Created
June 4, 2022 13:33
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Code for benchmarking sort!(unique!(df)) versus sort!(df) on a real-world example
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using CSV, DataFrames, Downloads, Tar | |
datadir = "biofast-data-v1" | |
tarball = "$datadir.tar.gz" | |
if !isfile(tarball) | |
dataurl = joinpath( | |
"https://github.com/lh3/biofast/releases/download", | |
datadir, | |
tarball, | |
) | |
Downloads.download(dataurl, tarball) | |
end | |
isdir(datadir) || mkdir(datadir) | |
bedfilenames = ["ex-anno.bed", "ex-rna.bed"] | |
if !all(nm -> isfile(joinpath(datadir, nm)), bedfilenames) | |
tmpdir = Tar.extract( | |
h -> endswith(h.path, ".bed"), `zcat ./$tarball`, | |
) | |
for nm in bedfilenames | |
mv(joinpath(tmpdir, datadir, nm), datadir) | |
end | |
end | |
rnadf = CSV.read( | |
joinpath(datadir, "ex-rna.bed"), | |
DataFrame; | |
delim='\t', | |
types=[String, Int32, Int32,], | |
header=[:chr, :start, :stop,], | |
) | |
tmpdf = copy(rnadf) # because it will be modified | |
@time copy(rnadf); # negligible compared to sort! and unique! | |
sort!(unique!(tmpdf)) | |
@time sort!(unique!(copy(rnadf))); | |
@time sort!(copy(rnadf)); |
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