Mercurial > repos > mvdbeek > r_goseq_1_22_0
comparison get_length_and_gc_content.r @ 6:d4b5942ed347 draft
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/goseq_1_22_0 commit fdd0811efc61c31f88ff17096fbe8ee8cfacd766-dirty
author | mvdbeek |
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date | Thu, 25 Feb 2016 05:49:08 -0500 |
parents | f9b964d1d386 |
children | 15ce6435ab83 |
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5:f9b964d1d386 | 6:d4b5942ed347 |
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1 # originally by Devon Ryan, https://www.biostars.org/p/84467/ | 1 # originally by Devon Ryan, https://www.biostars.org/p/84467/ |
2 sink(stdout(), type = "message") | |
2 | 3 |
3 library(GenomicRanges) | 4 library(GenomicRanges) |
4 library(rtracklayer) | 5 library(rtracklayer) |
5 library(Rsamtools) | 6 library(Rsamtools) |
6 library(optparse) | 7 library(optparse) |
17 GTFfile = args$gtf | 18 GTFfile = args$gtf |
18 FASTAfile = args$fasta | 19 FASTAfile = args$fasta |
19 output = args$output | 20 output = args$output |
20 | 21 |
21 #Load the annotation and reduce it | 22 #Load the annotation and reduce it |
22 GTF <- import.gff(GTFfile, format="gtf", genome=NA, asRangedData=F, feature.type="exon") | 23 GTF <- import.gff(GTFfile, format="gtf", genome=NA, feature.type="exon") |
23 grl <- reduce(split(GTF, elementMetadata(GTF)$gene_name)) | 24 grl <- reduce(split(GTF, elementMetadata(GTF)$gene_name)) |
24 reducedGTF <- unlist(grl, use.names=T) | 25 reducedGTF <- unlist(grl, use.names=T) |
25 elementMetadata(reducedGTF)$gene_name <- rep(names(grl), elementLengths(grl)) | 26 elementMetadata(reducedGTF)$gene_name <- rep(names(grl), elementLengths(grl)) |
26 | 27 |
27 #Open the fasta file | 28 #Open the fasta file |