def test_trans_trans(self):
# DNA with 1 protein that's 1 AA long; no non-coding DNA
chr = 'ATGGAATGA'
self.assertEqual(self.trans_translator.trans_trans(chr),
(['E'], 0, False))
# DNA with 1 protein that's 1 AA long; trailing non-coding DNA; nucleotides not a multiple of 3
chr = 'ATG CGT TAA CGT A'.replace(' ', '')
self.assertEqual(self.trans_translator.trans_trans(chr),
(['R'], 4, False))
# DNA with no protein
chr = 'ATTATTATT'
self.assertEqual(self.trans_translator.trans_trans(chr),
([], len(chr), True))
# DNA with a 0-length protein; no non-coding DNA
chr = 'ATGTAA'
self.assertEqual(self.trans_translator.trans_trans(chr), ([], 0, True))
# DNA failure: ends while encoding a protein
chr = 'ATGCGTCGT'
self.assertEqual(self.trans_translator.trans_trans(chr), ([], 0, True))
# test exceptions
chr = 'ABD'
with self.assertRaisesRegex(
ValueError, re.escape("bad bases in ABD at positions [1, 2]")):
self.trans_translator.trans_trans(chr)
# RNA_PROTEIN covers all possible codons, so must delete one to generate the unknown codon error
# copy TransTranslator.RNA_PROTEIN so that the one in TransTranslator does not get changed
rna_protein_copy = copy.deepcopy(TransTranslator.RNA_PROTEIN)
del rna_protein_copy['UCU']
# use the rna_protein keyword argument to use the changed RNA_PROTEIN dict
trans_translator = TransTranslator(rna_protein=rna_protein_copy)
chr = 'ATGTCTTGA'
with self.assertRaisesRegex(
ValueError, "unknown codon 'UCU' at pos 3 in AUGUCUUGA"):
trans_translator.trans_trans(chr)
def test_init(self):
self.assertEqual(self.trans_translator.dna_rna,
TransTranslator.DNA_RNA)
self.assertEqual(self.trans_translator.rna_protein,
TransTranslator.RNA_PROTEIN)
self.assertEqual(self.trans_translator.start_codons,
TransTranslator.START_CODONS)
alternate_dna_rna = {'x': 'y'}
alternate_rna_protein = {'x': 'y', 'a': 'b'}
alternate_start_codons = {'x'}
trans_translator = TransTranslator(dna_rna=alternate_dna_rna,
rna_protein=alternate_rna_protein,
start_codons=alternate_start_codons)
self.assertEqual(trans_translator.dna_rna, alternate_dna_rna)
self.assertEqual(trans_translator.rna_protein, alternate_rna_protein)
self.assertEqual(trans_translator.start_codons, alternate_start_codons)
def trans_trans_genome(self, genome):
trans_translator = TransTranslator()
trans_translator.trans_trans_genome(genome)
return trans_translator
def setUp(self):
self.trans_translator = TransTranslator()
class TestTransTranslator(unittest.TestCase):
def setUp(self):
self.trans_translator = TransTranslator()
def test_init(self):
self.assertEqual(self.trans_translator.dna_rna,
TransTranslator.DNA_RNA)
self.assertEqual(self.trans_translator.rna_protein,
TransTranslator.RNA_PROTEIN)
self.assertEqual(self.trans_translator.start_codons,
TransTranslator.START_CODONS)
alternate_dna_rna = {'x': 'y'}
alternate_rna_protein = {'x': 'y', 'a': 'b'}
alternate_start_codons = {'x'}
trans_translator = TransTranslator(dna_rna=alternate_dna_rna,
rna_protein=alternate_rna_protein,
start_codons=alternate_start_codons)
self.assertEqual(trans_translator.dna_rna, alternate_dna_rna)
self.assertEqual(trans_translator.rna_protein, alternate_rna_protein)
self.assertEqual(trans_translator.start_codons, alternate_start_codons)
def test_trans_trans(self):
# DNA with 1 protein that's 1 AA long; no non-coding DNA
chr = 'ATGGAATGA'
self.assertEqual(self.trans_translator.trans_trans(chr),
(['E'], 0, False))
# DNA with 1 protein that's 1 AA long; trailing non-coding DNA; nucleotides not a multiple of 3
chr = 'ATG CGT TAA CGT A'.replace(' ', '')
self.assertEqual(self.trans_translator.trans_trans(chr),
(['R'], 4, False))
# DNA with no protein
chr = 'ATTATTATT'
self.assertEqual(self.trans_translator.trans_trans(chr),
([], len(chr), True))
# DNA with a 0-length protein; no non-coding DNA
chr = 'ATGTAA'
self.assertEqual(self.trans_translator.trans_trans(chr), ([], 0, True))
# DNA failure: ends while encoding a protein
chr = 'ATGCGTCGT'
self.assertEqual(self.trans_translator.trans_trans(chr), ([], 0, True))
# test exceptions
chr = 'ABD'
with self.assertRaisesRegex(
ValueError, re.escape("bad bases in ABD at positions [1, 2]")):
self.trans_translator.trans_trans(chr)
# RNA_PROTEIN covers all possible codons, so must delete one to generate the unknown codon error
# copy TransTranslator.RNA_PROTEIN so that the one in TransTranslator does not get changed
rna_protein_copy = copy.deepcopy(TransTranslator.RNA_PROTEIN)
del rna_protein_copy['UCU']
# use the rna_protein keyword argument to use the changed RNA_PROTEIN dict
trans_translator = TransTranslator(rna_protein=rna_protein_copy)
chr = 'ATGTCTTGA'
with self.assertRaisesRegex(
ValueError, "unknown codon 'UCU' at pos 3 in AUGUCUUGA"):
trans_translator.trans_trans(chr)
def trans_trans_genome(self, genome):
trans_translator = TransTranslator()
trans_translator.trans_trans_genome(genome)
return trans_translator
def test_trans_trans_genome(self):
genome = ['ABD', 'ATTATTATT', 'ATGGAATGA']
trans_translator = self.trans_trans_genome(genome)
self.assertEqual(trans_translator.proteins, [[], ['E']])
self.assertEqual(trans_translator.num_noncoding_bases, len(genome[1]))
self.assertEqual(trans_translator.num_DNA_failures, 1)
genome = ['ATTATTATT', 'ATGGAATGA']
trans_translator = self.trans_trans_genome(genome)
self.assertEqual(trans_translator.proteins, [[], ['E']])
def test_genome_stats(self):
genome = ['ATTATTATT', 'ATGGAATGA']
trans_translator = self.trans_trans_genome(genome)
data = trans_translator.genome_stats()
self.assertEqual(data['proteins'], [[], ['E']])
self.assertEqual(data['number_proteins'][0], 2)
self.assertEqual(data['len_shortest_protein'][0], 0)
self.assertEqual(data['len_longest_protein'][0], 1)
self.assertEqual(data['mean_protein_length'][0], 0.5)
self.assertEqual(data['num_DNA_failures'][0], 1)
self.assertEqual(data['total_noncoding_bases'][0], len(genome[1]))