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comparison lib.r @ 8:198b035d4848 draft

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planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
author lecorguille
date Fri, 07 Apr 2017 07:42:38 -0400
parents 87570e9b71f5
children 837c6955e4e9
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7:c23aa0cbc550 8:198b035d4848
1 # lib.r version="2.2.1" 1 # lib.r
2 2
3 #@author G. Le Corguille
3 #The function create a pdf from the different png generated by diffreport 4 #The function create a pdf from the different png generated by diffreport
4 diffreport_png2pdf <- function(filebase, new_file_path) { 5 diffreport_png2pdf <- function(filebase) {
5 6 dir.create("pdf")
6 pdfEicOutput = paste(new_file_path,filebase,"-eic_visible_pdf",sep="") 7
7 pdfBoxOutput = paste(new_file_path,filebase,"-box_visible_pdf",sep="") 8 pdfEicOutput = paste0("pdf/",filebase,"-eic_pdf.pdf")
8 9 pdfBoxOutput = paste0("pdf/",filebase,"-box_pdf.pdf")
9 system(paste("gm convert ",filebase,"_eic/*.png ",filebase,"_eic.pdf",sep="")) 10
10 system(paste("gm convert ",filebase,"_box/*.png ",filebase,"_box.pdf",sep="")) 11 system(paste0("gm convert ",filebase,"_eic/*.png ",pdfEicOutput))
11 12 system(paste0("gm convert ",filebase,"_box/*.png ",pdfBoxOutput))
12 file.copy(paste(filebase,"_eic.pdf",sep=""), pdfEicOutput) 13
13 file.copy(paste(filebase,"_box.pdf",sep=""), pdfBoxOutput) 14 }
15
16 #@author G. Le Corguille
17 #This function convert if it is required the Retention Time in minutes
18 RTSecondToMinute <- function(variableMetadata, convertRTMinute) {
19 if (convertRTMinute){
20 #converting the retention times (seconds) into minutes
21 print("converting the retention times into minutes in the variableMetadata")
22 variableMetadata[,"rt"]=variableMetadata[,"rt"]/60
23 variableMetadata[,"rtmin"]=variableMetadata[,"rtmin"]/60
24 variableMetadata[,"rtmax"]=variableMetadata[,"rtmax"]/60
25 }
26 return (variableMetadata)
27 }
28
29 #@author G. Le Corguille
30 #This function format ions identifiers
31 formatIonIdentifiers <- function(variableMetadata, numDigitsRT=0, numDigitsMZ=0) {
32 splitDeco = strsplit(as.character(variableMetadata$name),"_")
33 idsDeco = sapply(splitDeco, function(x) { deco=unlist(x)[2]; if (is.na(deco)) return ("") else return(paste0("_",deco)) })
34 namecustom = make.unique(paste0("M",round(variableMetadata[,"mz"],numDigitsMZ),"T",round(variableMetadata[,"rt"],numDigitsRT),idsDeco))
35 variableMetadata=cbind(name=variableMetadata$name, namecustom=namecustom, variableMetadata[,!(colnames(variableMetadata) %in% c("name"))])
36 return(variableMetadata)
14 } 37 }
15 38
16 #The function annotateDiffreport without the corr function which bugs 39 #The function annotateDiffreport without the corr function which bugs
17 annotatediff <- function(xset=xset, listArguments=listArguments, variableMetadataOutput="variableMetadata.tsv", dataMatrixOutput="dataMatrix.tsv",new_file_path=NULL) { 40 annotatediff <- function(xset=xset, listArguments=listArguments, variableMetadataOutput="variableMetadata.tsv", dataMatrixOutput="dataMatrix.tsv") {
18 # Resolve the bug with x11, with the function png 41 # Resolve the bug with x11, with the function png
19 options(bitmapType='cairo') 42 options(bitmapType='cairo')
20 43
21 #Check if the fillpeaks step has been done previously, if it hasn't, there is an error message and the execution is stopped.
22 res=try(is.null(xset@filled))
23
24 # ------ annot -------
25 listArguments[["calcCiS"]]=as.logical(listArguments[["calcCiS"]])
26 listArguments[["calcIso"]]=as.logical(listArguments[["calcIso"]])
27 listArguments[["calcCaS"]]=as.logical(listArguments[["calcCaS"]])
28
29 #graphMethod parameter bugs where this parameter is not defined in quick=true
30 if(listArguments[["quick"]]==TRUE) {
31 xa= annotate(object=xset,nSlaves=1,sigma=listArguments[["sigma"]],perfwhm=listArguments[["perfwhm"]],maxcharge=listArguments[["maxcharge"]],maxiso=listArguments[["maxiso"]],minfrac=listArguments[["minfrac"]],ppm=listArguments[["ppm"]],mzabs=listArguments[["mzabs"]],quick=listArguments[["quick"]],polarity=listArguments[["polarity"]],max_peaks=listArguments[["max_peaks"]],intval=listArguments[["intval"]])
32 }
33 else {
34 xa= annotate(object=xset,nSlaves=1,sigma=listArguments[["sigma"]],perfwhm=listArguments[["perfwhm"]],graphMethod=listArguments[["graphMethod"]],cor_eic_th=listArguments[["cor_eic_th"]],pval=listArguments[["pval"]],calcCiS=listArguments[["calcCiS"]],calcIso=listArguments[["calcIso"]],calcCaS=listArguments[["calcCaS"]],multiplier=listArguments[["multiplier"]],maxcharge=listArguments[["maxcharge"]],maxiso=listArguments[["maxiso"]],minfrac=listArguments[["minfrac"]],ppm=listArguments[["ppm"]],mzabs=listArguments[["mzabs"]],quick=listArguments[["quick"]],polarity=listArguments[["polarity"]],max_peaks=listArguments[["max_peaks"]],intval=listArguments[["intval"]])
35
36 }
37 peakList=getPeaklist(xa,intval=listArguments[["intval"]])
38 peakList=cbind(groupnames(xa@xcmsSet),peakList); colnames(peakList)[1] = c("name");
39
40
41 # --- Multi condition : diffreport ---
42 diffrep=NULL
43 if (!is.null(listArguments[["runDiffreport"]]) & nlevels(sampclass(xset))>=2) {
44 #Check if the fillpeaks step has been done previously, if it hasn't, there is an error message and the execution is stopped. 44 #Check if the fillpeaks step has been done previously, if it hasn't, there is an error message and the execution is stopped.
45 res=try(is.null(xset@filled)) 45 res=try(is.null(xset@filled))
46 classes=levels(sampclass(xset)) 46
47 x=1:(length(classes)-1) 47 # ------ annot -------
48 for (i in seq(along=x) ) { 48 listArguments[["calcCiS"]]=as.logical(listArguments[["calcCiS"]])
49 y=1:(length(classes)) 49 listArguments[["calcIso"]]=as.logical(listArguments[["calcIso"]])
50 for (n in seq(along=y)){ 50 listArguments[["calcCaS"]]=as.logical(listArguments[["calcCaS"]])
51 if(i+n <= length(classes)){ 51
52 filebase=paste(classes[i],class2=classes[i+n],sep="-vs-") 52 # common parameters
53 53 listArguments4annotate = list(object=xset,
54 diffrep=diffreport(object=xset,class1=classes[i],class2=classes[i+n],filebase=filebase,eicmax=listArguments[["eicmax"]],eicwidth=listArguments[["eicwidth"]],sortpval=TRUE,value=listArguments[["value"]],h=listArguments[["h"]],w=listArguments[["w"]],mzdec=listArguments[["mzdec"]]) 54 nSlaves=listArguments[["nSlaves"]],sigma=listArguments[["sigma"]],perfwhm=listArguments[["perfwhm"]],
55 #combines results 55 maxcharge=listArguments[["maxcharge"]],maxiso=listArguments[["maxiso"]],minfrac=listArguments[["minfrac"]],
56 diffreportTSV=merge(peakList, diffrep[,c("name","fold","tstat","pvalue")], by.x="name", by.y="name", sort=F) 56 ppm=listArguments[["ppm"]],mzabs=listArguments[["mzabs"]],quick=listArguments[["quick"]],
57 diffreportTSV=cbind(diffreportTSV[,!(colnames(diffreportTSV) %in% c(sampnames(xa@xcmsSet)))],diffreportTSV[,(colnames(diffreportTSV) %in% c(sampnames(xa@xcmsSet)))]) 57 polarity=listArguments[["polarity"]],max_peaks=listArguments[["max_peaks"]],intval=listArguments[["intval"]])
58 58
59 if(listArguments[["sortpval"]]){ 59 # quick == FALSE
60 diffreportTSV=diffreportTSV[order(diffreportTSV$pvalue), ] 60 if(listArguments[["quick"]]==FALSE) {
61 } 61 listArguments4annotate = append(listArguments4annotate,
62 62 list(graphMethod=listArguments[["graphMethod"]],cor_eic_th=listArguments[["cor_eic_th"]],pval=listArguments[["pval"]],
63 if (listArguments[["convert_param"]]){ 63 calcCiS=listArguments[["calcCiS"]],calcIso=listArguments[["calcIso"]],calcCaS=listArguments[["calcCaS"]]))
64 #converting the retention times (seconds) into minutes 64 # no ruleset
65 diffreportTSV$rt=diffreportTSV$rt/60;diffreportTSV$rtmin=diffreportTSV$rtmin/60; diffreportTSV$rtmax=diffreportTSV$rtmax/60; 65 if (!is.null(listArguments[["multiplier"]])) {
66 } 66 listArguments4annotate = append(listArguments4annotate,
67 write.table(diffreportTSV, sep="\t", quote=FALSE, row.names=FALSE, file=paste(new_file_path,filebase,"-tabular_visible_tabular",sep="")) 67 list(multiplier=listArguments[["multiplier"]]))
68 68 }
69 if (listArguments[["eicmax"]] != 0) { 69 # ruleset
70 diffreport_png2pdf(filebase, new_file_path) 70 else {
71 } 71 rulset=read.table(listArguments[["rules"]], h=T, sep=";")
72 } 72 if (ncol(rulset) < 4) rulset=read.table(listArguments[["rules"]], h=T, sep="\t")
73 } 73 if (ncol(rulset) < 4) rulset=read.table(listArguments[["rules"]], h=T, sep=",")
74 } 74 if (ncol(rulset) < 4) {
75 } 75 error_message="Your ruleset file seems not well formatted. The column separators accepted are ; , and tabulation"
76 76 print(error_message)
77 77 stop(error_message)
78 78 }
79 79
80 # --- variableMetadata --- 80 listArguments4annotate = append(listArguments4annotate,
81 variableMetadata=peakList[,!(make.names(colnames(peakList)) %in% c(make.names(sampnames(xa@xcmsSet))))] 81 list(rules=rulset))
82 # if we have 2 conditions, we keep stat of diffrep 82 }
83 if (!is.null(listArguments[["runDiffreport"]]) & nlevels(sampclass(xset))==2) { 83 }
84 variableMetadata = merge(variableMetadata, diffrep[,c("name","fold","tstat","pvalue")],by.x="name", by.y="name", sort=F) 84
85 if(exists("listArguments[[\"sortpval\"]]")){ 85
86 variableMetadata=variableMetadata[order(variableMetadata$pvalue), ] 86 # launch annotate
87 } 87 xa = do.call("annotate", listArguments4annotate)
88 } 88 peakList=getPeaklist(xa,intval=listArguments[["intval"]])
89 89 peakList=cbind(groupnames(xa@xcmsSet),peakList); colnames(peakList)[1] = c("name");
90 variableMetadataOri=variableMetadata 90
91 if (listArguments[["convert_param"]]){ 91 # --- dataMatrix ---
92 #converting the retention times (seconds) into minutes 92 dataMatrix = peakList[,(make.names(colnames(peakList)) %in% c("name", make.names(sampnames(xa@xcmsSet))))]
93 print("converting the retention times into minutes in the variableMetadata") 93 write.table(dataMatrix, sep="\t", quote=FALSE, row.names=FALSE, file=dataMatrixOutput)
94 variableMetadata$rt=variableMetadata$rt/60;variableMetadata$rtmin=variableMetadata$rtmin/60; variableMetadata$rtmax=variableMetadata$rtmax/60; 94
95 } 95
96 #Transform metabolites name 96 # --- Multi condition : diffreport ---
97 variableMetadata$name= paste("M",round(variableMetadata$mz,digits=listArguments[["num_digits"]]),"T",round(variableMetadata$rt),sep="") 97 diffrepOri=NULL
98 write.table(variableMetadata, sep="\t", quote=FALSE, row.names=FALSE, file=variableMetadataOutput) 98 if (!is.null(listArguments[["runDiffreport"]]) & nlevels(sampclass(xset))>=2) {
99 99 #Check if the fillpeaks step has been done previously, if it hasn't, there is an error message and the execution is stopped.
100 # --- dataMatrix --- 100 res=try(is.null(xset@filled))
101 dataMatrix = peakList[,(make.names(colnames(peakList)) %in% c(make.names(sampnames(xa@xcmsSet))))] 101 classes=levels(sampclass(xset))
102 dataMatrix=cbind(peakList$name,dataMatrix); colnames(dataMatrix)[1] = c("name"); 102 x=1:(length(classes)-1)
103 103 for (i in seq(along=x) ) {
104 if (listArguments[["convert_param"]]){ 104 y=1:(length(classes))
105 #converting the retention times (seconds) into minutes 105 for (n in seq(along=y)){
106 print("converting the retention times into minutes in the dataMatrix ids") 106 if(i+n <= length(classes)){
107 peakList$rt=peakList$rt/60 107 filebase=paste(classes[i],class2=classes[i+n],sep="-vs-")
108 } 108
109 dataMatrix$name= paste("M",round(peakList$mz,digits=listArguments[["num_digits"]]),"T",round(peakList$rt),sep="") 109 diffrep=diffreport(object=xset,class1=classes[i],class2=classes[i+n],filebase=filebase,eicmax=listArguments[["eicmax"]],eicwidth=listArguments[["eicwidth"]],sortpval=TRUE,value=listArguments[["value"]],h=listArguments[["h"]],w=listArguments[["w"]],mzdec=listArguments[["mzdec"]])
110 write.table(dataMatrix, sep="\t", quote=FALSE, row.names=FALSE, file=dataMatrixOutput) 110
111 111 diffrepOri = diffrep
112 return(list("xa"=xa,"diffrep"=diffrep,"variableMetadata"=variableMetadataOri)); 112
113 113 # renamming of the column rtmed to rt to fit with camera peaklist function output
114 } 114 colnames(diffrep)[colnames(diffrep)=="rtmed"] <- "rt"
115 115 colnames(diffrep)[colnames(diffrep)=="mzmed"] <- "mz"
116 116
117 combinexsAnnos_function <- function(xaP, xaN, listOFlistArgumentsP,listOFlistArgumentsN, diffrepP=NULL,diffrepN=NULL,convert_param=FALSE,pos=TRUE,tol=2,ruleset=NULL,keep_meta=TRUE, variableMetadataOutput="variableMetadata.tsv"){ 117 # combines results and reorder columns
118 118 diffrep = merge(peakList, diffrep[,c("name","fold","tstat","pvalue")], by.x="name", by.y="name", sort=F)
119 #Load the two Rdata to extract the xset objects from positive and negative mode 119 diffrep = cbind(diffrep[,!(colnames(diffrep) %in% c(sampnames(xa@xcmsSet)))],diffrep[,(colnames(diffrep) %in% c(sampnames(xa@xcmsSet)))])
120 cat("\tObject xset from positive mode\n") 120
121 print(xaP) 121 diffrep = RTSecondToMinute(diffrep, listArguments[["convertRTMinute"]])
122 cat("\n") 122 diffrep = formatIonIdentifiers(diffrep, numDigitsRT=listArguments[["numDigitsRT"]], numDigitsMZ=listArguments[["numDigitsMZ"]])
123 123
124 cat("\tObject xset from negative mode\n") 124 if(listArguments[["sortpval"]]){
125 print(xaN) 125 diffrep=diffrep[order(diffrep$pvalue), ]
126 cat("\n") 126 }
127 127
128 cat("\n") 128 dir.create("tabular")
129 cat("\tCombining...\n") 129 write.table(diffrep, sep="\t", quote=FALSE, row.names=FALSE, file=paste("tabular/",filebase,"_tsv.tabular",sep=""))
130 #Convert the string to numeric for creating matrix 130
131 row=as.numeric(strsplit(ruleset,",")[[1]][1]) 131 if (listArguments[["eicmax"]] != 0) {
132 column=as.numeric(strsplit(ruleset,",")[[1]][2]) 132 diffreport_png2pdf(filebase)
133 ruleset=cbind(row,column) 133 }
134 #Test if the file comes from an older version tool 134 }
135 if ((!is.null(xaP)) & (!is.null(xaN))) { 135 }
136 #Launch the combinexsannos function from CAMERA 136 }
137 cAnnot=combinexsAnnos(xaP, xaN,pos=pos,tol=tol,ruleset=ruleset) 137 }
138 } else { 138
139 stop("You must relauch the CAMERA.annotate step with the lastest version.") 139
140 } 140 # --- variableMetadata ---
141 141 variableMetadata=peakList[,!(make.names(colnames(peakList)) %in% c(make.names(sampnames(xa@xcmsSet))))]
142 142 variableMetadata = RTSecondToMinute(variableMetadata, listArguments[["convertRTMinute"]])
143 143 variableMetadata = formatIonIdentifiers(variableMetadata, numDigitsRT=listArguments[["numDigitsRT"]], numDigitsMZ=listArguments[["numDigitsMZ"]])
144 if(pos){ 144 # if we have 2 conditions, we keep stat of diffrep
145 xa=xaP 145 if (!is.null(listArguments[["runDiffreport"]]) & nlevels(sampclass(xset))==2) {
146 listOFlistArgumentsP=listOFlistArguments 146 variableMetadata = merge(variableMetadata, diffrep[,c("name","fold","tstat","pvalue")],by.x="name", by.y="name", sort=F)
147 mode="neg. Mode" 147 if(exists("listArguments[[\"sortpval\"]]")){
148 } else { 148 variableMetadata=variableMetadata[order(variableMetadata$pvalue), ]
149 xa=xaN 149 }
150 listOFlistArgumentsN=listOFlistArguments 150 }
151 mode="pos. Mode" 151
152 } 152 variableMetadataOri=variableMetadata
153 intval = "into"; for (steps in names(listOFlistArguments)) { if (!is.null(listOFlistArguments[[steps]]$intval)) intval = listOFlistArguments[[steps]]$intval } 153 write.table(variableMetadata, sep="\t", quote=FALSE, row.names=FALSE, file=variableMetadataOutput)
154 peakList=getPeaklist(xa,intval=intval) 154
155 peakList=cbind(groupnames(xa@xcmsSet),peakList); colnames(peakList)[1] = c("name"); 155 return(list("xa"=xa,"diffrep"=diffrepOri,"variableMetadata"=variableMetadataOri));
156 variableMetadata=cbind(peakList, cAnnot[, c("isotopes", "adduct", "pcgroup",mode)]); 156
157 variableMetadata=variableMetadata[,!(colnames(variableMetadata) %in% c(sampnames(xa@xcmsSet)))] 157 }
158 158
159 #Test if there are more than two classes (conditions) 159
160 if ( nlevels(sampclass(xaP@xcmsSet))==2 & (!is.null(diffrepN)) & (!is.null(diffrepP))) { 160 combinexsAnnos_function <- function(xaP, xaN, listOFlistArgumentsP,listOFlistArgumentsN, diffrepP=NULL,diffrepN=NULL,pos=TRUE,tol=2,ruleset=NULL,keep_meta=TRUE, convertRTMinute=F, numDigitsMZ=0, numDigitsRT=0, variableMetadataOutput="variableMetadata.tsv"){
161 diffrepP = diffrepP[,c("name","fold","tstat","pvalue")]; colnames(diffrepP) = paste("P.",colnames(diffrepP),sep="") 161
162 diffrepN = diffrepN[,c("name","fold","tstat","pvalue")]; colnames(diffrepN) = paste("N.",colnames(diffrepN),sep="") 162 #Load the two Rdata to extract the xset objects from positive and negative mode
163 163 cat("\tObject xset from positive mode\n")
164 variableMetadata = merge(variableMetadata, diffrepP, by.x="name", by.y="P.name") 164 print(xaP)
165 variableMetadata = merge(variableMetadata, diffrepN, by.x="name", by.y="N.name") 165 cat("\n")
166 } 166
167 167 cat("\tObject xset from negative mode\n")
168 rownames(variableMetadata) = NULL 168 print(xaN)
169 #TODO: checker 169 cat("\n")
170 #colnames(variableMetadata)[1:2] = c("name","mz/rt"); 170
171 171 cat("\n")
172 #If the user want to convert the retention times (seconds) into minutes. 172 cat("\tCombining...\n")
173 if (listArguments[["convert_param"]]){ 173 #Convert the string to numeric for creating matrix
174 #converting the retention times (seconds) into minutes 174 row=as.numeric(strsplit(ruleset,",")[[1]][1])
175 cat("\tConverting the retention times into minutes\n") 175 column=as.numeric(strsplit(ruleset,",")[[1]][2])
176 variableMetadata$rtmed=cAnnot$rt/60; variableMetadata$rtmin=cAnnot$rtmin/60; variableMetadata$rtmax=cAnnot$rtmax/60; 176 ruleset=cbind(row,column)
177 } 177 #Test if the file comes from an older version tool
178 178 if ((!is.null(xaP)) & (!is.null(xaN))) {
179 #If the user want to keep only the metabolites which match a difference 179 #Launch the combinexsannos function from CAMERA
180 if(keep_meta){ 180 cAnnot=combinexsAnnos(xaP, xaN,pos=pos,tol=tol,ruleset=ruleset)
181 variableMetadata=variableMetadata[variableMetadata[,c(mode)]!="",] 181 } else {
182 } 182 stop("You must relauch the CAMERA.annotate step with the lastest version.")
183 183 }
184 #Write the output into a tsv file 184
185 write.table(variableMetadata, sep="\t", quote=FALSE, row.names=FALSE, file=variableMetadataOutput) 185 if(pos){
186 return(variableMetadata); 186 xa=xaP
187 187 listOFlistArgumentsP=listOFlistArguments
188 } 188 mode="neg. Mode"
189 } else {
190 xa=xaN
191 listOFlistArgumentsN=listOFlistArguments
192 mode="pos. Mode"
193 }
194
195 peakList=getPeaklist(xa)
196 peakList=cbind(groupnames(xa@xcmsSet),peakList); colnames(peakList)[1] = c("name");
197 variableMetadata=cbind(peakList, cAnnot[, c("isotopes", "adduct", "pcgroup",mode)]);
198 variableMetadata=variableMetadata[,!(colnames(variableMetadata) %in% c(sampnames(xa@xcmsSet)))]
199
200 #Test if there are more than two classes (conditions)
201 if ( nlevels(sampclass(xaP@xcmsSet))==2 & (!is.null(diffrepN)) & (!is.null(diffrepP))) {
202 diffrepP = diffrepP[,c("name","fold","tstat","pvalue")]; colnames(diffrepP) = paste("P.",colnames(diffrepP),sep="")
203 diffrepN = diffrepN[,c("name","fold","tstat","pvalue")]; colnames(diffrepN) = paste("N.",colnames(diffrepN),sep="")
204
205 variableMetadata = merge(variableMetadata, diffrepP, by.x="name", by.y="P.name")
206 variableMetadata = merge(variableMetadata, diffrepN, by.x="name", by.y="N.name")
207 }
208
209 rownames(variableMetadata) = NULL
210 #TODO: checker
211 #colnames(variableMetadata)[1:2] = c("name","mz/rt");
212
213 variableMetadata = RTSecondToMinute(variableMetadata, convertRTMinute)
214 variableMetadata = formatIonIdentifiers(variableMetadata, numDigitsRT=numDigitsRT, numDigitsMZ=numDigitsMZ)
215
216 #If the user want to keep only the metabolites which match a difference
217 if(keep_meta){
218 variableMetadata=variableMetadata[variableMetadata[,c(mode)]!="",]
219 }
220
221 #Write the output into a tsv file
222 write.table(variableMetadata, sep="\t", quote=FALSE, row.names=FALSE, file=variableMetadataOutput)
223 return(variableMetadata);
224
225 }
226
227 # This function get the raw file path from the arguments
228 getRawfilePathFromArguments <- function(singlefile, zipfile, listArguments) {
229 if (!is.null(listArguments[["zipfile"]])) zipfile = listArguments[["zipfile"]]
230 if (!is.null(listArguments[["zipfilePositive"]])) zipfile = listArguments[["zipfilePositive"]]
231 if (!is.null(listArguments[["zipfileNegative"]])) zipfile = listArguments[["zipfileNegative"]]
232
233 if (!is.null(listArguments[["singlefile_galaxyPath"]])) {
234 singlefile_galaxyPaths = listArguments[["singlefile_galaxyPath"]];
235 singlefile_sampleNames = listArguments[["singlefile_sampleName"]]
236 }
237 if (!is.null(listArguments[["singlefile_galaxyPathPositive"]])) {
238 singlefile_galaxyPaths = listArguments[["singlefile_galaxyPathPositive"]];
239 singlefile_sampleNames = listArguments[["singlefile_sampleNamePositive"]]
240 }
241 if (!is.null(listArguments[["singlefile_galaxyPathNegative"]])) {
242 singlefile_galaxyPaths = listArguments[["singlefile_galaxyPathNegative"]];
243 singlefile_sampleNames = listArguments[["singlefile_sampleNameNegative"]]
244 }
245 if (exists("singlefile_galaxyPaths")){
246 singlefile_galaxyPaths = unlist(strsplit(singlefile_galaxyPaths,","))
247 singlefile_sampleNames = unlist(strsplit(singlefile_sampleNames,","))
248
249 singlefile=NULL
250 for (singlefile_galaxyPath_i in seq(1:length(singlefile_galaxyPaths))) {
251 singlefile_galaxyPath=singlefile_galaxyPaths[singlefile_galaxyPath_i]
252 singlefile_sampleName=singlefile_sampleNames[singlefile_galaxyPath_i]
253 singlefile[[singlefile_sampleName]] = singlefile_galaxyPath
254 }
255 }
256 for (argument in c("zipfile","zipfilePositive","zipfileNegative","singlefile_galaxyPath","singlefile_sampleName","singlefile_galaxyPathPositive","singlefile_sampleNamePositive","singlefile_galaxyPathNegative","singlefile_sampleNameNegative")) {
257 listArguments[[argument]]=NULL
258 }
259 return(list(zipfile=zipfile, singlefile=singlefile, listArguments=listArguments))
260 }
261
262
263 # This function retrieve the raw file in the working directory
264 # - if zipfile: unzip the file with its directory tree
265 # - if singlefiles: set symlink with the good filename
266 retrieveRawfileInTheWorkingDirectory <- function(singlefile, zipfile) {
267 if(!is.null(singlefile) && (length("singlefile")>0)) {
268 for (singlefile_sampleName in names(singlefile)) {
269 singlefile_galaxyPath = singlefile[[singlefile_sampleName]]
270 if(!file.exists(singlefile_galaxyPath)){
271 error_message=paste("Cannot access the sample:",singlefile_sampleName,"located:",singlefile_galaxyPath,". Please, contact your administrator ... if you have one!")
272 print(error_message); stop(error_message)
273 }
274
275 file.symlink(singlefile_galaxyPath,singlefile_sampleName)
276 }
277 directory = "."
278
279 }
280 if(!is.null(zipfile) && (zipfile!="")) {
281 if(!file.exists(zipfile)){
282 error_message=paste("Cannot access the Zip file:",zipfile,". Please, contact your administrator ... if you have one!")
283 print(error_message)
284 stop(error_message)
285 }
286
287 #list all file in the zip file
288 #zip_files=unzip(zipfile,list=T)[,"Name"]
289
290 #unzip
291 suppressWarnings(unzip(zipfile, unzip="unzip"))
292
293 #get the directory name
294 filesInZip=unzip(zipfile, list=T);
295 directories=unique(unlist(lapply(strsplit(filesInZip$Name,"/"), function(x) x[1])));
296 directories=directories[!(directories %in% c("__MACOSX")) & file.info(directories)$isdir]
297 directory = "."
298 if (length(directories) == 1) directory = directories
299
300 cat("files_root_directory\t",directory,"\n")
301
302 }
303 return (directory)
304 }