Mercurial > repos > mvdbeek > r_goseq_1_22_0

annotate getgo.r @ 6:0e9424413ab0 draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/goseq_1_22_0 commit f95b47ed1a09ce14d3b565e8ea56d8bf12c35814-dirty
author mvdbeek
date Thu, 03 Mar 2016 09:56:51 -0500
parents b79c65c90744
children 04b9c519d3e1
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0e9424413ab0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/goseq_1_22_0 commit f95b47ed1a09ce14d3b565e8ea56d8bf12c35814-dirty
mvdbeek
parents: 5
diff changeset
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
mvdbeek
parents: 5
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0e9424413ab0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/goseq_1_22_0 commit f95b47ed1a09ce14d3b565e8ea56d8bf12c35814-dirty
mvdbeek
parents: 5
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3 # we need that to not crash galaxy with an UTF8 error on German LC settings.
0e9424413ab0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/goseq_1_22_0 commit f95b47ed1a09ce14d3b565e8ea56d8bf12c35814-dirty
mvdbeek
parents: 5
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4 loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
0e9424413ab0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/goseq_1_22_0 commit f95b47ed1a09ce14d3b565e8ea56d8bf12c35814-dirty
mvdbeek
parents: 5
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0e9424413ab0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/goseq_1_22_0 commit f95b47ed1a09ce14d3b565e8ea56d8bf12c35814-dirty
mvdbeek
parents: 5
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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
mvdbeek
parents: 5
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7 library("goseq")
0e9424413ab0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/goseq_1_22_0 commit f95b47ed1a09ce14d3b565e8ea56d8bf12c35814-dirty
mvdbeek
parents: 5
diff changeset
8 library("optparse")
0e9424413ab0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/goseq_1_22_0 commit f95b47ed1a09ce14d3b565e8ea56d8bf12c35814-dirty
mvdbeek
parents: 5
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9 library("rtracklayer")
0e9424413ab0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/goseq_1_22_0 commit f95b47ed1a09ce14d3b565e8ea56d8bf12c35814-dirty
mvdbeek
parents: 5
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10 library("reshape2")
0e9424413ab0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/goseq_1_22_0 commit f95b47ed1a09ce14d3b565e8ea56d8bf12c35814-dirty
mvdbeek
parents: 5
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11 })
0e9424413ab0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/goseq_1_22_0 commit f95b47ed1a09ce14d3b565e8ea56d8bf12c35814-dirty
mvdbeek
parents: 5
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b79c65c90744 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/goseq_1_22_0 commit 81aedf1b50849160f6c048c0da4bb1038bb813a5
mvdbeek
parents:
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13 sink(stdout(), type = "message")
b79c65c90744 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/goseq_1_22_0 commit 81aedf1b50849160f6c048c0da4bb1038bb813a5
mvdbeek
parents:
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b79c65c90744 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/goseq_1_22_0 commit 81aedf1b50849160f6c048c0da4bb1038bb813a5
mvdbeek
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15 option_list <- list(
b79c65c90744 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/goseq_1_22_0 commit 81aedf1b50849160f6c048c0da4bb1038bb813a5
mvdbeek
parents:
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16 make_option(c("-gtf", "--gtf"), type="character", help = "Path to GTF file for which to fetch GO data"),
b79c65c90744 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/goseq_1_22_0 commit 81aedf1b50849160f6c048c0da4bb1038bb813a5
mvdbeek
parents:
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17 make_option(c("-g", "--genome"), type="character", help = "Genome [used for looking up GO categories]"),
b79c65c90744 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/goseq_1_22_0 commit 81aedf1b50849160f6c048c0da4bb1038bb813a5
mvdbeek
parents:
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18 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
mvdbeek
parents:
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19 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
mvdbeek
parents:
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20 make_option(c("-o", "--output"), type="character", help="Path to output file")
b79c65c90744 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/goseq_1_22_0 commit 81aedf1b50849160f6c048c0da4bb1038bb813a5
mvdbeek
parents:
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21 )
b79c65c90744 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/goseq_1_22_0 commit 81aedf1b50849160f6c048c0da4bb1038bb813a5
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b79c65c90744 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/goseq_1_22_0 commit 81aedf1b50849160f6c048c0da4bb1038bb813a5
mvdbeek
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23 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
mvdbeek
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24 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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0e9424413ab0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/goseq_1_22_0 commit f95b47ed1a09ce14d3b565e8ea56d8bf12c35814-dirty
mvdbeek
parents: 5
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26 # vars
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b79c65c90744 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/goseq_1_22_0 commit 81aedf1b50849160f6c048c0da4bb1038bb813a5
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b79c65c90744 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/goseq_1_22_0 commit 81aedf1b50849160f6c048c0da4bb1038bb813a5
mvdbeek
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28 gtf = args$gtf
b79c65c90744 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/goseq_1_22_0 commit 81aedf1b50849160f6c048c0da4bb1038bb813a5
mvdbeek
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29 genome = args$genome
b79c65c90744 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/goseq_1_22_0 commit 81aedf1b50849160f6c048c0da4bb1038bb813a5
mvdbeek
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30 gene_id = args$gene_id
b79c65c90744 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/goseq_1_22_0 commit 81aedf1b50849160f6c048c0da4bb1038bb813a5
mvdbeek
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31 output = args$output
b79c65c90744 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/goseq_1_22_0 commit 81aedf1b50849160f6c048c0da4bb1038bb813a5
mvdbeek
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32 cats = unlist(strsplit(args$cats, ','))
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0e9424413ab0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/goseq_1_22_0 commit f95b47ed1a09ce14d3b565e8ea56d8bf12c35814-dirty
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0e9424413ab0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/goseq_1_22_0 commit f95b47ed1a09ce14d3b565e8ea56d8bf12c35814-dirty
mvdbeek
parents: 5
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34 # retrieve and transform data
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b79c65c90744 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/goseq_1_22_0 commit 81aedf1b50849160f6c048c0da4bb1038bb813a5
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35 genes = unique(import.gff(gtf)$gene_id)
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0e9424413ab0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/goseq_1_22_0 commit f95b47ed1a09ce14d3b565e8ea56d8bf12c35814-dirty
mvdbeek
parents: 5
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36 go_categories = getgo(genes, genome, gene_id, fetch.cats=cats)
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b79c65c90744 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/goseq_1_22_0 commit 81aedf1b50849160f6c048c0da4bb1038bb813a5
mvdbeek
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37 go_categories = goseq:::reversemapping(go_categories)
b79c65c90744 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/goseq_1_22_0 commit 81aedf1b50849160f6c048c0da4bb1038bb813a5
mvdbeek
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38 go_categories = melt(go_categories)
b79c65c90744 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/goseq_1_22_0 commit 81aedf1b50849160f6c048c0da4bb1038bb813a5
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0e9424413ab0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/goseq_1_22_0 commit f95b47ed1a09ce14d3b565e8ea56d8bf12c35814-dirty
mvdbeek
parents: 5
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40 write.table(go_categories, output, sep="\t", col.names = FALSE, row.names = FALSE, quote = FALSE)
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b79c65c90744 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/goseq_1_22_0 commit 81aedf1b50849160f6c048c0da4bb1038bb813a5
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41 sessionInfo()