#!/usr/bin/env bats # generated on 2022-11-02T20:59:34Z load bats-extra load bats-jq @test 'Empty RNA sequence results in no proteins' { #[[ $BATS_RUN_SKIPPED == "true" ]] || skip run jq -c -f protein-translation.jq << 'END_INPUT' { "strand": "" } END_INPUT assert_success expected='[]' assert_equal "$output" "$expected" } @test 'Methionine RNA sequence' { [[ $BATS_RUN_SKIPPED == "true" ]] || skip run jq -c -f protein-translation.jq << 'END_INPUT' { "strand": "AUG" } END_INPUT assert_success expected='["Methionine"]' assert_equal "$output" "$expected" } @test 'Phenylalanine RNA sequence 1' { [[ $BATS_RUN_SKIPPED == "true" ]] || skip run jq -c -f protein-translation.jq << 'END_INPUT' { "strand": "UUU" } END_INPUT assert_success expected='["Phenylalanine"]' assert_equal "$output" "$expected" } @test 'Phenylalanine RNA sequence 2' { [[ $BATS_RUN_SKIPPED == "true" ]] || skip run jq -c -f protein-translation.jq << 'END_INPUT' { "strand": "UUC" } END_INPUT assert_success expected='["Phenylalanine"]' assert_equal "$output" "$expected" } @test 'Leucine RNA sequence 1' { [[ $BATS_RUN_SKIPPED == "true" ]] || skip run jq -c -f protein-translation.jq << 'END_INPUT' { "strand": "UUA" } END_INPUT assert_success expected='["Leucine"]' assert_equal "$output" "$expected" } @test 'Leucine RNA sequence 2' { [[ $BATS_RUN_SKIPPED == "true" ]] || skip run jq -c -f protein-translation.jq << 'END_INPUT' { "strand": "UUG" } END_INPUT assert_success expected='["Leucine"]' assert_equal "$output" "$expected" } @test 'Serine RNA sequence 1' { [[ $BATS_RUN_SKIPPED == "true" ]] || skip run jq -c -f protein-translation.jq << 'END_INPUT' { "strand": "UCU" } END_INPUT assert_success expected='["Serine"]' assert_equal "$output" "$expected" } @test 'Serine RNA sequence 2' { [[ $BATS_RUN_SKIPPED == "true" ]] || skip run jq -c -f protein-translation.jq << 'END_INPUT' { "strand": "UCC" } END_INPUT assert_success expected='["Serine"]' assert_equal "$output" "$expected" } @test 'Serine RNA sequence 3' { [[ $BATS_RUN_SKIPPED == "true" ]] || skip run jq -c -f protein-translation.jq << 'END_INPUT' { "strand": "UCA" } END_INPUT assert_success expected='["Serine"]' assert_equal "$output" "$expected" } @test 'Serine RNA sequence 4' { [[ $BATS_RUN_SKIPPED == "true" ]] || skip run jq -c -f protein-translation.jq << 'END_INPUT' { "strand": "UCG" } END_INPUT assert_success expected='["Serine"]' assert_equal "$output" "$expected" } @test 'Tyrosine RNA sequence 1' { [[ $BATS_RUN_SKIPPED == "true" ]] || skip run jq -c -f protein-translation.jq << 'END_INPUT' { "strand": "UAU" } END_INPUT assert_success expected='["Tyrosine"]' assert_equal "$output" "$expected" } @test 'Tyrosine RNA sequence 2' { [[ $BATS_RUN_SKIPPED == "true" ]] || skip run jq -c -f protein-translation.jq << 'END_INPUT' { "strand": "UAC" } END_INPUT assert_success expected='["Tyrosine"]' assert_equal "$output" "$expected" } @test 'Cysteine RNA sequence 1' { [[ $BATS_RUN_SKIPPED == "true" ]] || skip run jq -c -f protein-translation.jq << 'END_INPUT' { "strand": "UGU" } END_INPUT assert_success expected='["Cysteine"]' assert_equal "$output" "$expected" } @test 'Cysteine RNA sequence 2' { [[ $BATS_RUN_SKIPPED == "true" ]] || skip run jq -c -f protein-translation.jq << 'END_INPUT' { "strand": "UGC" } END_INPUT assert_success expected='["Cysteine"]' assert_equal "$output" "$expected" } @test 'Tryptophan RNA sequence' { [[ $BATS_RUN_SKIPPED == "true" ]] || skip run jq -c -f protein-translation.jq << 'END_INPUT' { "strand": "UGG" } END_INPUT assert_success expected='["Tryptophan"]' assert_equal "$output" "$expected" } @test 'STOP codon RNA sequence 1' { [[ $BATS_RUN_SKIPPED == "true" ]] || skip run jq -c -f protein-translation.jq << 'END_INPUT' { "strand": "UAA" } END_INPUT assert_success expected='[]' assert_equal "$output" "$expected" } @test 'STOP codon RNA sequence 2' { [[ $BATS_RUN_SKIPPED == "true" ]] || skip run jq -c -f protein-translation.jq << 'END_INPUT' { "strand": "UAG" } END_INPUT assert_success expected='[]' assert_equal "$output" "$expected" } @test 'STOP codon RNA sequence 3' { [[ $BATS_RUN_SKIPPED == "true" ]] || skip run jq -c -f protein-translation.jq << 'END_INPUT' { "strand": "UGA" } END_INPUT assert_success expected='[]' assert_equal "$output" "$expected" } @test 'Sequence of two protein codons translates into proteins' { [[ $BATS_RUN_SKIPPED == "true" ]] || skip run jq -c -f protein-translation.jq << 'END_INPUT' { "strand": "UUUUUU" } END_INPUT assert_success expected='["Phenylalanine","Phenylalanine"]' assert_equal "$output" "$expected" } @test 'Sequence of two different protein codons translates into proteins' { [[ $BATS_RUN_SKIPPED == "true" ]] || skip run jq -c -f protein-translation.jq << 'END_INPUT' { "strand": "UUAUUG" } END_INPUT assert_success expected='["Leucine","Leucine"]' assert_equal "$output" "$expected" } @test 'Translate RNA strand into correct protein list' { [[ $BATS_RUN_SKIPPED == "true" ]] || skip run jq -c -f protein-translation.jq << 'END_INPUT' { "strand": "AUGUUUUGG" } END_INPUT assert_success expected='["Methionine","Phenylalanine","Tryptophan"]' assert_equal "$output" "$expected" } @test 'Translation stops if STOP codon at beginning of sequence' { [[ $BATS_RUN_SKIPPED == "true" ]] || skip run jq -c -f protein-translation.jq << 'END_INPUT' { "strand": "UAGUGG" } END_INPUT assert_success expected='[]' assert_equal "$output" "$expected" } @test 'Translation stops if STOP codon at end of two-codon sequence' { [[ $BATS_RUN_SKIPPED == "true" ]] || skip run jq -c -f protein-translation.jq << 'END_INPUT' { "strand": "UGGUAG" } END_INPUT assert_success expected='["Tryptophan"]' assert_equal "$output" "$expected" } @test 'Translation stops if STOP codon at end of three-codon sequence' { [[ $BATS_RUN_SKIPPED == "true" ]] || skip run jq -c -f protein-translation.jq << 'END_INPUT' { "strand": "AUGUUUUAA" } END_INPUT assert_success expected='["Methionine","Phenylalanine"]' assert_equal "$output" "$expected" } @test 'Translation stops if STOP codon in middle of three-codon sequence' { [[ $BATS_RUN_SKIPPED == "true" ]] || skip run jq -c -f protein-translation.jq << 'END_INPUT' { "strand": "UGGUAGUGG" } END_INPUT assert_success expected='["Tryptophan"]' assert_equal "$output" "$expected" } @test 'Translation stops if STOP codon in middle of six-codon sequence' { [[ $BATS_RUN_SKIPPED == "true" ]] || skip run jq -c -f protein-translation.jq << 'END_INPUT' { "strand": "UGGUGUUAUUAAUGGUUU" } END_INPUT assert_success expected='["Tryptophan","Cysteine","Tyrosine"]' assert_equal "$output" "$expected" } @test 'Sequence of two non-STOP codons does not translate to a STOP codon' { [[ $BATS_RUN_SKIPPED == "true" ]] || skip run jq -c -f protein-translation.jq << 'END_INPUT' { "strand": "AUGAUG" } END_INPUT assert_success expected='["Methionine","Methionine"]' assert_equal "$output" "$expected" } @test 'Non-existing codon can'\''t translate' { [[ $BATS_RUN_SKIPPED == "true" ]] || skip run jq -c -f protein-translation.jq << 'END_INPUT' { "strand": "AAA" } END_INPUT assert_failure expected='Invalid codon' assert_equal "$output" "$expected" } @test 'Unknown amino acids, not part of a codon, can'\''t translate' { [[ $BATS_RUN_SKIPPED == "true" ]] || skip run jq -c -f protein-translation.jq << 'END_INPUT' { "strand": "XYZ" } END_INPUT assert_failure expected='Invalid codon' assert_equal "$output" "$expected" } @test 'Incomplete RNA sequence can'\''t translate' { [[ $BATS_RUN_SKIPPED == "true" ]] || skip run jq -c -f protein-translation.jq << 'END_INPUT' { "strand": "AUGU" } END_INPUT assert_failure expected='Invalid codon' assert_equal "$output" "$expected" } @test 'Incomplete RNA sequence can translate if valid until a STOP codon' { [[ $BATS_RUN_SKIPPED == "true" ]] || skip run jq -c -f protein-translation.jq << 'END_INPUT' { "strand": "UUCUUCUAAUGGU" } END_INPUT assert_success expected='["Phenylalanine","Phenylalanine"]' assert_equal "$output" "$expected" }