Function TestAddCodonTable

synthesis/codon/codon_test.go:293–332

(t *testing.T)

}

func TestAddCodonTable(t *testing.T) {
	sequence, _ := genbank.Read("../../data/puc19.gbk")

	// weight our codon optimization table using the regions we collected from the genbank file above

	optimizationTable, err := NewTranslationTable(11)
	if err != nil {
		t.Fatalf("failed to initialise codon table: %s", err)
	}

	err = optimizationTable.UpdateWeightsWithSequence(sequence)
	if err != nil {
		t.Error(err)
	}

	sequence2, _ := genbank.Read("../../data/phix174.gb")
	optimizationTable2, err := NewTranslationTable(11)
	if err != nil {
		t.Fatalf("failed to initialise codon table: %s", err)
	}

	err = optimizationTable2.UpdateWeightsWithSequence(sequence2)
	if err != nil {
		t.Error(err)
	}

	// replace chooser fn with test one
	newChooserFn = func(choices ...weightedRand.Choice) (*weightedRand.Chooser, error) {
		return nil, errors.New("new chooser rigged to fail")
	}

	defer func() {
		newChooserFn = weightedRand.NewChooser
	}()

	_, err = AddCodonTable(optimizationTable, optimizationTable2)
	if err == nil {
		t.Errorf("Compromise table should fail when new chooser func rigged")
	}
}

func TestCapitalizationRegression(t *testing.T) {
	// Tests to make sure that amino acids are capitalized