Mercurial > repos > galaxyp > custom_pro_db_annotation_data_manager

annotate data_manager/customProDB_annotation.R @ 1:4c77cf5a2977 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/data_manager_customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
author galaxyp
date Mon, 25 Jan 2016 18:00:15 -0500
parents 663ee21a8609
children 20a1b026b798
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1 #!/usr/bin/env Rscript
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3 initial.options <- commandArgs(trailingOnly = FALSE)
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4 script_parent_dir <- dirname(sub("--file=", "", initial.options[grep("--file=", initial.options)]))
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6 ## begin warning handler
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7 withCallingHandlers({
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9 library(methods) # Because Rscript does not always do this
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11 options('useFancyQuotes' = FALSE)
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13 suppressPackageStartupMessages(library("optparse"))
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14 suppressPackageStartupMessages(library("RGalaxy"))
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17 option_list <- list()
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18 option_list$dbkey <- make_option('--dbkey', type='character')
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19 option_list$outputFile <- make_option('--outputFile', type='character')
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21 opt <- parse_args(OptionParser(option_list=option_list))
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24 customProDB_annotation <- function(
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25 dbkey = GalaxyCharacterParam(required=TRUE),
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26 outputFile = GalaxyOutput("output","json"))
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27 {
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28 if (!file.exists(outputFile))
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29 {
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30 gstop("json params file does not exist")
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31 }
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33 suppressPackageStartupMessages(library(rjson))
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34 params = fromJSON(file=outputFile)
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35 target_directory = params$output_data[[1]]$extra_files_path
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36 data_description = params$param_dict$advanced$data_description
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37 data_id = params$param_dict$advanced$data_id
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38 dir.create(target_directory)
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40 tryCatch(
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41 {
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42 #file.remove(outputFile)
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43 }, error=function(err)
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44 {
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45 gstop("failed to remove json params file after reading")
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46 })
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48 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="")
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49 ucscTableProteinFastaURL = paste("http://genome.ucsc.edu/cgi-bin/hgTables?db=", dbkey, "&hgta_geneSeqType=protein&hgta_doGenePredSequence=submit&hgta_track=refGene&hgta_table=refGene", sep="")
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50 codingFastaFilepath = paste(target_directory, "/", dbkey, ".cds.fa", sep="")
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51 proteinFastaFilepath = paste(target_directory, "/", dbkey, ".protein.fa", sep="")
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52 suppressPackageStartupMessages(library(customProDB))
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53 options(timeout=3600)
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54 cat(paste("Downloading coding FASTA from:", ucscTableCodingFastaURL, "\n"))
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55 download.file(ucscTableCodingFastaURL, codingFastaFilepath, quiet=T, mode='wb')
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56 cat(paste("Downloading protein FASTA from:", ucscTableProteinFastaURL, "\n"))
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57 download.file(ucscTableProteinFastaURL, proteinFastaFilepath, quiet=T, mode='wb')
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58 customProDB::PrepareAnnotationRefseq(genome=dbkey, CDSfasta=codingFastaFilepath, pepfasta=proteinFastaFilepath, annotation_path=target_directory)
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60 outputPath = paste("customProDB/", dbkey, sep="")
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61 output = list(data_tables = list())
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62 output[["data_tables"]][["customProDB"]]=c(path=outputPath, name=dbkey, value=dbkey)
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63 write(toJSON(output), file=outputFile)
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64 }
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67 params <- list()
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68 for(param in names(opt))
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69 {
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70 if (!param == "help")
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71 params[param] <- opt[param]
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72 }
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74 setClass("GalaxyRemoteError", contains="character")
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75 wrappedFunction <- function(f)
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76 {
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77 tryCatch(do.call(f, params),
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78 error=function(e) new("GalaxyRemoteError", conditionMessage(e)))
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79 }
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80
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81
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82 suppressPackageStartupMessages(library(RGalaxy))
663ee21a8609 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/data_manager_customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
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83 do.call(customProDB_annotation, params)
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84
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85 ## end warning handler
663ee21a8609 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/data_manager_customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
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86 }, warning = function(w) {
663ee21a8609 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/data_manager_customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
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87 cat(paste("Warning:", conditionMessage(w), "\n"))
663ee21a8609 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/data_manager_customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
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88 invokeRestart("muffleWarning")
663ee21a8609 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/data_manager_customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
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89 })