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| Original file line number | Diff line number | Diff line change |
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@@ -2,7 +2,7 @@ | |
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| # Author: Tim Sterne-Weiler, 2014 | ||
| # [email protected] | ||
| # Modifications Ulrich Braunschweig 2018 | ||
| # Modifications Ulrich Braunschweig 2018-2019 | ||
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| # Copyright (C) 2014 Tim Sterne-Weiler | ||
| # | ||
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@@ -70,7 +70,7 @@ option.list <- list( | |
| help = "Threshold for min diff where P( (psi1 - psi2) > threshold ) > --prob [default %default]"), | ||
| make_option(c("-e", "--minReads"), type = "numeric", default = 10, | ||
| help = "Threshold for min reads in a sample (use this flag unless you believe the prior) [default %default]"), | ||
| make_option(c("-S","--minSamples"), type = "numeric", default = 1, | ||
| make_option(c("-S","--minSamples"), type = "integer", default = 1, | ||
| help = "Threshold for min samples with min reads in a group [default %default]"), | ||
| make_option(c("--alpha"), type = "numeric", default = 1, | ||
| help = "First shape parameter for the Beta prior distribution P(psi), Uniform by default [default %default]"), | ||
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@@ -101,6 +101,16 @@ if (length(commandArgs(TRUE)) == 2 & commandArgs(TRUE)[1] == "-o") { | |
| stop("No input") | ||
| } | ||
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| ## input checks | ||
| if (opt$prob < 0 | opt$prob >= 1) { | ||
| stop ("--prob must be a positive number < 1") | ||
| } | ||
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| if (opt$minDiff < 0 | opt$minDiff >= 1) { | ||
| stop ("--minDiff must be a positive number < 1") | ||
| } | ||
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| loadPackages(c("MASS", "RColorBrewer", "reshape2", "ggplot2", "grid", "parallel"), local.lib=paste(c(scriptPath,"/Rlib"), collapse="")) | ||
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| ## move to output directory | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
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@@ -6,8 +6,17 @@ | |
| # Updates: Manuel Irimia, 2015-present | ||
| # [email protected] | ||
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| argv <- commandArgs(trailingOnly = F) | ||
| scriptPath <- dirname(sub("--file=","",argv[grep("--file",argv)])) | ||
| suppressPackageStartupMessages(require(optparse)) | ||
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| option_list <- list( | ||
| make_option(c("-p", "--prompt"), action="store_true", default=TRUE, type="logical", help="User prompt during installation [default %default]"), | ||
| make_option(c("-q", "--quiet"), action="store_false", dest="prompt", type="logical", help="Quiet installation, no prompt"), | ||
| make_option(c("-f", "--file"), action="store", default=".", type='character', help="From where to run install script") | ||
| ) | ||
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| opt <- parse_args(OptionParser(option_list=option_list)) | ||
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| scriptPath <- dirname( opt$file ) | ||
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| joinStr <- function(x,y) { | ||
| return(paste(c(as.character(x), as.character(y)), collapse="")) | ||
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@@ -57,64 +66,66 @@ planariaUrl <- joinStr("http://vastdb.crg.eu/libs/", planariaDbFile) | |
| NveUrl <- joinStr("http://vastdb.crg.eu/libs/", NveDbFile) | ||
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| # | ||
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| writeLines("Looking for VAST Database [VASTDB]") | ||
| auto <- "invalid" | ||
| if(!file.exists("VASTDB")) { | ||
| cat("Cannot find 'VASTDB'.. Do you want to download it? [y/n]: ") | ||
| auto <- readLines(file("stdin"),1) | ||
| close(file("stdin")) | ||
| } | ||
| if(file.exists("VASTDB")) { | ||
| cat("Found 'VASTDB'.. Do you want to download yet uninstalled datasets or update installed datasets? [y/n]: ") | ||
| auto <- readLines(file("stdin"),1) | ||
| close(file("stdin")) | ||
| } | ||
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| if(as.character(auto) == 'y') { | ||
| cat("Please choose one or more, e.g. Hsa,Mmu,Dre, from [all, Hsa, Mmu, Dre, Bla, Spu, Dme, Sma, Cel, Sme, Nve] : ") | ||
| db <- readLines(file("stdin"),1) | ||
| db <- as.character(db) | ||
| close(file("stdin")) | ||
| if ( opt$prompt ) { | ||
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| writeLines("Looking for VAST Database [VASTDB]") | ||
| auto <- "invalid" | ||
| if(!file.exists("VASTDB")) { | ||
| cat("Cannot find 'VASTDB'.. Do you want to download it? [y/n]: ") | ||
| auto <- readLines(file("stdin"),1) | ||
| close(file("stdin")) | ||
| } | ||
| if(file.exists("VASTDB")) { | ||
| cat("Found 'VASTDB'.. Do you want to download yet uninstalled datasets or update installed datasets? [y/n]: ") | ||
| auto <- readLines(file("stdin"),1) | ||
| close(file("stdin")) | ||
| } | ||
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| dbs<-strsplit(db,"\\s*,\\s*",perl=TRUE)[[1]] | ||
| for(db in dbs){ | ||
| if(db == 'Hsa' || db == 'all') { | ||
| downloadDb(humanUrl, humanDbFile) | ||
| } | ||
| if(db == 'Mmu' || db == 'all') { | ||
| downloadDb(mouseUrl, mouseDbFile) | ||
| } | ||
| if(db == 'Gga' || db == 'all') { | ||
| downloadDb(chickenUrl, chickenDbFile) | ||
| } | ||
| if(db == 'Dre' || db == 'all') { | ||
| downloadDb(DreUrl, DreDbFile) | ||
| } | ||
| if(db == 'Bla' || db == 'all') { | ||
| downloadDb(BlaUrl, BlaDbFile) | ||
| } | ||
| if(db == 'Spu' || db == 'all') { | ||
| downloadDb(SpuUrl, SpuDbFile) | ||
| } | ||
| if(db == 'Dme' || db == 'all') { | ||
| downloadDb(DmeUrl, DmeDbFile) | ||
| } | ||
| if(db == 'Sma' || db == 'all') { | ||
| downloadDb(SmaUrl, SmaDbFile) | ||
| } | ||
| if(db == 'Cel' || db == 'all') { | ||
| downloadDb(CelUrl, CelDbFile) | ||
| } | ||
| if(db == 'Sme' || db == 'all') { | ||
| downloadDb(planariaUrl, planariaDbFile) | ||
| } | ||
| if(db == 'Nve' || db == 'all') { | ||
| downloadDb(NveUrl, NveDbFile) | ||
| if(as.character(auto) == 'y') { | ||
| cat("Please choose one or more, e.g. Hsa,Mmu,Dre, from [all, Hsa, Mmu, Dre, Bla, Spu, Dme, Sma, Cel, Sme, Nve] : ") | ||
| db <- readLines(file("stdin"),1) | ||
| db <- as.character(db) | ||
| close(file("stdin")) | ||
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| dbs<-strsplit(db,"\\s*,\\s*",perl=TRUE)[[1]] | ||
| for(db in dbs){ | ||
| if(db == 'Hsa' || db == 'all') { | ||
| downloadDb(humanUrl, humanDbFile) | ||
| } | ||
| if(db == 'Mmu' || db == 'all') { | ||
| downloadDb(mouseUrl, mouseDbFile) | ||
| } | ||
| if(db == 'Gga' || db == 'all') { | ||
| downloadDb(chickenUrl, chickenDbFile) | ||
| } | ||
| if(db == 'Dre' || db == 'all') { | ||
| downloadDb(DreUrl, DreDbFile) | ||
| } | ||
| if(db == 'Bla' || db == 'all') { | ||
| downloadDb(BlaUrl, BlaDbFile) | ||
| } | ||
| if(db == 'Spu' || db == 'all') { | ||
| downloadDb(SpuUrl, SpuDbFile) | ||
| } | ||
| if(db == 'Dme' || db == 'all') { | ||
| downloadDb(DmeUrl, DmeDbFile) | ||
| } | ||
| if(db == 'Sma' || db == 'all') { | ||
| downloadDb(SmaUrl, SmaDbFile) | ||
| } | ||
| if(db == 'Cel' || db == 'all') { | ||
| downloadDb(CelUrl, CelDbFile) | ||
| } | ||
| if(db == 'Sme' || db == 'all') { | ||
| downloadDb(planariaUrl, planariaDbFile) | ||
| } | ||
| if(db == 'Nve' || db == 'all') { | ||
| downloadDb(NveUrl, NveDbFile) | ||
| } | ||
| } | ||
| } | ||
| } | ||
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| } | ||
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| # custom install from include.R | ||
| loadPackages(c("MASS", "getopt", "optparse", "RColorBrewer", "reshape2", "ggplot2", "grid", "parallel", "devtools"), local.lib=paste(c(scriptPath,"/R/Rlib"), collapse="")) | ||
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