Mercurial > repos > mvdbeek > r_goseq_1_22_0
comparison get_length_and_gc_content.r @ 5:f9b964d1d386 draft
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 |
comparison
equal
deleted
inserted
replaced
| 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) |