| Previous changeset 5:f9b964d1d386 (2016-02-25) Next changeset 7:15ce6435ab83 (2016-02-25) |
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Commit message:
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/goseq_1_22_0 commit fdd0811efc61c31f88ff17096fbe8ee8cfacd766-dirty |
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modified:
get_length_and_gc_content.r |
| b |
| diff -r f9b964d1d386 -r d4b5942ed347 get_length_and_gc_content.r --- a/get_length_and_gc_content.r Thu Feb 25 05:47:38 2016 -0500 +++ b/get_length_and_gc_content.r Thu Feb 25 05:49:08 2016 -0500 |
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| @@ -1,4 +1,5 @@ # originally by Devon Ryan, https://www.biostars.org/p/84467/ +sink(stdout(), type = "message") library(GenomicRanges) library(rtracklayer) @@ -19,7 +20,7 @@ output = args$output #Load the annotation and reduce it -GTF <- import.gff(GTFfile, format="gtf", genome=NA, asRangedData=F, feature.type="exon") +GTF <- import.gff(GTFfile, format="gtf", genome=NA, feature.type="exon") grl <- reduce(split(GTF, elementMetadata(GTF)$gene_name)) reducedGTF <- unlist(grl, use.names=T) elementMetadata(reducedGTF)$gene_name <- rep(names(grl), elementLengths(grl)) |