Mercurial > repos > galaxyp > custom_pro_db_annotation_data_manager
view data_manager/customProDB_annotation.R @ 3:af0a098e15bd draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/data_manager_customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
author | galaxyp |
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date | Wed, 27 Jan 2016 16:46:54 -0500 |
parents | 20a1b026b798 |
children | b42974daa659 |
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#!/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$dbkey <- make_option('--dbkey', type='character') option_list$outputFile <- make_option('--outputFile', type='character') option_list$dbkey_description <- make_option('--dbkey_description', type='character') opt <- parse_args(OptionParser(option_list=option_list)) customProDB_annotation <- function( dbkey = GalaxyCharacterParam(required=TRUE), dbkey_description = GalaxyCharacterParam(required=FALSE), outputFile = GalaxyOutput("output","json")) { if (!file.exists(outputFile)) { gstop("json params file does not exist") } if (length(dbkey_description) < 1) { dbkey_description = dbkey } suppressPackageStartupMessages(library(rjson)) params = fromJSON(file=outputFile) target_directory = params$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) outputPath = paste(dbkey, "/customProDB", sep="") output = list(data_tables = list()) output[["data_tables"]][["customProDB"]]=c(path=outputPath, name=dbkey_description, dbkey=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") })