Orf

ORFR — Finding Genes with ORFs

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# Rosalind: ORFR — Finding Genes with ORFs
# https://rosalind.info/problems/orfr/
#
# Given: A DNA string s of length at most 1 kbp.
# Return: The longest protein string from any ORF (all six reading frames).

let s = dna"AGCCATGTAGCTAACTCAGGTTACATGGGGATGACCCCGCGACTTGGATTAGAGTCTCTTTTGGAATAAGCCTGAATGATCCGAGTAGCATCTCAG"

# find_orfs searches 3 forward reading frames; we also need the reverse complement
let fwd_orfs = find_orfs(s, 1)
let rc = reverse_complement(s)
let rev_orfs = find_orfs(rc, 1)
let all_orfs = fwd_orfs + rev_orfs

# Find the longest protein
let longest = all_orfs |> reduce(|a, b| {
    if seq_len(a.protein) >= seq_len(b.protein) then a else b
})

let result = longest.protein
let expected = protein"MLLGSFRLIPKETLIQVAGSSPCNLS"

println("Result:   " + str(result))
println("Expected: " + str(expected))
println("Match:    " + str(result == expected))

println("\nAll ORFs found (" + str(len(all_orfs)) + "):")
all_orfs |> each(|o| println("  frame=" + str(o.frame) + " len=" + str(seq_len(o.protein)) + " " + str(o.protein)))

fn test_orfr_longest_protein() {
    assert result == expected, "ORFR: expected " + str(expected) + ", got " + str(result)
}