The Computer Language
22.05 Benchmarks Game

regex-redux Julia program

source code

# The Computer Language Benchmarks Game
# https://salsa.debian.org/benchmarksgame-team/benchmarksgame/
#
# contributed by Daniel Jones
# fixed by David Campbell
# modified by Jarret Revels, Alex Arslan, Yichao Yu

using Printf

const variants = [
      "agggtaaa|tttaccct",
      "[cgt]gggtaaa|tttaccc[acg]",
      "a[act]ggtaaa|tttacc[agt]t",
      "ag[act]gtaaa|tttac[agt]ct",
      "agg[act]taaa|ttta[agt]cct",
      "aggg[acg]aaa|ttt[cgt]ccct",
      "agggt[cgt]aa|tt[acg]accct",
      "agggta[cgt]a|t[acg]taccct",
      "agggtaa[cgt]|[acg]ttaccct"
]

const subs = [
    (r"tHa[Nt]", "<4>"),
    (r"aND|caN|Ha[DS]|WaS", "<3>"),
    (r"a[NSt]|BY", "<2>"),
    (r"<[^>]*>", "|"),
    (r"\|[^|][^|]*\|", "-")
]

function perf_regex_dna()
    seq = read(stdin, String)
    l1 = length(seq)

    seq = replace(seq, r">.*\n|\n" => "")
    l2 = length(seq)

    for v in variants
        k = 0
        for m in eachmatch(Regex(v), seq)
            k += 1
        end
        @printf("%s %d\n", v, k)
    end

    for (u, v) in subs
        seq = replace(seq, u => v)
    end

    println()
    println(l1)
    println(l2)
    println(length(seq))
end

perf_regex_dna()

    

notes, command-line, and program output

NOTES:
64-bit Ubuntu quad core
julia version 1.7.2


Wed, 04 May 2022 22:05:06 GMT

MAKE:
printenv JULIA_NUM_THREADS
4

0.10s to complete and log all make actions

COMMAND LINE:
/opt/src/julia-1.7.2/bin/julia -O3 --cpu-target=ivybridge --math-mode=ieee  -- regexredux.julia 0 < regexredux-input5000000.txt

PROGRAM OUTPUT:
agggtaaa|tttaccct 356
[cgt]gggtaaa|tttaccc[acg] 1250
a[act]ggtaaa|tttacc[agt]t 4252
ag[act]gtaaa|tttac[agt]ct 2894
agg[act]taaa|ttta[agt]cct 5435
aggg[acg]aaa|ttt[cgt]ccct 1537
agggt[cgt]aa|tt[acg]accct 1431
agggta[cgt]a|t[acg]taccct 1608
agggtaa[cgt]|[acg]ttaccct 2178

50833411
50000000
27388361