Mercurial > repos > sblanck > mpagenomics_wrappers

comparison segmentFracB.R @ 8:d5ed62b4d3ac draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
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 #!/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("--settings_type",type="character",default=NULL, dest="settingsType"),
17 make_option("--output_graph",type="character",default=NULL, dest="outputgraph"),
18 make_option("--zip_figures",type="character",default=NULL, dest="zipfigures"),
19 make_option("--settings_tumor",type="character",default=NULL, dest="settingsTypeTumor"),
20 make_option("--outputlog",type="character",default=NULL, dest="outputlog"),
21 make_option("--log",type="character",default=NULL, dest="log"),
22 make_option("--userid",type="character",default=NULL, dest="userid"),
23 make_option("--method",type="character",default=NULL, dest="method")
24 );
25
26 opt_parser = OptionParser(option_list=option_list);
27 opt = parse_args(opt_parser);
28
29 if(is.null(opt$input)){
30 print_help(opt_parser)
31 stop("input required.", call.=FALSE)
32 }
33
34 #loading libraries
35
1 args<-commandArgs(TRUE) 36 args<-commandArgs(TRUE)
2 37
3 chrom=args[1] 38 chrom=opt$chrom
4 dataset=args[2] 39 datasetFile=opt$input
5 output=args[3] 40 output=opt$output
6 tmp_dir=args[4] 41 tmp_dir=opt$new_file_path
7 input=args[5] 42 input=opt$settingsType
8 outputfigures=type.convert(args[6]) 43 outputfigures=type.convert(opt$outputgraph)
9 tumorcsv=args[7] 44 tumorcsv=opt$settingsTypeTumor
10 user=args[8] 45 user=opt$userid
11 method=args[9] 46 method=opt$method
47 log=opt$log
48 outputlog=opt$outputlog
49 outputgraph=opt$outputgraph
50 zipfigures=opt$zipfigures
51
52 #chrom=opt$chrom
53 #datasetFile=opt$input
54 #output=opt$output
55 #tmp_dir=opt$new_file_path
56 #nbcall=as.numeric(opt$nbcall)
57 #settingsType=opt$settingsType
58 #outputfigures=type.convert(opt$outputgraph)
59 #snp=type.convert(opt$snp)
60 #tumorcsv=opt$settingsTypeTumor
61 #cellularity=as.numeric(opt$cellularity)
62 #user=opt$userid
63 #method=opt$method
64 #log=opt$log
65 #outputlog=opt$outputlog
66 #outputgraph=opt$outputgraph
67 #zipfigures=opt$zipfigures
12 68
13 library(MPAgenomics) 69 library(MPAgenomics)
14 workdir=file.path(tmp_dir, "mpagenomics",user) 70 workdir=file.path(tmp_dir, "mpagenomics",user)
15 setwd(workdir) 71 setwd(workdir)
16 72
20 chrom_tmp <- strsplit(chrom,",") 76 chrom_tmp <- strsplit(chrom,",")
21 chrom_vecstring <-unlist(chrom_tmp) 77 chrom_vecstring <-unlist(chrom_tmp)
22 chrom_vec <- as.numeric(chrom_vecstring) 78 chrom_vec <- as.numeric(chrom_vecstring)
23 } 79 }
24 80
25 input_tmp <- strsplit(input,",") 81
26 input_tmp_vecstring <-unlist(input_tmp) 82 if (outputlog){
83 sinklog <- file(log, open = "wt")
84 sink(sinklog ,type = "output")
85 sink(sinklog, type = "message")
86 }
27 87
28 88
29 input_vecstring = sub("^([^.]*).*", "\\1", input_tmp_vecstring) 89 inputDataset=read.table(file=datasetFile,stringsAsFactors=FALSE)
90 dataset=inputDataset[1,2]
30 91
31 if (dataset == input) { 92
93
94 library(MPAgenomics)
95 workdir=file.path(tmp_dir, "mpagenomics",user)
96 setwd(workdir)
97
98 if (grepl("all",tolower(chrom)) | chrom=="None") {
99 chrom_vec=c(1:25)
100 } else {
101 chrom_tmp <- strsplit(chrom,",")
102 chrom_vecstring <-unlist(chrom_tmp)
103 chrom_vec <- as.numeric(chrom_vecstring)
104 }
105
106 fig_dir = file.path("mpagenomics", user, "figures", dataset, "segmentation","fracB")
107 abs_fig_dir = file.path(tmp_dir, fig_dir)
108
109 if (outputgraph) {
110 if (dir.exists(abs_fig_dir)) {
111 system(paste0("rm -r ", abs_fig_dir))
112 }
113 }
114
115 if (input == 'dataset') {
32 segcall=segFracBSignal(dataset,chromosome=chrom_vec, normalTumorArray=tumorcsv, savePlot=outputfigures, method=method) 116 segcall=segFracBSignal(dataset,chromosome=chrom_vec, normalTumorArray=tumorcsv, savePlot=outputfigures, method=method)
33 117
34 } else { 118 } else {
119 input_tmp <- strsplit(input,",")
120 input_tmp_vecstring <-unlist(input_tmp)
121 input_vecstring = sub("^([^.]*).*", "\\1", input_tmp_vecstring)
35 segcall=segFracBSignal(dataset,chromosome=chrom_vec, normalTumorArray=tumorcsv, listOfFiles=input_vecstring, savePlot=outputfigures, method=method) 122 segcall=segFracBSignal(dataset,chromosome=chrom_vec, normalTumorArray=tumorcsv, listOfFiles=input_vecstring, savePlot=outputfigures, method=method)
36 123
37 } 124 }
38 sink(output) 125 write.table(segcall,output,row.names = FALSE, quote=FALSE, sep = "\t")
39 print(format(segcall))
40 sink()
41 #write.table(segcall,output,row.names = FALSE, quote=FALSE, sep = "\t")
42 126
43 quit() 127 if (outputgraph) {
128 setwd(abs_fig_dir)
129 files2zip <- dir(abs_fig_dir)
130 zip(zipfile = "figures.zip", files = files2zip)
131 file.rename("figures.zip",zipfigures)
132 }
133
134 if (outputlog){
135 sink(type="output")
136 sink(type="message")
137 close(sinklog)
138 }
139
140 #sink(output)
141 #print(format(segcall))
142 #sink()
143
144