Mercurial > repos > mvdbeek > r_goseq_1_22_0

comparison get_length_and_gc_content.r @ 5:f9b964d1d386 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 Thu, 25 Feb 2016 05:47:38 -0500
parents 3ab168143b69
children d4b5942ed347
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4:a6198fc1116f 5:f9b964d1d386
12 ) 12 )
13 13
14 parser <- OptionParser(usage = "%prog [options] file", option_list=option_list) 14 parser <- OptionParser(usage = "%prog [options] file", option_list=option_list)
15 args = parse_args(parser) 15 args = parse_args(parser)
16 16
17 GTFfile = args.gtf 17 GTFfile = args$gtf
18 FASTAfile = args.fasta 18 FASTAfile = args$fasta
19 output = args.output 19 output = args$output
20 20
21 #Load the annotation and reduce it 21 #Load the annotation and reduce it
22 GTF <- import.gff(GTFfile, format="gtf", genome=NA, asRangedData=F, feature.type="exon") 22 GTF <- import.gff(GTFfile, format="gtf", genome=NA, asRangedData=F, feature.type="exon")
23 grl <- reduce(split(GTF, elementMetadata(GTF)$gene_name)) 23 grl <- reduce(split(GTF, elementMetadata(GTF)$gene_name))
24 reducedGTF <- unlist(grl, use.names=T) 24 reducedGTF <- unlist(grl, use.names=T)