--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/customProDB_annotation.R	Tue Mar 14 14:11:55 2017 -0400
@@ -0,0 +1,125 @@
+#!/usr/bin/env Rscript
+
+initial.options <- commandArgs(trailingOnly = FALSE)
+script_parent_dir <- dirname(sub("--file=", "", initial.options[grep("--file=", initial.options)]))
+
+## begin warning handler
+withCallingHandlers({
+
+library(methods) # Because Rscript does not always do this
+
+options('useFancyQuotes' = FALSE)
+
+suppressPackageStartupMessages(library("optparse"))
+suppressPackageStartupMessages(library("RGalaxy"))
+
+
+option_list <- list()
+option_list$dbkey <- make_option('--dbkey', type='character')
+option_list$dbsnp <- make_option('--dbsnp', type='character')
+option_list$cosmic <- make_option('--cosmic', type='logical')
+option_list$outputFile <- make_option('--outputFile', type='character')
+option_list$dbkey_description <- make_option('--dbkey_description', type='character')
+
+opt <- parse_args(OptionParser(option_list=option_list))
+
+
+customProDB_annotation <- function(
+	dbkey = GalaxyCharacterParam(required=TRUE), 
+	dbsnp_str = GalaxyCharacterParam(required=FALSE), 
+	cosmic = GalaxyLogicalParam(required=FALSE), 
+	dbkey_description = GalaxyCharacterParam(required=FALSE), 
+	outputFile = GalaxyOutput("output","json"))
+{
+    if (!file.exists(outputFile))
+    {
+        gstop("json params file does not exist")
+    }
+
+    if (length(dbkey_description) < 1)
+    {
+        dbkey_description = dbkey
+    }
+
+    if (length(dbsnp_str) > 0)
+    {
+        dbsnp = dbsnp_str
+    }
+    else
+    {
+        dbsnp = NULL
+    }
+
+    use_cosmic = FALSE
+    if (length(cosmic) > 0)
+    {
+        if (grepl("^hg", dbkey))
+        {
+            use_cosmic = TRUE
+        }
+        else
+        {
+            gstop("COSMIC annotation requested but dbkey does not indicate a human genome (e.g. hg19)")
+        }
+    }
+
+    suppressPackageStartupMessages(library(rjson))
+    params = fromJSON(file=outputFile)
+    target_directory = params$output_data[[1]]$extra_files_path
+    dir.create(target_directory)
+
+    tryCatch(
+    {
+        file.remove(outputFile)
+    }, error=function(err)
+    {
+        gstop("failed to remove json params file after reading")
+    })
+
+    ucscTableCodingFastaURL = paste("http://genome.ucsc.edu/cgi-bin/hgTables?db=", dbkey, "&hgSeq.cdsExon=on&hgSeq.granularity=gene&hgSeq.casing=exon&hgSeq.repMasking=lower&hgta_doGenomicDna=get+sequence&hgta_group=genes&hgta_track=refGene&hgta_table=refGene&hgta_regionType=genome", sep="")
+    ucscTableProteinFastaURL = paste("http://genome.ucsc.edu/cgi-bin/hgTables?db=", dbkey, "&hgta_geneSeqType=protein&hgta_doGenePredSequence=submit&hgta_track=refGene&hgta_table=refGene", sep="")
+    codingFastaFilepath = paste(target_directory, "/", dbkey, ".cds.fa", sep="")
+    proteinFastaFilepath = paste(target_directory, "/", dbkey, ".protein.fa", sep="")
+
+    suppressPackageStartupMessages(library(customProDB))
+    options(timeout=3600)
+
+    cat(paste("Downloading coding FASTA from:", ucscTableCodingFastaURL, "\n"))
+    download.file(ucscTableCodingFastaURL, codingFastaFilepath, quiet=T, mode='wb')
+
+    cat(paste("Downloading protein FASTA from:", ucscTableProteinFastaURL, "\n"))
+    download.file(ucscTableProteinFastaURL, proteinFastaFilepath, quiet=T, mode='wb')
+
+    cat(paste("Preparing Refseq annotation files\n"))
+    customProDB::PrepareAnnotationRefseq(genome=dbkey, CDSfasta=codingFastaFilepath, pepfasta=proteinFastaFilepath, annotation_path=target_directory, dbsnp=dbsnp, COSMIC=use_cosmic)
+    
+    outputPath = paste(dbkey, "/customProDB", sep="")
+    output = list(data_tables = list())
+    output[["data_tables"]][["customProDB"]]=c(path=outputPath, name=dbkey_description, dbkey=dbkey, value=dbkey)
+    write(toJSON(output), file=outputFile)
+}
+
+
+params <- list()
+for(param in names(opt))
+{
+    if (!param == "help")
+        params[param] <- opt[param]
+}
+
+setClass("GalaxyRemoteError", contains="character")
+wrappedFunction <- function(f)
+{
+    tryCatch(do.call(f, params),
+        error=function(e) new("GalaxyRemoteError", conditionMessage(e)))
+}
+
+
+suppressPackageStartupMessages(library(RGalaxy))
+do.call(customProDB_annotation, params)
+
+## end warning handler
+}, warning = function(w) {
+    cat(paste("Warning:", conditionMessage(w), "\n"))
+    invokeRestart("muffleWarning")
+})