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1 #!/usr/bin/env Rscript
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2 suppressPackageStartupMessages(library(rtracklayer))
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3 g = import(commandArgs(T)[1])
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4 attribute_name = commandArgs(T)[2]
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5
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6 m = mcols(g)
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7 w = width(g)
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8 total_lengths = by(w, INDICES=m[,attribute_name] , sum)
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9 total_counts = by(w, INDICES=m[,attribute_name] , length)
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10 d = data.frame(attribute = names(total_counts), cbind(counts = total_counts, length=total_lengths))
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11 colnames(d)[1] = attribute_name
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12 d = d[order(d$length, decreasing = TRUE),]
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13 write.table(d, sep = "\t", row.names = FALSE, quote = FALSE)
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