Mercurial > repos > galaxyp > custom_pro_db_annotation_data_manager

annotate data_manager/customProDB_annotation.R @ 8:f4badf0bf23a draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/data_manager_customProDB commit 98f3323d4b92a4a3668788b3e1bad1a6529fd6df-dirty
author galaxyp
date Wed, 08 Jun 2016 16:00:30 -0400
parents 7399b23db662
children 9fec6c7f46eb
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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$dbkey <- make_option('--dbkey', type='character')
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19 option_list$dbsnp <- make_option('--dbsnp', type='character')
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20 option_list$cosmic <- make_option('--cosmic', type='logical')
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21 option_list$outputFile <- make_option('--outputFile', type='character')
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22 option_list$dbkey_description <- make_option('--dbkey_description', type='character')
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24 opt <- parse_args(OptionParser(option_list=option_list))
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27 customProDB_annotation <- function(
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28 dbkey = GalaxyCharacterParam(required=TRUE),
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29 dbsnp_str = GalaxyCharacterParam(required=FALSE),
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30 cosmic = GalaxyLogicalParam(required=FALSE),
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31 dbkey_description = GalaxyCharacterParam(required=FALSE),
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32 outputFile = GalaxyOutput("output","json"))
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33 {
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34 if (!file.exists(outputFile))
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35 {
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36 gstop("json params file does not exist")
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37 }
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38
3
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39 if (length(dbkey_description) < 1)
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40 {
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41 dbkey_description = dbkey
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42 }
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43
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44 if (length(dbsnp_str) > 0)
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45 {
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46 dbsnp = dbsnp_str
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47 }
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48 else
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49 {
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50 dbsnp = NULL
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51 }
7
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52
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53 use_cosmic = NULL
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54 if (length(cosmic) > 0)
5
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55 {
7
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56 if (grepl("^hg", dbkey))
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57 {
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58 use_cosmic = TRUE
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59 }
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60 else
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61 {
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62 gstop("COSMIC annotation requested but dbkey does not indicate a human genome (e.g. hg19)")
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63 }
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64 }
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65
0
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66 suppressPackageStartupMessages(library(rjson))
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67 params = fromJSON(file=outputFile)
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68 target_directory = params$output_data[[1]]$extra_files_path
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69 dir.create(target_directory)
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70
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71 tryCatch(
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72 {
3
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73 file.remove(outputFile)
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74 }, error=function(err)
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75 {
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76 gstop("failed to remove json params file after reading")
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77 })
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78
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79 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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80 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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81 codingFastaFilepath = paste(target_directory, "/", dbkey, ".cds.fa", sep="")
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82 proteinFastaFilepath = paste(target_directory, "/", dbkey, ".protein.fa", sep="")
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83
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84 suppressPackageStartupMessages(library(customProDB))
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85 options(timeout=3600)
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86
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87 cat(paste("Downloading coding FASTA from:", ucscTableCodingFastaURL, "\n"))
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88 download.file(ucscTableCodingFastaURL, codingFastaFilepath, quiet=T, mode='wb')
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89
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90 cat(paste("Downloading protein FASTA from:", ucscTableProteinFastaURL, "\n"))
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91 download.file(ucscTableProteinFastaURL, proteinFastaFilepath, quiet=T, mode='wb')
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92
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93 cat(paste("Preparing Refseq annotation files\n"))
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94 customProDB::PrepareAnnotationRefseq(genome=dbkey, CDSfasta=codingFastaFilepath, pepfasta=proteinFastaFilepath, annotation_path=target_directory, dbsnp=dbsnp, COSMIC=use_cosmic)
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95
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96 outputPath = paste(dbkey, "/customProDB", sep="")
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97 output = list(data_tables = list())
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98 output[["data_tables"]][["customProDB"]]=c(path=outputPath, name=dbkey_description, dbkey=dbkey, value=dbkey)
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99 write(toJSON(output), file=outputFile)
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100 }
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101
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102
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103 params <- list()
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104 for(param in names(opt))
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105 {
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106 if (!param == "help")
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107 params[param] <- opt[param]
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108 }
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109
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110 setClass("GalaxyRemoteError", contains="character")
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111 wrappedFunction <- function(f)
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112 {
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113 tryCatch(do.call(f, params),
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114 error=function(e) new("GalaxyRemoteError", conditionMessage(e)))
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115 }
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116
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117
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118 suppressPackageStartupMessages(library(RGalaxy))
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119 do.call(customProDB_annotation, params)
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120
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121 ## end warning handler
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122 }, warning = function(w) {
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123 cat(paste("Warning:", conditionMessage(w), "\n"))
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124 invokeRestart("muffleWarning")
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125 })