-1] = getMultiplexSampleName(sampleNames[i-1], 1, coreSampleNames) | |
106 sampleNames[i] = getMultiplexSampleName(sampleNames[i], 2, coreSampleNames) | |
107 sampleNames[i+1] = getMultiplexSampleName(sampleNames[i+1], 3, coreSampleNames) | |
108 print(sampleNames[i-1]) | |
109 print(sampleNames[i]) | |
110 print(sampleNames[i+1]) | |
111 #ratios[,firstGroupNum] = ZeroSafeDivide(multiplexData[,i], multiplexData[,i+3]) | |
112 #ratios[,firstGroupNum+1] = ZeroSafeDivide(multiplexData[,i+1], multiplexData[,i+3]) | |
113 #ratios[,firstGroupNum+2] = ZeroSafeDivide(multiplexData[,i+2], multiplexData[,i+3]) | |
114 } | |
115 sampleNames = colnames(multiplexData)[-1]#[c(F, rep(c(T,T,T,F), numSamples/3))] | |
116 incrementChar = function(c, step=1) { return(rawToChar(as.raw(as.integer(charToRaw(c))+step))); } | |
117 getMultiplexSampleName = function(mergedSampleName, tokenIndex, coreSampleNames) | |
118 { | |
119 sample = sub("(\\S+?)_(\\S+?)_(\\S+?)\\.iTRAQ\\.\\d+", paste0("\\", tokenIndex), mergedSampleName, perl=T) | |
120 if(is.null(coreSampleNames[[sample]])) | |
121 { | |
122 coreSampleNames[[sample]] = 1 | |
123 } | |
124 else | |
125 { | |
126 oldCount = coreSampleNames[[sample]] | |
127 sample = paste0(sample, "-", incrementChar("A", oldCount)) | |
128 coreSampleNames[[sample]] = oldCount + 1 | |
129 } | |
130 channel = sub("\\S+?\\.(iTRAQ\\.\\d+)", "\\1", mergedSampleName, perl=T) | |
131 coreSampleNames <<- coreSampleNames | |
132 return(paste0(sample, "-", channel)) | |
133 } | |
134 coreSampleNames = list() | |
135 for(i in seq(2, length(multiplexData), 4)) | |
136 { | |
137 firstGroupNum = 0.75 * i | |
138 sampleNames[i-1] = getMultiplexSampleName(sampleNames[i-1], 1, coreSampleNames) | |
139 sampleNames[i] = getMultiplexSampleName(sampleNames[i], 2, coreSampleNames) | |
140 sampleNames[i+1] = getMultiplexSampleName(sampleNames[i+1], 3, coreSampleNames) | |
141 print(sampleNames[i-1]) | |
142 print(sampleNames[i]) | |
143 print(sampleNames[i+1]) | |
144 #ratios[,firstGroupNum] = ZeroSafeDivide(multiplexData[,i], multiplexData[,i+3]) | |
145 #ratios[,firstGroupNum+1] = ZeroSafeDivide(multiplexData[,i+1], multiplexData[,i+3]) | |
146 #ratios[,firstGroupNum+2] = ZeroSafeDivide(multiplexData[,i+2], multiplexData[,i+3]) | |
147 } | |
148 sort(coreSampleNames) | |
149 sort(coreSampleNames[1]) | |
150 coreSampleNames[1] | |
151 coreSampleNames[2] | |
152 coreSampleNames[1,] | |
153 coreSampleNames[,1] | |
154 simplify2array(coreSampleNames) | |
155 order(coreSampleNames) | |
156 order(coreSampleNames[1]) | |
157 sort(simplify2array(coreSampleNames)) | |
158 order(coreSampleNames) | |
159 as.matrix(cores) | |
160 as.matrix(coreSampleNames) | |
161 order(as.matrix(coreSampleNames)) | |
162 names(as.matrix(coreSampleNames)) | |
163 names(coreSampleNames) | |
164 sort(names(coreSampleNames)) | |
165 sort(sampleNames) | |
166 sampleNames = sampleNames[c(rep(c(T,T,T,F), numSamples/3))] | |
167 sort(sampleNames) | |
168 ratios = matrix(nrow=dim(multiplexData)[1], ncol=numSamples, dimnames=list(multiplexData[,1], sampleNames)) | |
169 View(ratios) | |
170 for(i in seq(2, length(multiplexData), 4)) | |
171 { | |
172 firstGroupNum = 0.75 * i | |
173 ratios[,firstGroupNum] = ZeroSafeDivide(multiplexData[,i], multiplexData[,i+3]) | |
174 ratios[,firstGroupNum+1] = ZeroSafeDivide(multiplexData[,i+1], multiplexData[,i+3]) | |
175 ratios[,firstGroupNum+2] = ZeroSafeDivide(multiplexData[,i+2], multiplexData[,i+3]) | |
176 } | |
177 View(ratios) | |
178 filepath = "H:/data/CPTAC/TCGA-Broad-Breast/global-Broad.cct" | |
179 outputFilepath = sub(".cct", "-demultiplexed-ratios.cct", filepath, fixed=T) | |
180 source('~/.active-rstudio-document') | |
181 write.csv(format(ratios, digits=4), file=outputFilepath, quote=F) | |
182 demultiplexNetGestaltITRAQ_CCT = function(filepath) | |
183 { | |
184 outputFilepath = sub(".cct", "-demultiplexed-ratios.cct", filepath, fixed=T) | |
185 multiplexData = read.table(filepath, sep="\t", header=T) | |
186 numSamples = 0.75*(dim(multiplexData)[2]-1) | |
187 sampleNames = colnames(multiplexData)[-1]#[c(F, rep(c(T,T,T,F), numSamples/3))] | |
188 coreSampleNames = list() | |
189 for(i in seq(2, length(multiplexData), 4)) | |
190 { | |
191 firstGroupNum = 0.75 * i | |
192 sampleNames[i-1] = getMultiplexSampleName(sampleNames[i-1], 1, coreSampleNames) | |
193 sampleNames[i] = getMultiplexSampleName(sampleNames[i], 2, coreSampleNames) | |
194 sampleNames[i+1] = getMultiplexSampleName(sampleNames[i+1], 3, coreSampleNames) | |
195 } | |
196 sampleNames = sampleNames[c(rep(c(T,T,T,F), numSamples/3))] | |
197 ratios = matrix(nrow=dim(multiplexData)[1], ncol=numSamples, dimnames=list(multiplexData[,1], sampleNames)) | |
198 for(i in seq(2, length(multiplexData), 4)) | |
199 { | |
200 firstGroupNum = 0.75 * i | |
201 ratios[,firstGroupNum] = ZeroSafeDivide(multiplexData[,i], multiplexData[,i+3]) | |
202 ratios[,firstGroupNum+1] = ZeroSafeDivide(multiplexData[,i+1], multiplexData[,i+3]) | |
203 ratios[,firstGroupNum+2] = ZeroSafeDivide(multiplexData[,i+2], multiplexData[,i+3]) | |
204 } | |
205 write.csv(format(ratios, digits=4), file=outputFilepath, quote=F) | |
206 } | |
207 source('~/.active-rstudio-document') | |
208 source('~/.active-rstudio-document') | |
209 write.table(format(ratios, digits=4), file=outputFilepath, quote=F, row.names=T, sep="\t") | |
210 write.table(format(ratios, digits=4), file=outputFilepath, quote=F, row.names=T, col.names=T, sep="\t") | |
211 write.table(format(cbind(rownames(ratios), ratios), digits=4), file=outputFilepath, quote=F, row.names=F, sep="\t") | |
212 write.table(format(cbind(c("GeneSymbol", rownames(ratios)), ratios), digits=4), file=outputFilepath, quote=F, row.names=F, sep="\t") | |
213 c("GeneSymbol", rownames(ratios)) | |
214 head(c("GeneSymbol", rownames(ratios))) | |
215 cbind(c("GeneSymbol", rownames(ratios)), ratios), digits=4) | |
216 cbind(c("GeneSymbol", rownames(ratios)) | |
217 ) | |
218 cbind(c("GeneSymbol", rownames(ratios)), ratios) | |
219 write.table(format(cbind(c(GeneSymbol=rownames(ratios)), ratios), digits=4), file=outputFilepath, quote=F, row.names=F, sep="\t") | |
220 write.table(format(cbind(c(GeneSymbol=rownames(ratios)), ratios), digits=4), file=outputFilepath, quote=F, row.names=F, sep="\t") | |
221 write.table(format(cbind(GeneSymbol=rownames(ratios), ratios), digits=4), file=outputFilepath, quote=F, row.names=F, sep="\t") | |
222 source('~/.active-rstudio-document') | |
223 write.table(format(cbind(GeneSymbol=rownames(ratios), ratios), digits=4), file=outputFilepath, quote=F, row.names=F, sep="\t", options(digits=2)) | |
224 write.table(cbind(GeneSymbol=rownames(ratios), ratios), file=outputFilepath, quote=F, row.names=F, sep="\t", options(digits=4)) | |
225 options(digits=4) | |
226 write.table(cbind(GeneSymbol=rownames(ratios), ratios), file=outputFilepath, quote=F, row.names=F, sep="\t") | |
227 source('~/.active-rstudio-document') | |
228 demultiplexNetGestaltITRAQ_CCT("H:/data/CPTAC/TCGA-Broad-Breast/phospho-Broad.cct") | |
229 demultiplexNetGestaltITRAQ_CCT("H:/data/CPTAC/TCGA-Broad-Breast/phospho-Broad.cct") | |
230 rm("*") | |
231 rm("") | |
232 rm | |
233 rm() | |
234 ?rm | |
235 getMultiplexSampleName = function(mergedSampleName, tokenIndex, coreSampleNames) | |
236 { | |
237 innerSampleNames = coreSampleNames | |
238 sample = sub("(\\S+?)_(\\S+?)_(\\S+?)\\.iTRAQ\\.\\d+", paste0("\\", tokenIndex), mergedSampleName, perl=T) | |
239 if(is.null(innerSampleNames[[sample]])) | |
240 { | |
241 innerSampleNames[[sample]] = 1 | |
242 } | |
243 else | |
244 { | |
245 oldCount = innerSampleNames[[sample]] | |
246 sample = paste0(sample, "-", incrementChar("A", oldCount)) | |
247 innerSampleNames[[sample]] = oldCount + 1 | |
248 } | |
249 channel = sub("\\S+?\\.(iTRAQ\\.\\d+)", "\\1", mergedSampleName, perl=T) | |
250 eval.parent(substitute(coreSampleNames = innerSampleNames)) | |
251 return(paste0(sample, "-", channel)) | |
252 } | |
253 demultiplexNetGestaltITRAQ_CCT = function(filepath) | |
254 { | |
255 outputFilepath = sub(".cct", "-demultiplexed-ratios.cct", filepath, fixed=T) | |
256 multiplexData = read.table(filepath, sep="\t", header=T) | |
257 numSamples = 0.75*(dim(multiplexData)[2]-1) | |
258 sampleNames = colnames(multiplexData)[-1]#[c(F, rep(c(T,T,T,F), numSamples/3))] | |
259 coreSampleNames = list() | |
260 for(i in seq(2, length(multiplexData), 4)) | |
261 { | |
262 firstGroupNum = 0.75 * i | |
263 sampleNames[i-1] = getMultiplexSampleName(sampleNames[i-1], 1, coreSampleNames) | |
264 sampleNames[i] = getMultiplexSampleName(sampleNames[i], 2, coreSampleNames) | |
265 sampleNames[i+1] = getMultiplexSampleName(sampleNames[i+1], 3, coreSampleNames) | |
266 } | |
267 sampleNames = sampleNames[c(rep(c(T,T,T,F), numSamples/3))] | |
268 ratios = matrix(nrow=dim(multiplexData)[1], ncol=numSamples, dimnames=list(multiplexData[,1], sampleNames)) | |
269 for(i in seq(2, length(multiplexData), 4)) | |
270 { | |
271 firstGroupNum = 0.75 * i | |
272 ratios[,firstGroupNum] = ZeroSafeDivide(multiplexData[,i], multiplexData[,i+3]) | |
273 ratios[,firstGroupNum+1] = ZeroSafeDivide(multiplexData[,i+1], multiplexData[,i+3]) | |
274 ratios[,firstGroupNum+2] = ZeroSafeDivide(multiplexData[,i+2], multiplexData[,i+3]) | |
275 } | |
276 options(digits=4) | |
277 write.table(cbind(GeneSymbol=rownames(ratios), ratios), file=outputFilepath, quote=F, row.names=F, sep="\t") | |
278 } | |
279 demultiplexNetGestaltITRAQ_CCT("H:/data/CPTAC/TCGA-Broad-Breast/phospho-Broad.cct") | |
280 ?substittue | |
281 ?substitute | |
282 getMultiplexSampleName = function(mergedSampleName, tokenIndex, coreSampleNames) | |
283 { | |
284 innerSampleNames = coreSampleNames | |
285 sample = sub("(\\S+?)_(\\S+?)_(\\S+?)\\.iTRAQ\\.\\d+", paste0("\\", tokenIndex), mergedSampleName, perl=T) | |
286 if(is.null(innerSampleNames[[sample]])) | |
287 { | |
288 innerSampleNames[[sample]] = 1 | |
289 } | |
290 else | |
291 { | |
292 oldCount = innerSampleNames[[sample]] | |
293 sample = paste0(sample, "-", incrementChar("A", oldCount)) | |
294 innerSampleNames[[sample]] = oldCount + 1 | |
295 } | |
296 channel = sub("\\S+?\\.(iTRAQ\\.\\d+)", "\\1", mergedSampleName, perl=T) | |
297 eval.parent(substitute(coreSampleNames<-innerSampleNames)) | |
298 return(paste0(sample, "-", channel)) | |
299 } | |
300 demultiplexNetGestaltITRAQ_CCT = function(filepath) | |
301 { | |
302 outputFilepath = sub(".cct", "-demultiplexed-ratios.cct", filepath, fixed=T) | |
303 multiplexData = read.table(filepath, sep="\t", header=T) | |
304 numSamples = 0.75*(dim(multiplexData)[2]-1) | |
305 sampleNames = colnames(multiplexData)[-1]#[c(F, rep(c(T,T,T,F), numSamples/3))] | |
306 coreSampleNames = list() | |
307 for(i in seq(2, length(multiplexData), 4)) | |
308 { | |
309 firstGroupNum = 0.75 * i | |
310 sampleNames[i-1] = getMultiplexSampleName(sampleNames[i-1], 1, coreSampleNames) | |
311 sampleNames[i] = getMultiplexSampleName(sampleNames[i], 2, coreSampleNames) | |
312 sampleNames[i+1] = getMultiplexSampleName(sampleNames[i+1], 3, coreSampleNames) | |
313 } | |
314 sampleNames = sampleNames[c(rep(c(T,T,T,F), numSamples/3))] | |
315 ratios = matrix(nrow=dim(multiplexData)[1], ncol=numSamples, dimnames=list(multiplexData[,1], sampleNames)) | |
316 for(i in seq(2, length(multiplexData), 4)) | |
317 { | |
318 firstGroupNum = 0.75 * i | |
319 ratios[,firstGroupNum] = ZeroSafeDivide(multiplexData[,i], multiplexData[,i+3]) | |
320 ratios[,firstGroupNum+1] = ZeroSafeDivide(multiplexData[,i+1], multiplexData[,i+3]) | |
321 ratios[,firstGroupNum+2] = ZeroSafeDivide(multiplexData[,i+2], multiplexData[,i+3]) | |
322 } | |
323 options(digits=4) | |
324 write.table(cbind(GeneSymbol=rownames(ratios), ratios), file=outputFilepath, quote=F, row.names=F, sep="\t") | |
325 } | |
326 demultiplexNetGestaltITRAQ_CCT("H:/data/CPTAC/TCGA-Broad-Breast/phospho-Broad.cct") | |
327 demultiplexNetGestaltITRAQ_CCT("H:/data/CPTAC/TCGA-Broad-Breast/global-Broad.cct") | |
328 demultiplexNetGestaltITRAQ_CCT("H:/data/CPTAC/TCGA-PNNL-Ovarian/phospho-PNNL.cct") | |
329 demultiplexNetGestaltITRAQ_CCT("H:/data/CPTAC/TCGA-PNNL-Ovarian/global-PNNL.cct") | |
330 demultiplexNetGestaltITRAQ_CCT("H:/data/CPTAC/TCGA-PNNL-Ovarian/phospho-PNNL.cct") | |
331 demultiplexNetGestaltITRAQ_CCT("H:/data/CPTAC/TCGA-PNNL-Ovarian/global-PNNL.cct") | |
332 ratios_ordered = ratios[,order(names(ratios))] | |
333 ratios_ordered = ratios[order(names(ratios)),] | |
334 names(ratios) | |
335 colnames(ratios) | |
336 ratios_ordered = ratios[order(colnames(ratios)),] | |
337 ratios_ordered = ratios[,order(colnames(ratios))] | |
338 View(ratios_ordered) | |
339 source('~/.active-rstudio-document') | |
340 source('~/.active-rstudio-document') | |
341 source('~/.active-rstudio-document') | |
342 source('~/.active-rstudio-document') | |
343 biocLite("RGalaxy") | |
344 source("https://bioconductor.org/biocLite.R") | |
345 biocLite("RGalaxy") | |
346 source('~/.active-rstudio-document') | |
347 source('~/.active-rstudio-document') | |
348 source('~/.active-rstudio-document') | |
349 galaxyHome="/galaxy-central" | |
350 galaxy("addTwoNumbers", | |
351 galaxyConfig= | |
352 GalaxyConfig(galaxyHome, "mytool", "Test Section", | |
353 "testSectionId") | |
354 ) | |
355 galaxyHome="C:\\Users\\chambem2\\.vagrant\\precise64\\bingomics-galaxy\\vagrant\\export\\src\\galaxy" | |
356 galaxy("addTwoNumbers", | |
357 galaxyConfig= | |
358 GalaxyConfig(galaxyHome, "mytool", "Test Section", | |
359 "testSectionId") | |
360 ) | |
361 galaxyHome="C:\\Users\\chambem2\\.vagrant\\precise64\\bingomics-galaxy\\vagrant\\export\\src\\galaxy" | |
362 galaxy("addTwoNumbers", | |
363 galaxyConfig= | |
364 GalaxyConfig(galaxyHome, "mytool", "Test Section", | |
365 "testSectionId") | |
366 ) | |
367 ?GalaxyConfig | |
368 galaxyHome="C:\\Users\\chambem2\\.vagrant\\precise64\\bingomics-galaxy\\vagrant\\export\\src\\galaxy" | |
369 galaxy("addTwoNumbers", | |
370 galaxyConfig= | |
371 GalaxyConfig(galaxyHome, "mytool", "Test Section", | |
372 "testSectionId") | |
373 ) | |
374 galaxyHome="C:\\Users\\chambem2\\.vagrant\\precise64\\bingomics-galaxy\\vagrant\\export\\src\\galaxy" | |
375 galaxy("addTwoNumbers", | |
376 galaxyConfig= | |
377 GalaxyConfig(galaxyHome, "mytool", "Test Section", | |
378 "testSectionId") | |
379 ) | |
380 source('~/.active-rstudio-document') | |
381 galaxyHome="C:\\Users\\chambem2\\.vagrant\\precise64\\bingomics-galaxy\\vagrant\\export\\src\\galaxy" | |
382 galaxy("addTwoNumbers", | |
383 galaxyConfig= | |
384 GalaxyConfig(galaxyHome, "mytool", "Test Section", | |
385 "testSectionId") | |
386 ) | |
387 galaxyHome="C:\\Users\\chambem2\\.vagrant\\precise64\\bingomics-galaxy\\vagrant\\export\\src\\galaxy" | |
388 galaxy("addTwoNumbers", | |
389 galaxyConfig= | |
390 GalaxyConfig(galaxyHome, "mytool", "Test Section", | |
391 "testSectionId") | |
392 ) | |
393 galaxyHome="C:\\Users\\chambem2\\.vagrant\\precise64\\bingomics-galaxy\\vagrant\\export\\src\\galaxy" | |
394 galaxy("PrepareAnnotationGENCODE_g", | |
395 galaxyConfig= | |
396 GalaxyConfig(galaxyHome, "mytool", "Test Section", | |
397 "testSectionId") | |
398 ) | |
399 PrepareAnnotationGENCODE_g <- function() {} | |
400 galaxyHome="C:\\Users\\chambem2\\.vagrant\\precise64\\bingomics-galaxy\\vagrant\\export\\src\\galaxy" | |
401 galaxy("PrepareAnnotationGENCODE_g", | |
402 galaxyConfig= | |
403 GalaxyConfig(galaxyHome, "mytool", "Test Section", | |
404 "testSectionId") | |
405 ) | |
406 PrepareAnnotationGENCODE_g <- function(gtfFile = GalaxyInputFile(required = TRUE), | |
407 CDSfasta = GalaxyInputFile(required = TRUE), | |
408 pepfasta = GalaxyInputFile(required = TRUE), | |
409 annotation_path = GalaxyCharacterParam(required = TRUE), | |
410 dbsnp = GalaxySelectParam(c(`First Choice` = "NULL", `Second Choice` = | |
411 "snp135")), splice_matrix = GalaxyLogicalParam(checked = TRUE), | |
412 COSMIC = GalaxyLogicalParam(checked = TRUE), ...) | |
413 { | |
414 } | |
415 PrepareAnnotationGENCODE_g <- function(gtfFile = GalaxyInputFile(required = TRUE), | |
416 CDSfasta = GalaxyInputFile(required = TRUE), | |
417 pepfasta = GalaxyInputFile(required = TRUE), | |
418 annotation_path = GalaxyCharacterParam(required = TRUE), | |
419 dbsnp = GalaxySelectParam(c(`First Choice` = "NULL", `Second Choice` = | |
420 "snp135")), splice_matrix = GalaxyLogicalParam(checked = TRUE), | |
421 COSMIC = GalaxyLogicalParam(checked = TRUE), ...) | |
422 { | |
423 } | |
424 galaxyHome="C:\\Users\\chambem2\\.vagrant\\precise64\\bingomics-galaxy\\vagrant\\export\\src\\galaxy" | |
425 galaxy("PrepareAnnotationGENCODE_g", | |
426 galaxyConfig= | |
427 GalaxyConfig(galaxyHome, "mytool", "Test Section", | |
428 "testSectionId") | |
429 ) | |
430 source('~/.active-rstudio-document') | |
431 PrepareAnnotationGENCODE_g <- function(gtfFile = GalaxyInputFile(required = TRUE), | |
432 CDSfasta = GalaxyInputFile(required = TRUE), | |
433 pepfasta = GalaxyInputFile(required = TRUE), | |
434 annotation_path = GalaxyCharacterParam(required = TRUE), | |
435 dbsnp = GalaxySelectParam(c(`First Choice` = "NULL", `Second Choice` = | |
436 "snp135")), splice_matrix = GalaxyLogicalParam(checked = TRUE), | |
437 COSMIC = GalaxyLogicalParam(checked = TRUE), ...) | |
438 { | |
439 } | |
440 galaxyHome="C:\\Users\\chambem2\\.vagrant\\precise64\\bingomics-galaxy\\vagrant\\export\\src\\galaxy" | |
441 galaxy("PrepareAnnotationGENCODE_g", | |
442 galaxyConfig= | |
443 GalaxyConfig(galaxyHome, "mytool", "Test Section", | |
444 "testSectionId") | |
445 ) | |
446 source('~/.active-rstudio-document') | |
447 source('~/.active-rstudio-document') | |
448 source('~/.active-rstudio-document') | |
449 source('~/.active-rstudio-document') | |
450 source('~/.active-rstudio-document') | |
451 source('~/.active-rstudio-document') | |
452 source('~/.active-rstudio-document') | |
453 source('~/.active-rstudio-document') | |
454 ?wtf | |
455 print "why doesn't this work" | |
456 print( )"why doesn't this work") | |
457 print("why doesn't this work") | |
458 source('~/.active-rstudio-document') | |
459 galaxyHome="C:\\Users\\chambem2\\.vagrant\\precise64\\bingomics-galaxy\\vagrant\\export\\src\\galaxy" | |
460 galaxy("addTwoNumbers", | |
461 galaxyConfig= | |
462 GalaxyConfig(galaxyHome, "mytool", "Test Section", | |
463 "testSectionId") | |
464 ) | |
465 source('~/.active-rstudio-document') | |
466 source('~/.active-rstudio-document') | |
467 PrepareAnnotationGENCODE <- function(gtfFile = GalaxyInputFile(required = TRUE), | |
468 CDSfasta = GalaxyInputFile(required = TRUE), | |
469 pepfasta = GalaxyInputFile(required = TRUE), | |
470 annotation_path = GalaxyCharacterParam(required = TRUE), | |
471 COSMIC = GalaxyLogicalParam(checked = TRUE), | |
472 output = GalaxyOutput("sum", "txt")) | |
473 { | |
474 print("why doesn't this work") | |
475 } | |
476 source('~/.active-rstudio-document') | |
477 source('~/.active-rstudio-document') | |
478 source('~/.active-rstudio-document') | |
479 library(RGalaxy) | |
480 source('~/.active-rstudio-document') | |
481 galaxyHome="C:\\Users\\chambem2\\.vagrant\\precise64\\bingomics-galaxy\\vagrant\\export\\src\\galaxy" | |
482 galaxy("PrepareAnnotationGENCODE", | |
483 galaxyConfig= | |
484 GalaxyConfig(galaxyHome, "mytool", "Test Section", | |
485 "testSectionId") | |
486 ) | |
487 source('~/.active-rstudio-document') | |
488 str(addTwoNumbers) | |
489 addTwoNumbers | |
490 packageName() | |
491 packageName(addTwoNumbers) | |
492 packageName("addTwoNumbers") | |
493 source('~/.active-rstudio-document') | |
494 source('~/.active-rstudio-document', echo=TRUE) | |
495 source('~/.active-rstudio-document', echo=TRUE) | |
496 str(addTwoNumbers) | |
497 str(addTwoNumbers2) | |
498 env(addTwoNumbers) | |
499 environmentName | |
500 environmentName() | |
501 env.profile() | |
502 namespace:base | |
503 library(namespace) | |
504 source('~/.active-rstudio-document', echo=TRUE) | |
505 source("https://bioconductor.org/biocLite.R") | |
506 biocLite("customProDB") | |
507 library("customProDB", lib.loc="C:/Users/chambem2/Google Drive/Marvin Documents/R/win-library/3.1") | |
508 setwd("C:/Users/chambem2/.vagrant/precise64/bingomics-galaxy/vagrant/export/src/tools-galaxyp-chambm/tools/bumbershoot/psm_to_sam/tool-data") | |
509 bamFile <- system.file("extdata/bams", "test1_sort.bam", package="customProDB") | |
510 easyRun(bamFile=bamFile, annotation_path=".") | |
511 easyRun(bamFile=bamFile, annotation_path=".") | |
512 easyRun(bamFile=bamFile, annotation_path=".", outfile_path=".", outfile_name="test.fasta") |