Mercurial > repos > sblanck > mpagenomics_wrappers

comparison selection.R @ 8:d5ed62b4d3ac draft default tip

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planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233
author sblanck
date Tue, 12 May 2020 13:40:07 +0000
parents af4f63f27c77
children
comparison
equal deleted inserted replaced
7:f2d24110f65a 8:d5ed62b4d3ac
1 args<-commandArgs(TRUE) 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 ) } )
2 4
3 input=args[1] 5 # we need that to not crash galaxy with an UTF8 error on German LC settings.
4 dataResponse=args[2] 6 loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
5 chrom=args[3] 7
6 tmp_dir=args[4] 8 library("optparse")
7 signal=args[5] 9
8 snp=type.convert(args[6]) 10 ##### Read options
9 settingsType=args[7] 11 option_list=list(
10 tumor=args[8] 12 make_option("--chrom",type="character",default=NULL, dest="chrom"),
11 fold=as.integer(args[9]) 13 make_option("--input",type="character",default=NULL, dest="input"),
12 loss=args[10] 14 make_option("--output",type="character",default=NULL, dest="output"),
13 plot=type.convert(args[11]) 15 make_option("--new_file_path",type="character",default=NULL, dest="new_file_path"),
14 output=args[12] 16 make_option("--response",type="character",default=NULL, dest="response"),
15 user=args[13] 17 make_option("--settingsType",type="character",default=NULL, dest="settingsType"),
16 package=args[14] 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
17 58
18 59
19 library(MPAgenomics) 60 library(MPAgenomics)
20 library(glmnet) 61 library(glmnet)
21 library(spikeslab) 62 library(spikeslab)
22 library(lars) 63 library(lars)
64
65 inputDataset=read.table(file=dataset,stringsAsFactors=FALSE)
66 input=inputDataset[1,2]
23 workdir=file.path(tmp_dir, "mpagenomics",user) 67 workdir=file.path(tmp_dir, "mpagenomics",user)
68 print(workdir)
24 setwd(workdir) 69 setwd(workdir)
25 70
26 if (grepl("all",tolower(chrom)) | chrom=="None") { 71 if (grepl("all",tolower(chrom)) | chrom=="None") {
27 chrom_vec=c(1:25) 72 chrom_vec=c(1:25)
28 } else { 73 } else {
29 chrom_tmp <- strsplit(chrom,",") 74 chrom_tmp <- strsplit(chrom,",")
30 chrom_vecstring <-unlist(chrom_tmp) 75 chrom_vecstring <-unlist(chrom_tmp)
31 chrom_vec <- as.numeric(chrom_vecstring) 76 chrom_vec <- as.numeric(chrom_vecstring)
32 } 77 }
33 78
34 79 if (outputlog){
80 sinklog <- file(log, open = "wt")
81 sink(sinklog ,type = "output")
82 sink(sinklog, type = "message")
83 }
84
35 if (settingsType == "tumor") { 85 if (settingsType == "tumor") {
36 if (signal=="CN") { 86 if (signal=="CN") {
37 res=markerSelection(input,dataResponse, chromosome=chrom_vec, signal=signal, normalTumorArray=tumor, onlySNP=snp, loss=loss, plot=plot, nbFolds=fold, pkg=package) 87 res=markerSelection(input,dataResponse, chromosome=chrom_vec, signal=signal, normalTumorArray=tumor, onlySNP=snp, loss=loss, plot=outputfigures, nbFolds=folds, pkg=package)
38 } else { 88 } else {
39 res=markerSelection(input,dataResponse, chromosome=chrom_vec,signal=signal,normalTumorArray=tumor, loss=loss, plot=plot, nbFolds=fold,pkg=package) 89 res=markerSelection(input,dataResponse, chromosome=chrom_vec,signal=signal,normalTumorArray=tumor, loss=loss, plot=outputfigures, nbFolds=folds,pkg=package)
40 } 90 }
41 } else { 91 } else {
42 if (signal=="CN") { 92 if (signal=="CN") {
43 res=markerSelection(input,dataResponse, chromosome=chrom_vec, signal=signal, onlySNP=snp, loss=loss, plot=plot, nbFolds=fold,pkg=package) 93 res=markerSelection(input,dataResponse, chromosome=chrom_vec, signal=signal, onlySNP=snp, loss=loss, plot=outputfigures, nbFolds=folds,pkg=package)
44 } else { 94 } else {
45 res=markerSelection(input,dataResponse, chromosome=chrom_vec, signal=signal, loss=loss, plot=plot, nbFolds=fold,pkg=package) 95 res=markerSelection(input,dataResponse, chromosome=chrom_vec, signal=signal, loss=loss, plot=outputfigures, nbFolds=folds,pkg=package)
46 } 96 }
47 } 97 }
48 98
49 res 99 res
50 100
61 chrdf=data.frame(rep(i,len),chr_data$markers.position,chr_data$markers.index,chr_data$markers.names,chr_data$coefficient) 111 chrdf=data.frame(rep(i,len),chr_data$markers.position,chr_data$markers.index,chr_data$markers.names,chr_data$coefficient)
62 df=rbind(df,chrdf) 112 df=rbind(df,chrdf)
63 } 113 }
64 } 114 }
65 115
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
66 if (markerSelected) { 126 if (markerSelected) {
67 colnames(df) <- c("chr","position","index","names","coefficient") 127 colnames(df) <- c("chr","position","index","names","coefficient")
68 sink(output) 128 #sink(output)
69 print(format(df),row.names=FALSE) 129 #print(format(df),row.names=FALSE)
70 sink() 130 #sink()
71 #write.table(df,output,row.names = FALSE, quote = FALSE, sep = "\t") 131 write.table(df,output,row.names = FALSE, quote = FALSE, sep = "\t")
72 } else 132 } else
73 writeLines("no SNP selected", output) 133 writeLines("no SNP selected", output)
74 134
75 135