Sequence

2 problems from Rosalind — Bioinformatics Armory. Press Run on any block to execute it in your browser.

# Rosalind: INI — Introduction to the Bioinformatics Armory
# https://rosalind.info/problems/ini/
#
# Given: A DNA string s of length at most 1000 bp.
# Return: Four integers separated by spaces counting A, C, G, T occurrences.

let s = dna"AGCTTTTCATTCTGACTGCAACGGGCAATATGTCTCTGTGTGGATTAAAAAAAGAGTGTCTGATAGCAGC"

let counts = base_counts(s)
let result = str(counts.A) + " " + str(counts.C) + " " + str(counts.G) + " " + str(counts.T)

println("Result:   " + result)
println("Expected: 20 12 17 21")
println("Match:    " + str(result == "20 12 17 21"))

fn test_ini_base_counts() {
    assert result == "20 12 17 21", "INI: expected '20 12 17 21', got '" + result + "'"
}

# Rosalind: RVCO — Complementing a Strand of DNA
# https://rosalind.info/problems/rvco/
#
# Given: A collection of n (n <= 10) DNA strings.
# Return: The number of strings that match their own reverse complement.

let sequences = [
    dna"ATAT",
    dna"GCATA"
]

let palindrome_count = 0
for seq in sequences {
    let rc = reverse_complement(seq)
    if str(seq) == str(rc) then
        palindrome_count = palindrome_count + 1
}

println("Result:   " + str(palindrome_count))
println("Expected: 1")
println("Match:    " + str(palindrome_count == 1))

# Verify: ATAT -> rev_comp = ATAT (palindrome), GCATA -> rev_comp = TATGC (not)
println("\nDetail:")
for seq in sequences {
    let rc = reverse_complement(seq)
    let is_palindrome = str(seq) == str(rc)
    println("  " + str(seq) + " -> rc=" + str(rc) + " palindrome=" + str(is_palindrome))
}

fn test_rvco_palindrome_count() {
    assert palindrome_count == 1, "RVCO: expected 1, got " + str(palindrome_count)
}