Mercurial > repos > mvdbeek > r_goseq_1_22_0

annotate get_length_and_gc_content.r @ 6:0e9424413ab0 draft

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author mvdbeek
date Thu, 03 Mar 2016 09:56:51 -0500
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1 # originally by Devon Ryan, https://www.biostars.org/p/84467/
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3 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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5 # 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
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6 loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
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8 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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9 library("GenomicRanges")
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10 library("rtracklayer")
0e9424413ab0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/goseq_1_22_0 commit f95b47ed1a09ce14d3b565e8ea56d8bf12c35814-dirty
mvdbeek
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11 library("Rsamtools")
0e9424413ab0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/goseq_1_22_0 commit f95b47ed1a09ce14d3b565e8ea56d8bf12c35814-dirty
mvdbeek
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12 library("optparse")
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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13 library("data.table")
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14 })
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16 option_list <- list(
a6427f7893b0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/goseq_1_22_0 commit fdd0811efc61c31f88ff17096fbe8ee8cfacd766-dirty
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17 make_option(c("-g","--gtf"), type="character", help="Input GTF file with gene / exon information."),
a6427f7893b0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/goseq_1_22_0 commit fdd0811efc61c31f88ff17096fbe8ee8cfacd766-dirty
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18 make_option(c("-f","--fasta"), type="character", default=FALSE, help="Fasta file that corresponds to the supplied GTF."),
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19 make_option(c("-l","--length"), type="character", default=FALSE, help="Output file with gene name and length."),
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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20 make_option(c("-gc","--gc_content"), type="character", default=FALSE, help="Output file with gene name and GC content.")
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21 )
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23 parser <- OptionParser(usage = "%prog [options] file", option_list=option_list)
a6427f7893b0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/goseq_1_22_0 commit fdd0811efc61c31f88ff17096fbe8ee8cfacd766-dirty
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24 args = parse_args(parser)
a6427f7893b0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/goseq_1_22_0 commit fdd0811efc61c31f88ff17096fbe8ee8cfacd766-dirty
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26 GTFfile = args$gtf
a6427f7893b0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/goseq_1_22_0 commit fdd0811efc61c31f88ff17096fbe8ee8cfacd766-dirty
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27 FASTAfile = args$fasta
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28 length = args$length
0e9424413ab0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/goseq_1_22_0 commit f95b47ed1a09ce14d3b565e8ea56d8bf12c35814-dirty
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29 gc_content = args$gc_content
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31 #Load the annotation and reduce it
a6427f7893b0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/goseq_1_22_0 commit fdd0811efc61c31f88ff17096fbe8ee8cfacd766-dirty
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32 GTF <- import.gff(GTFfile, format="gtf", genome=NA, feature.type="exon")
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33 grl <- reduce(split(GTF, elementMetadata(GTF)$gene_id))
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34 reducedGTF <- unlist(grl, use.names=T)
a6427f7893b0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/goseq_1_22_0 commit fdd0811efc61c31f88ff17096fbe8ee8cfacd766-dirty
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35 elementMetadata(reducedGTF)$gene_id <- rep(names(grl), elementLengths(grl))
a6427f7893b0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/goseq_1_22_0 commit fdd0811efc61c31f88ff17096fbe8ee8cfacd766-dirty
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37 #Open the fasta file
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38 FASTA <- FaFile(FASTAfile)
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39 open(FASTA)
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41 #Add the GC numbers
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42 elementMetadata(reducedGTF)$nGCs <- letterFrequency(getSeq(FASTA, reducedGTF), "GC")[,1]
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43 elementMetadata(reducedGTF)$widths <- width(reducedGTF)
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45 #Create a list of the ensembl_id/GC/length
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46 calc_GC_length <- function(x) {
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47 nGCs = sum(elementMetadata(x)$nGCs)
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48 width = sum(elementMetadata(x)$widths)
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49 c(width, nGCs/width)
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50 }
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51 output <- t(sapply(split(reducedGTF, elementMetadata(reducedGTF)$gene_id), calc_GC_length))
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52 output <- data.frame(setDT(data.frame(output), keep.rownames = TRUE)[])
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55 write.table(output[,c(1,2)], file=length, col.names=FALSE, row.names=FALSE, quote=FALSE, sep="\t")
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56 write.table(output[,c(1,3)], file=gc_content, col.names=FALSE, row.names=FALSE, quote=FALSE, sep="\t")
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59 sessionInfo()