Mercurial > repos > galaxyp > custom_pro_db

annotate customProDB.R @ 4:5bf19713c281 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
author galaxyp
date Fri, 29 Jan 2016 14:27:31 -0500
parents 7e078d4e40f8
children 61e45c111ef7
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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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19 option_list$bam <- make_option('--bam', type='character')
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20 option_list$vcf <- make_option('--vcf', type='character')
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21 option_list$exon_anno <- make_option('--exon_anno', type='character')
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22 option_list$proteinseq <- make_option('--proteinseq', type='character')
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23 option_list$procodingseq <- make_option('--procodingseq', type='character')
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24 option_list$outputFile <- make_option('--outputFile', type='character')
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27 opt <- parse_args(OptionParser(option_list=option_list))
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30 customProDB <- function(
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31 bam_file = GalaxyInputFile(required=TRUE),
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32 vcf_file = GalaxyInputFile(required=TRUE),
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33 exon_anno_file = GalaxyInputFile(required=TRUE),
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34 proteinseq_file = GalaxyInputFile(required=TRUE),
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35 procodingseq_file = GalaxyInputFile(required=TRUE),
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36 outputFile = GalaxyOutput("FASTA","fasta"))
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37 {
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38 if (dirname(exon_anno_file) != dirname(proteinseq_file) ||
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39 dirname(exon_anno_file) != dirname(procodingseq_file))
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40 {
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41 gstop("parent directory of annotation files must all be the same")
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42 }
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44 if (file.exists(outputFile))
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45 {
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46 if (file.info(outputFile)$size > 0) { gstop("output file already exists") }
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47 else
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48 {
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49 tryCatch(
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50 {
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51 file.remove(outputFile)
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52 }, error=function(err)
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53 {
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54 gstop("failed to remove empty existing file")
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55 })
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56 }
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57 }
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59 suppressPackageStartupMessages(library(customProDB))
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61 easyRun(bamFile=bamFile, vcfFile=vcfFile, annotation_path=dirname(exon_anno_file), outfile_path=dirname(outputFile), outfile_name=basename(outputFile))
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62 }
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65 params <- list()
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66 for(param in names(opt))
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67 {
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68 if (!param == "help")
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69 params[param] <- opt[param]
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70 }
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72 setClass("GalaxyRemoteError", contains="character")
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73 wrappedFunction <- function(f)
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74 {
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75 tryCatch(do.call(f, params),
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76 error=function(e) new("GalaxyRemoteError", conditionMessage(e)))
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77 }
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80 suppressPackageStartupMessages(library(RGalaxy))
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81 do.call(customProDB, params)
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82
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83 ## end warning handler
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84 }, warning = function(w) {
7e078d4e40f8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
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85 cat(paste("Warning:", conditionMessage(w), "\n"))
7e078d4e40f8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
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86 invokeRestart("muffleWarning")
7e078d4e40f8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
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87 })