Compare old Automa parsers with Deferred parsing Automa parsers.

deferred-bench.jl

function scan(T, filename)
    reader = open(T, filename)
    record = eltype(reader)()
    n = 0
    try
        while true
            read!(reader, record)
            n += 1
        end
    catch ex
        if !isa(ex, EOFError)
            rethrow()
        end
    end
    return n
end

function collect(T, filename)
    return length(open(Base.collect, T, filename))
end

println("-- FASTAReader --")
scan(FASTAReader, "ccds.fasta")
@time scan(FASTAReader, "refseqgene.all.genomic.fna")
@time scan(FASTAReader, "ecoli_allreads.fasta")
@time scan(FASTAReader, "/Users/kenta/bioinfo/data/genome/hg38.fa")

println("-- FASTA.Reader --")
scan(FASTA.Reader, "ccds.fasta")
@time scan(FASTA.Reader, "refseqgene.all.genomic.fna")
@time scan(FASTA.Reader, "ecoli_allreads.fasta")
@time scan(FASTA.Reader, "/Users/kenta/bioinfo/data/genome/hg38.fa")

println("-- FASTAReader --")
collect(FASTAReader, "ccds.fasta")
@time collect(FASTAReader, "refseqgene.all.genomic.fna")
@time collect(FASTAReader, "ecoli_allreads.fasta")
@time collect(FASTAReader, "/Users/kenta/bioinfo/data/genome/hg38.fa")

println("-- FASTA.Reader --")
collect(FASTA.Reader, "ccds.fasta")
@time collect(FASTA.Reader, "refseqgene.all.genomic.fna")
@time collect(FASTA.Reader, "ecoli_allreads.fasta")
@time collect(FASTA.Reader, "/Users/kenta/bioinfo/data/genome/hg38.fa")