Mercurial > repos > mvdbeek > r_goseq_1_22_0

annotate getgo.r @ 5:b79c65c90744 draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/goseq_1_22_0 commit 81aedf1b50849160f6c048c0da4bb1038bb813a5
author mvdbeek
date Sun, 28 Feb 2016 11:52:10 -0500
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children 0e9424413ab0
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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:
diff changeset
1 suppressWarnings(suppressMessages(library(goseq)))
b79c65c90744 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/goseq_1_22_0 commit 81aedf1b50849160f6c048c0da4bb1038bb813a5
mvdbeek
parents:
diff changeset
2 suppressWarnings(suppressMessages(library(optparse)))
b79c65c90744 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/goseq_1_22_0 commit 81aedf1b50849160f6c048c0da4bb1038bb813a5
mvdbeek
parents:
diff changeset
3 suppressWarnings(suppressMessages(library(rtracklayer)))
b79c65c90744 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/goseq_1_22_0 commit 81aedf1b50849160f6c048c0da4bb1038bb813a5
mvdbeek
parents:
diff changeset
4 suppressWarnings(suppressMessages(library(reshape2)))
b79c65c90744 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/goseq_1_22_0 commit 81aedf1b50849160f6c048c0da4bb1038bb813a5
mvdbeek
parents:
diff changeset
5 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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6
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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7 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:
diff changeset
8 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:
diff changeset
9 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:
diff changeset
10 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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11 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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12 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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13 )
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
parents:
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15 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
parents:
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16 args = parse_args(parser)
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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18 # Vars:
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
parents:
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20 gtf = args$gtf
b79c65c90744 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/goseq_1_22_0 commit 81aedf1b50849160f6c048c0da4bb1038bb813a5
mvdbeek
parents:
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21 genome = args$genome
b79c65c90744 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/goseq_1_22_0 commit 81aedf1b50849160f6c048c0da4bb1038bb813a5
mvdbeek
parents:
diff changeset
22 gene_id = args$gene_id
b79c65c90744 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/goseq_1_22_0 commit 81aedf1b50849160f6c048c0da4bb1038bb813a5
mvdbeek
parents:
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23 output = args$output
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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24 cats = unlist(strsplit(args$cats, ','))
b79c65c90744 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/goseq_1_22_0 commit 81aedf1b50849160f6c048c0da4bb1038bb813a5
mvdbeek
parents:
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25 genes = unique(import.gff(gtf)$gene_id)
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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26 go_categories = getgo(genes, genome, id, fetch.cats=cats)
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
parents:
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28 # transform go category list to sth. more manipulatable in galaxy
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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29 go_categories <- lapply(go_categories, unlist)
b79c65c90744 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/goseq_1_22_0 commit 81aedf1b50849160f6c048c0da4bb1038bb813a5
mvdbeek
parents:
diff changeset
30 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
parents:
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31 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
mvdbeek
parents:
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32 colnames(go_categories) = c("#gene_id", "go_category")
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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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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34 write.table(go_categories, output, sep="\t", row.names = FALSE, quote = FALSE)
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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35 sessionInfo()