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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/goseq_1_22_0 commit 6574ffcb63770ff8de2d496894292cb7ce0492a8-dirty
author mvdbeek
date Thu, 31 Mar 2016 12:30:01 -0400
parents 04b9c519d3e1
children
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mvdbeek
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1 options( show.error.messages=F, error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } )
0e9424413ab0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/goseq_1_22_0 commit f95b47ed1a09ce14d3b565e8ea56d8bf12c35814-dirty
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mvdbeek
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3 # we need that to not crash galaxy with an UTF8 error on German LC settings.
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4 loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
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6 suppressPackageStartupMessages({
0e9424413ab0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/goseq_1_22_0 commit f95b47ed1a09ce14d3b565e8ea56d8bf12c35814-dirty
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7 library("goseq")
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8 library("optparse")
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9 library("reshape2")
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10 })
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12 sink(stdout(), type = "message")
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14 option_list <- list(
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15 make_option(c("-p", "--package"), type="character", help = "Genome [used for looking up GO categories]"),
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16 make_option(c("-i", "--gene_id"), type="character", help="Gene ID format"),
b79c65c90744 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/goseq_1_22_0 commit 81aedf1b50849160f6c048c0da4bb1038bb813a5
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17 make_option(c("-c", "--cats"), type="character", help="Comma-seperated list of categories to fetch"),
b79c65c90744 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/goseq_1_22_0 commit 81aedf1b50849160f6c048c0da4bb1038bb813a5
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18 make_option(c("-o", "--output"), type="character", help="Path to output file")
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19 )
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21 parser <- OptionParser(usage = "%prog [options] file", option_list=option_list)
b79c65c90744 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/goseq_1_22_0 commit 81aedf1b50849160f6c048c0da4bb1038bb813a5
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22 args = parse_args(parser)
b79c65c90744 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/goseq_1_22_0 commit 81aedf1b50849160f6c048c0da4bb1038bb813a5
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mvdbeek
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24 # vars
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26 package = args$package
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27 gene_id = args$gene_id
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28 output = args$output
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29 cats = unlist(strsplit(args$cats, ','))
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31 get_categories = function(package_str, gen, cat) {
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32 # gen should be ENSEMBL, UNIGENE, REFSEQ, SYMBOL or GENENAME
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33 # package should be org.Xx.eg.db
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34 # cat should be PMID, GO2ALLEGS, ENZYME or PATH
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35 library(package_str, character.only = TRUE)
04b9c519d3e1 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/goseq_1_22_0 commit 6574ffcb63770ff8de2d496894292cb7ce0492a8
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36 package = eval( parse( text=package_str ) )
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37 if( cat %in% c("GO2ALLEGS", "GO2ALLTAIRS", "GO2ALLORFS") ) {
04b9c519d3e1 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/goseq_1_22_0 commit 6574ffcb63770ff8de2d496894292cb7ce0492a8
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38 cat = "GOALL"
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39 }
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40 if(package_str == "org.Pf.plasmo.db") {
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41 keytype = "ORF"
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42 } else if(package_str == "org.At.tair.db") {
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43 keytype = "TAIR"
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44 } else {
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45 keytype = "ENTREZID"
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46 }
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47 entrez_cat = select(package, keys(package), cat, keytype)
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48 entrez_cat = entrez_cat[complete.cases(entrez_cat),]
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49 if( cat != "GOALL" ) {
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50 # add the origin of the term, so that there are no duplicate values e.g between ENZYME and PATH
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51 entrez_cat[,2] = sapply(entrez_cat[,2], function(x) paste(cat, x, sep=":"))
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52 } else {
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53 entrez_cat = entrez_cat[,c(1,2)] # we are discarding ontology (MF, CC, BP) and evidence class here
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54 }
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55 colnames(entrez_cat) = c(gen, "category")
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56 if( gen == "ENTREZ" ) {
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57 return( entrez_cat )
04b9c519d3e1 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/goseq_1_22_0 commit 6574ffcb63770ff8de2d496894292cb7ce0492a8
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58 } else {
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59 # We map ENTREZ to `gen`, but are potentially loosing gene identifiers where multiple identifiers match a single ENTREZ gene id.
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60 entrez_cat[,1] = mapIds(package, keys=as.character(entrez_cat[,1]), keytype=keytype, column=gen, multiVals="first")
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61 entrez_cat = entrez_cat[complete.cases(entrez_cat),]
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62 return(entrez_cat)
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63 }
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64 }
5
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66 result = lapply( cats, function(x) get_categories(package, gene_id, x ) )
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67 result = do.call(rbind, result)
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68
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69 write.table(result, output, sep="\t", col.names = FALSE, row.names = FALSE, quote = FALSE)
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70 sessionInfo()