Mercurial > repos > pavlo-lutsik > rnbeads

comparison RnBeadsGalaxy.R @ 43:39b78c48d064 draft

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author pavlo-lutsik
date Fri, 05 Jul 2013 17:39:25 -0400
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42:16f6ef2b3251 43:39b78c48d064
1 #msg.file<-file("RnBeads.messages.out", open="w")
2 #sink(file=msg.file)
3
4
5 ## add the RnBeads dependencies if we are on a cloud share-instance
6 if("Rsitelibrary" %in% list.files("/mnt")){
7
8 .libPaths("/mnt/galaxy/Rsitelibrary")
9
10
11 }
12
13 if(!'wordcloud' %in% rownames(installed.packages())){
14 install.packages('wordcloud',repos='http://cran.us.r-project.org')
15 }
16
17 suppressWarnings(suppressPackageStartupMessages(library(RnBeads)))
18 suppressWarnings(suppressPackageStartupMessages(library(getopt)))
19
20 #all.opts<-names(rnb.options())
21 opt.class<-RnBeads:::OPTION.TYPES[-28]
22 all.opts<-names(opt.class)
23 #all.opts<-paste("--", all.opts, sep="")
24 #all.opts<-gsub("\\.([a-z])", "\\U\\1", all.opts, perl=TRUE)
25 all.opts<-gsub("\\.","-", all.opts)
26 #opt.class<-sapply(rnb.options(), class)
27
28 rnb.opt.spec<-data.frame(
29 Long=all.opts,
30 Short=as.character(1:length(all.opts)),
31 Mask=c(1,2)[as.integer((opt.class=="logical"))+1],
32 Type=opt.class)
33
34 ### automated xml file preparation
35 xml.strings<-apply(rnb.opt.spec,1, function(row){
36
37 opt.lab<-gsub("-", ".", row[1])
38 opt.def.val<-rnb.getOption(opt.lab)
39 opt.name<-gsub("-([0-9a-z])", "\\U\\1", row[1], perl=TRUE)
40 tf.opt<-"\t\t\t<option value=\"True\">True</option>\n\t\t\t<option value=\"False\">False</option>"
41 opt.lab<-paste(opt.lab, gsub("\\."," ", row[4]), sep=", ")
42 if(row[4]=="logical"){
43 opt.type<-'select'
44 if(!is.null(opt.def.val) && opt.def.val)
45 opt.def.val<-"1" else
46 opt.def.val<-"0"
47 string<-sprintf("\t\t<param name=\"%s\" type=\"%s\" label=\"%s\" value=\"%s\">\n%s\n\t\t</param>\n", opt.name, opt.type, opt.lab, opt.def.val, tf.opt)
48 }else{
49 opt.type<-'text'
50 if(!is.null(opt.def.val) && opt.def.val!="")
51 opt.def.val<-paste(opt.def.val, collapse=",") else
52 opt.def.val<-""
53 string<-sprintf("\t\t<param name=\"%s\" type=\"%s\" label=\"%s\" value=\"%s\"/>\n", opt.name, opt.type, opt.lab, opt.def.val)
54 }
55 string
56 })
57
58 cat(xml.strings, sep="", file="automated.settings.xml.txt")
59
60 opt.def.strings<-apply(rnb.opt.spec,1, function(row){
61
62 opt.name<-gsub("-([0-9a-z])", "\\U\\1", row[1], perl=TRUE)
63 opt.long<-row[1]
64 opt.short<-row[2]
65
66 if(row[4]=="logical"){
67 def.string<-sprintf("#if str( $options.%s ) == \"True\"\n\t--%s\n#end if\n", opt.name, opt.long)
68 }else{
69 def.string<-sprintf("#if str( $options.%s ) != \"\"\n\t--%s=\"$options.%s\" \n#end if\n", opt.name, opt.long, opt.name)
70 }
71 def.string
72
73 })
74 cat(opt.def.strings, sep="", file="automated.option.assignments.txt")
75
76
77 rnb.opt.spec$Type<-gsub("\\.vector", "", rnb.opt.spec$Type)
78 rnb.opt.spec$Type<-gsub("numeric", "double", rnb.opt.spec$Type)
79 rnb.opt.spec<-rbind(data.frame(
80 Long=c("data-type", "pheno", "idat-dir","idat-files","bed-files", "gs-report", "geo-series", "betas", "pvals","output-file", "report-dir"),
81 Short=c("d","s","a","i","f","g","e","b","p","r","o"),
82 Mask=c(1,2,2,2,2,2,2,2,2,1,1),
83 Type=c("character","character","character","character","character","character","character","character","character","character", "character")),
84 rnb.opt.spec)
85
86 opts<-getopt(as.matrix(rnb.opt.spec))
87 #opts<-getopt(as.matrix(rnb.opt.spec), opt=list("--data-type=idats","--report-dir=dir", "--idats=file1\tfile2"))
88 print(opts)
89
90 if(opts[["data-type"]]=="idatDir"){
91
92 data.source<-list()
93 data.type<-"idat.dir"
94 data.source[["idat.dir"]]<-opts[["idat-dir"]]
95 data.source[["sample.sheet"]]<-opts[["pheno"]]
96
97 }else if(opts[["data-type"]]=="idatFiles"){
98
99 data.type<-"idat.dir"
100 file.string<-gsub(" ","", opts[["idat-files"]])
101 files<-strsplit(file.string, ",")[[1]]
102 files<-files[files!=""]
103 bed.dir<-sprintf("%s_beds",opts[["report-dir"]])
104 dir.create(bed.dir)
105 file.copy(files, bed.dir)
106 for(dat.file in list.files(bed.dir, full.names = TRUE)){
107 file.rename(dat.file, gsub("\\.dat", ".bed", dat.file))
108 }
109 data.source<-list()
110 data.source[["bed.dir"]]<-bed.dir
111 data.source[["sample.sheet"]]<-opts[["pheno"]]
112
113
114 }else if(opts[["data-type"]]=="GS.report"){
115
116 data.type<-"GS.report"
117 data.source<-opts[["gs-report"]]
118
119 }else if(opts[["data-type"]]=="GEO"){
120
121 data.type<-"GEO"
122 data.source<-opts[["geo-series"]]
123
124 }else if(opts[["data-type"]]=="data.files"){
125
126 data.type<-"GEO"
127 data.source<-opts[["geo-series"]]
128
129 }else if(opts[["data-type"]]=="data.files"){
130
131 data.type<-"data.files"
132 data.source<-c(opts[["pheno"]], opts[["betas"]])
133 if(!is.null(opts[["pvals"]]))
134 data.source<-c(data.source, opts[["pvals"]])
135
136 }else if(opts[["data-type"]]=="bed.dir"){
137
138 data.type<-"bed.dir"
139 file.string<-gsub(" ","", opts[["bed-files"]])
140 files<-strsplit(file.string, ",")[[1]]
141 files<-files[files!=""]
142 bed.dir<-sprintf("%s_beds",opts[["report-dir"]])
143 dir.create(bed.dir)
144 file.copy(files, bed.dir)
145 for(dat.file in list.files(bed.dir, full.names = TRUE)){
146 file.rename(dat.file, gsub("\\.dat", ".bed", dat.file))
147 }
148 data.source<-list()
149 data.source[["bed.dir"]]<-bed.dir
150
151 logger.start(fname="NA")
152 sample.sheet<-rnb.read.annotation(opts[["pheno"]])
153 logger.close()
154 if(length(files) < nrow(sample.sheet))
155 stop("Not all bed files are present")
156
157 cn<-colnames(sample.sheet)
158 dat.files<-sapply(strsplit(files, "\\/"), function(el) el[length(el)])
159 sample.sheet<-cbind(sample.sheet, gsub("\\.dat", ".bed", dat.files))
160 colnames(sample.sheet)<-c(cn, "BED_files")
161 data.source[["sample.sheet"]]<-sample.sheet
162 }
163
164 if("logging" %in% names(opts)){ # TODO create a cleaner way of checking whether the full options set was supplied
165
166 dump<-sapply(names(opt.class), function(on){
167 getoptname<-gsub("-", "\\.","-",on)
168 if(getoptname %in% names(opts)){
169 if(opt.class[on]=="logical"){
170 ov<-TRUE
171 }else if(opt.class %in% c("character","character.vector")){
172 ov<-opts[[getoptname]]
173 ov<-gsub("\"", "", ov)
174 if(opt.class=="character.vector"){
175 ov<-as.character(strsplit(ov,","))
176 }
177
178 }else if(opt.class %in% c("integer","numeric","integer.vector","numeric.vector")){
179 ov<-opts[[getoptname]]
180 ov<-gsub("\"", "", ov)
181 if(opt.class %in% c("integer.vector","numeric.vector")){
182 ov<-as.character(strsplit(ov,","))
183 }
184 }
185 eval(parse(text=sprintf("rnb.options(%s=ov)",on)))
186 }
187 })
188
189 logical.opts<-names(opt.class[opt.class=="logical"])
190 logical.opts.false<-logical.opts[!logical.opts %in% gsub("-",".",names(opts))]
191
192
193 dump<-sapply(logical.opts.false, function(on){
194 eval(parse(text=sprintf("rnb.options(%s=FALSE)",on)))
195 })
196 }
197
198 print(rnb.options())
199
200 #report.out.dir<-sprintf("%s_rnbReport", tempdir())
201 report.out.dir<-opts[["report-dir"]]
202 print("Starting RnBeads with the following inputs:")
203 print(data.source)
204 print(report.out.dir)
205 print(data.type)
206 rnb.run.analysis(data.source=data.source, dir.report=report.out.dir, data.type=data.type)
207
208
209 #sink(file=NULL)
210 #flush(msg.file)
211 #close(msg.file)