Mercurial > repos > petr-novak > repeat_annotation_pipeline2
comparison summarize_gff_by_attribute.R @ 0:cf3cea0a3039 draft
Uploaded
| author | petr-novak |
|---|---|
| date | Thu, 07 Oct 2021 06:07:34 +0000 |
| parents | |
| children |
comparison
equal
deleted
inserted
replaced
| -1:000000000000 | 0:cf3cea0a3039 |
|---|---|
| 1 #!/usr/bin/env Rscript | |
| 2 suppressPackageStartupMessages(library(rtracklayer)) | |
| 3 g = import(commandArgs(T)[1]) | |
| 4 attribute_name = commandArgs(T)[2] | |
| 5 | |
| 6 m = mcols(g) | |
| 7 w = width(g) | |
| 8 total_lengths = by(w, INDICES=m[,attribute_name] , sum) | |
| 9 total_counts = by(w, INDICES=m[,attribute_name] , length) | |
| 10 d = data.frame(attribute = names(total_counts), cbind(counts = total_counts, length=total_lengths)) | |
| 11 colnames(d)[1] = attribute_name | |
| 12 d = d[order(d$length, decreasing = TRUE),] | |
| 13 write.table(d, sep = "\t", row.names = FALSE, quote = FALSE) |