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comparison selection.R @ 0:4d539083cf7f draft

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planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
author sblanck
date Tue, 12 May 2020 10:40:36 -0400
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-1:000000000000 0:4d539083cf7f
1 #!/usr/bin/env Rscript
2 # setup R error handling to go to stderr
3 options( show.error.messages=F, error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } )
4
5 # we need that to not crash galaxy with an UTF8 error on German LC settings.
6 loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
7
8 library("optparse")
9
10 ##### Read options
11 option_list=list(
12 make_option("--chrom",type="character",default=NULL, dest="chrom"),
13 make_option("--input",type="character",default=NULL, dest="input"),
14 make_option("--output",type="character",default=NULL, dest="output"),
15 make_option("--new_file_path",type="character",default=NULL, dest="new_file_path"),
16 make_option("--response",type="character",default=NULL, dest="response"),
17 make_option("--settingsType",type="character",default=NULL, dest="settingsType"),
18 make_option("--outputgraph",type="character",default=NULL, dest="outputgraph"),
19 make_option("--settingsSnp",type="character",default=NULL, dest="settingsSnp"),
20 make_option("--settingsSignal",type="character",default=NULL, dest="settingsSignal"),
21 make_option("--settingsLoss",type="character",default=NULL, dest="settingsLoss"),
22 make_option("--pdffigures",type="character",default=NULL, dest="pdffigures"),
23 make_option("--folds",type="character",default=NULL, dest="folds"),
24 make_option("--outputlog",type="character",default=NULL, dest="outputlog"),
25 make_option("--log",type="character",default=NULL, dest="log"),
26 make_option("--userId",type="character",default=NULL, dest="userid"),
27 make_option("--settingsPackage",type="character",default=NULL, dest="settingsPackage")
28 );
29
30 opt_parser = OptionParser(option_list=option_list);
31 opt = parse_args(opt_parser);
32
33 if(is.null(opt$input)){
34 print_help(opt_parser)
35 stop("input required.", call.=FALSE)
36 }
37
38 #loading libraries
39
40
41 chrom=opt$chrom
42 dataset=opt$input
43 dataResponse=opt$response
44 output=opt$output
45 tmp_dir=opt$new_file_path
46 signal=opt$settingsSignal
47 settingsType=opt$settingsType
48 outputfigures=type.convert(opt$outputgraph)
49 snp=type.convert(opt$settingsSnp)
50 user=opt$userid
51 folds=as.numeric(opt$folds)
52 loss=opt$settingsLoss
53 log=opt$log
54 outputlog=opt$outputlog
55 outputgraph=opt$outputgraph
56 pdffigures=opt$pdffigures
57 package=opt$settingsPackage
58
59
60 library(MPAgenomics)
61 library(glmnet)
62 library(spikeslab)
63 library(lars)
64
65 inputDataset=read.table(file=dataset,stringsAsFactors=FALSE)
66 input=inputDataset[1,2]
67 workdir=file.path(tmp_dir, "mpagenomics",user)
68 print(workdir)
69 setwd(workdir)
70
71 if (grepl("all",tolower(chrom)) | chrom=="None") {
72 chrom_vec=c(1:25)
73 } else {
74 chrom_tmp <- strsplit(chrom,",")
75 chrom_vecstring <-unlist(chrom_tmp)
76 chrom_vec <- as.numeric(chrom_vecstring)
77 }
78
79 if (outputlog){
80 sinklog <- file(log, open = "wt")
81 sink(sinklog ,type = "output")
82 sink(sinklog, type = "message")
83 }
84
85 if (settingsType == "tumor") {
86 if (signal=="CN") {
87 res=markerSelection(input,dataResponse, chromosome=chrom_vec, signal=signal, normalTumorArray=tumor, onlySNP=snp, loss=loss, plot=outputfigures, nbFolds=folds, pkg=package)
88 } else {
89 res=markerSelection(input,dataResponse, chromosome=chrom_vec,signal=signal,normalTumorArray=tumor, loss=loss, plot=outputfigures, nbFolds=folds,pkg=package)
90 }
91 } else {
92 if (signal=="CN") {
93 res=markerSelection(input,dataResponse, chromosome=chrom_vec, signal=signal, onlySNP=snp, loss=loss, plot=outputfigures, nbFolds=folds,pkg=package)
94 } else {
95 res=markerSelection(input,dataResponse, chromosome=chrom_vec, signal=signal, loss=loss, plot=outputfigures, nbFolds=folds,pkg=package)
96 }
97 }
98
99 res
100
101 df=data.frame()
102 list_chr=names(res)
103 markerSelected=FALSE
104
105 for (i in list_chr) {
106 chr_data=res[[i]]
107 len=length(chr_data$markers.index)
108 if (len != 0)
109 {
110 markerSelected=TRUE
111 chrdf=data.frame(rep(i,len),chr_data$markers.position,chr_data$markers.index,chr_data$markers.names,chr_data$coefficient)
112 df=rbind(df,chrdf)
113 }
114 }
115
116 if (outputgraph){
117 file.rename(file.path(tmp_dir,"mpagenomics",user,"Rplots.pdf"), pdffigures)
118 }
119
120 if (outputlog){
121 sink(type="output")
122 sink(type="message")
123 close(sinklog)
124 }
125
126 if (markerSelected) {
127 colnames(df) <- c("chr","position","index","names","coefficient")
128 #sink(output)
129 #print(format(df),row.names=FALSE)
130 #sink()
131 write.table(df,output,row.names = FALSE, quote = FALSE, sep = "\t")
132 } else
133 writeLines("no SNP selected", output)
134
135