Mercurial > repos > petrn > repeat_annotation_pipeline
comparison summarize_gff_by_attribute.R @ 0:d14182506989 draft default tip
"planemo upload commit d7966a292ed4209f4058e77ab8c0e49a67847b16-dirty"
| author | petrn |
|---|---|
| date | Tue, 15 Feb 2022 16:44:31 +0000 |
| parents | |
| children |
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| -1:000000000000 | 0:d14182506989 |
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| 1 #!/usr/bin/env Rscript | |
| 2 suppressPackageStartupMessages(library(rtracklayer)) | |
| 3 g = import(commandArgs(T)[1], format = "GFF") | |
| 4 attribute_name = commandArgs(T)[2] | |
| 5 | |
| 6 m = mcols(g) | |
| 7 AN = commandArgs(T)[2] | |
| 8 ## check if attribute is in gff: | |
| 9 if (!AN %in% colnames(m)){ | |
| 10 stop(paste0("attribute ", AN," not in input gff\n", "Available attributes are:\n", paste(colnames(m), collapse = "\n "))) | |
| 11 } | |
| 12 | |
| 13 w = width(g) | |
| 14 total_lengths = by(w, INDICES=m[,attribute_name] , sum) | |
| 15 total_counts = by(w, INDICES=m[,attribute_name] , length) | |
| 16 total_length_summary = do.call(rbind,as.list(by(w, INDICES=m[,attribute_name] , summary))) | |
| 17 colnames(total_length_summary) = paste0("length.", colnames(total_length_summary)) | |
| 18 | |
| 19 d = data.frame(attribute = names(total_counts), cbind(count = total_counts, total_length=total_lengths, length=total_length_summary)) | |
| 20 colnames(d)[1] = attribute_name | |
| 21 d = d[order(d$total_length, decreasing = TRUE),] | |
| 22 write.table(d, sep = "\t", row.names = FALSE, quote = FALSE, file = commandArgs(T)[3]) |