Mercurial > repos > mvdbeek > r_goseq_1_22_0

annotate get_length_and_gc_content.r @ 17:1b03f6232900 draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/goseq_1_22_0 commit fdd0811efc61c31f88ff17096fbe8ee8cfacd766-dirty
author mvdbeek
date Fri, 26 Feb 2016 08:49:59 -0500
parents 8ce951313688
children
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mvdbeek
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1 # originally by Devon Ryan, https://www.biostars.org/p/84467/
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2 sink(stdout(), type = "message")
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3ab168143b69 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/goseq_1_22_0 commit fdd0811efc61c31f88ff17096fbe8ee8cfacd766-dirty
mvdbeek
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4 library(GenomicRanges)
3ab168143b69 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/goseq_1_22_0 commit fdd0811efc61c31f88ff17096fbe8ee8cfacd766-dirty
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5 library(rtracklayer)
3ab168143b69 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/goseq_1_22_0 commit fdd0811efc61c31f88ff17096fbe8ee8cfacd766-dirty
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6 library(Rsamtools)
3ab168143b69 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/goseq_1_22_0 commit fdd0811efc61c31f88ff17096fbe8ee8cfacd766-dirty
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7 library(optparse)
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8 library(data.table)
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10 option_list <- list(
3ab168143b69 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/goseq_1_22_0 commit fdd0811efc61c31f88ff17096fbe8ee8cfacd766-dirty
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11 make_option(c("-g","--gtf"), type="character", help="Input GTF file with gene / exon information."),
3ab168143b69 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/goseq_1_22_0 commit fdd0811efc61c31f88ff17096fbe8ee8cfacd766-dirty
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12 make_option(c("-f","--fasta"), type="character", default=FALSE, help="Fasta file that corresponds to the supplied GTF."),
3ab168143b69 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/goseq_1_22_0 commit fdd0811efc61c31f88ff17096fbe8ee8cfacd766-dirty
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13 make_option(c("-o","--output"), type="character", default=FALSE, help="Output file with gene name, length and GC content.")
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14 )
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16 parser <- OptionParser(usage = "%prog [options] file", option_list=option_list)
3ab168143b69 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 args = parse_args(parser)
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19 GTFfile = args$gtf
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20 FASTAfile = args$fasta
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21 output_file = args$output
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23 #Load the annotation and reduce it
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24 GTF <- import.gff(GTFfile, format="gtf", genome=NA, feature.type="exon")
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25 grl <- reduce(split(GTF, elementMetadata(GTF)$gene_id))
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26 reducedGTF <- unlist(grl, use.names=T)
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27 elementMetadata(reducedGTF)$gene_id <- rep(names(grl), elementLengths(grl))
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29 #Open the fasta file
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30 FASTA <- FaFile(FASTAfile)
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31 open(FASTA)
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33 #Add the GC numbers
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34 elementMetadata(reducedGTF)$nGCs <- letterFrequency(getSeq(FASTA, reducedGTF), "GC")[,1]
3ab168143b69 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)$widths <- width(reducedGTF)
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37 #Create a list of the ensembl_id/GC/length
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38 calc_GC_length <- function(x) {
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39 nGCs = sum(elementMetadata(x)$nGCs)
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40 width = sum(elementMetadata(x)$widths)
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41 c(width, nGCs/width)
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42 }
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43 output <- t(sapply(split(reducedGTF, elementMetadata(reducedGTF)$gene_id), calc_GC_length))
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44 output <- setDT(data.frame(output), keep.rownames = TRUE)[]
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45 colnames(output) <- c("#gene_id", "length", "GC")
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47 write.table(output, file=output_file, row.names=FALSE, quote=FALSE, sep="\t")
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49 sessionInfo()