#!/usr/bin/env bats load bats-extra # Translate input RNA sequences into proteins @test "Empty RNA sequence results in no proteins" { #[[ $BATS_RUN_SKIPPED == "true" ]] || skip run gawk -f protein-translation.awk <<< "" assert_success assert_output "" } @test "Methionine RNA sequence" { [[ $BATS_RUN_SKIPPED == "true" ]] || skip run gawk -f protein-translation.awk <<< "AUG" assert_success assert_output "Methionine" } @test "Phenylalanine RNA sequence 1" { [[ $BATS_RUN_SKIPPED == "true" ]] || skip run gawk -f protein-translation.awk <<< "UUU" assert_success assert_output "Phenylalanine" } @test "Phenylalanine RNA sequence 2" { [[ $BATS_RUN_SKIPPED == "true" ]] || skip run gawk -f protein-translation.awk <<< "UUC" assert_success assert_output "Phenylalanine" } @test "Leucine RNA sequence 1" { [[ $BATS_RUN_SKIPPED == "true" ]] || skip run gawk -f protein-translation.awk <<< "UUA" assert_success assert_output "Leucine" } @test "Leucine RNA sequence 2" { [[ $BATS_RUN_SKIPPED == "true" ]] || skip run gawk -f protein-translation.awk <<< "UUG" assert_success assert_output "Leucine" } @test "Serine RNA sequence 1" { [[ $BATS_RUN_SKIPPED == "true" ]] || skip run gawk -f protein-translation.awk <<< "UCU" assert_success assert_output "Serine" } @test "Serine RNA sequence 2" { [[ $BATS_RUN_SKIPPED == "true" ]] || skip run gawk -f protein-translation.awk <<< "UCC" assert_success assert_output "Serine" } @test "Serine RNA sequence 3" { [[ $BATS_RUN_SKIPPED == "true" ]] || skip run gawk -f protein-translation.awk <<< "UCA" assert_success assert_output "Serine" } @test "Serine RNA sequence 4" { [[ $BATS_RUN_SKIPPED == "true" ]] || skip run gawk -f protein-translation.awk <<< "UCG" assert_success assert_output "Serine" } @test "Tyrosine RNA sequence 1" { [[ $BATS_RUN_SKIPPED == "true" ]] || skip run gawk -f protein-translation.awk <<< "UAU" assert_success assert_output "Tyrosine" } @test "Tyrosine RNA sequence 2" { [[ $BATS_RUN_SKIPPED == "true" ]] || skip run gawk -f protein-translation.awk <<< "UAC" assert_success assert_output "Tyrosine" } @test "Cysteine RNA sequence 1" { [[ $BATS_RUN_SKIPPED == "true" ]] || skip run gawk -f protein-translation.awk <<< "UGU" assert_success assert_output "Cysteine" } @test "Cysteine RNA sequence 2" { [[ $BATS_RUN_SKIPPED == "true" ]] || skip run gawk -f protein-translation.awk <<< "UGC" assert_success assert_output "Cysteine" } @test "Tryptophan RNA sequence" { [[ $BATS_RUN_SKIPPED == "true" ]] || skip run gawk -f protein-translation.awk <<< "UGG" assert_success assert_output "Tryptophan" } @test "STOP codon RNA sequence 1" { [[ $BATS_RUN_SKIPPED == "true" ]] || skip run gawk -f protein-translation.awk <<< "UAA" assert_success assert_output "" } @test "STOP codon RNA sequence 2" { [[ $BATS_RUN_SKIPPED == "true" ]] || skip run gawk -f protein-translation.awk <<< "UAG" assert_success assert_output "" } @test "STOP codon RNA sequence 3" { [[ $BATS_RUN_SKIPPED == "true" ]] || skip run gawk -f protein-translation.awk <<< "UGA" assert_success assert_output "" } @test "Sequence of two protein codons translates into proteins" { [[ $BATS_RUN_SKIPPED == "true" ]] || skip run gawk -f protein-translation.awk <<< "UUUUUU" assert_success assert_output "Phenylalanine Phenylalanine" } @test "Sequence of two different protein codons translates into proteins" { [[ $BATS_RUN_SKIPPED == "true" ]] || skip run gawk -f protein-translation.awk <<< "UUAUUG" assert_success assert_output "Leucine Leucine" } @test "Translate RNA strand into correct protein list" { [[ $BATS_RUN_SKIPPED == "true" ]] || skip run gawk -f protein-translation.awk <<< "AUGUUUUGG" assert_success assert_output "Methionine Phenylalanine Tryptophan" } @test "Translation stops if STOP codon at beginning of sequence" { [[ $BATS_RUN_SKIPPED == "true" ]] || skip run gawk -f protein-translation.awk <<< "UAGUGG" assert_success assert_output "" } @test "Translation stops if STOP codon at end of two-codon sequence" { [[ $BATS_RUN_SKIPPED == "true" ]] || skip run gawk -f protein-translation.awk <<< "UGGUAG" assert_success assert_output "Tryptophan" } @test "Translation stops if STOP codon at end of three-codon sequence" { [[ $BATS_RUN_SKIPPED == "true" ]] || skip run gawk -f protein-translation.awk <<< "AUGUUUUAA" assert_success assert_output "Methionine Phenylalanine" } @test "Translation stops if STOP codon in middle of three-codon sequence" { [[ $BATS_RUN_SKIPPED == "true" ]] || skip run gawk -f protein-translation.awk <<< "UGGUAGUGG" assert_success assert_output "Tryptophan" } @test "Translation stops if STOP codon in middle of six-codon sequence" { [[ $BATS_RUN_SKIPPED == "true" ]] || skip run gawk -f protein-translation.awk <<< "UGGUGUUAUUAAUGGUUU" assert_success assert_output "Tryptophan Cysteine Tyrosine" } @test "Sequence of two non-STOP codons does not translate to a STOP codon" { [[ $BATS_RUN_SKIPPED == "true" ]] || skip run gawk -f protein-translation.awk <<< "AUGAUG" assert_success assert_output "Methionine Methionine" } @test "Error case" { [[ $BATS_RUN_SKIPPED == "true" ]] || skip run gawk -f protein-translation.awk <<< "UGG---AUG" assert_failure assert_output "Invalid codon" } @test "Non-existing codon can't translate" { [[ $BATS_RUN_SKIPPED == "true" ]] || skip run gawk -f protein-translation.awk <<< "AAA" assert_failure assert_output "Invalid codon" } @test "Unknown amino acids, not part of a codon, can't translate" { [[ $BATS_RUN_SKIPPED == "true" ]] || skip run gawk -f protein-translation.awk <<< "XYZ" assert_failure assert_output "Invalid codon" } @test "Incomplete RNA sequence can't translate" { [[ $BATS_RUN_SKIPPED == "true" ]] || skip run gawk -f protein-translation.awk <<< "AUGU" assert_failure assert_output "Invalid codon" } @test "Incomplete RNA sequence can translate if valid until a STOP codon" { [[ $BATS_RUN_SKIPPED == "true" ]] || skip run gawk -f protein-translation.awk <<< "UUCUUCUAAUGGU" assert_success assert_output "Phenylalanine Phenylalanine" }