def get_codu_per_group(groups):
""" Compute codon usage per group
"""
group_codu = {}
dnana = DNAAnalyzer(strict=False)
for label, genes in groups.items():
group_codu[label] = dnana.get_avg_codon_usage(genes)
return group_codu
def generate_codon_usage_summary(groups, out_fname):
""" Save codon usage tables per group
"""
dnana = DNAAnalyzer(strict=False)
with open(out_fname, 'w') as fd:
for label, genes in groups.items():
codu = dnana.get_avg_codon_usage(genes)
fd.write(label + '\n')
pprint.pprint(codu, fd)
fd.write('\n')
def main():
""" Generate overview
"""
farser = FastaParser(sys.argv[1])
genes = farser.parse()
dnana = DNAAnalyzer(strict=False)
codu = dnana.get_avg_codon_usage(genes)
with open('results/plain_codon_usage_table.txt', 'w') as fd:
output_data(codu, fd)
def get_codu(genes, group):
""" Compute codon usage for all genes or only for certain expression group if file is given
"""
exprs = extract_expression_levels(sys.argv[2]) if len(
sys.argv) == 3 else None
groups = {
'all': genes
} if exprs is None else group_expression_levels(genes, exprs)
select = 'all' if exprs is None else group
dnana = DNAAnalyzer(strict=False)
codu = dnana.get_avg_codon_usage(groups[select])
return codu, select
class TestCodonUsage(TestCase):
def setUp(self):
self.dnana = DNAAnalyzer()
self.seq = 'AAAAAGAAA'
self.genes = [
SeqRecord(Seq('AAAAAAAAG')),
SeqRecord(Seq('AAAAAGAAA')),
SeqRecord(Seq('TTTTTCTTT')),
SeqRecord(Seq('TTCTTTTTC'))
]
def test_codon_counter(self):
count = self.dnana._count_codons(self.seq)
self.assertEqual(count['AAA'], 2)
self.assertEqual(count['AAG'], 1)
self.assertEqual(count['AAT'], 0)
self.assertEqual(count['AAC'], 0)
def test_codon_usage(self):
codu = self.dnana.get_codon_usage(self.seq)
self.assertEqual(round(codu['AAA'], 3), round(0.6666, 3))
self.assertEqual(round(codu['AAG'], 3), round(0.3333, 3))
self.assertEqual(codu['AAT'], None)
self.assertEqual(codu['AAC'], None)
def test_average_codon_usage(self):
avg_codu = self.dnana.get_avg_codon_usage(self.genes)
self.assertEqual(round(avg_codu['AAA'], 3), round(0.6666, 3))
self.assertEqual(round(avg_codu['AAG'], 3), round(0.3333, 3))
self.assertEqual(avg_codu['AAT'], None)
self.assertEqual(avg_codu['AAC'], None)
self.assertEqual(round(avg_codu['TTT'], 3), round(0.5, 3))
self.assertEqual(round(avg_codu['TTC'], 3), round(0.5, 3))
def test_codon_frequencies(self):
avg_cod_freqs = self.dnana.get_codon_freqs(self.genes)
self.assertEqual(round(avg_cod_freqs['AAA'], 3), 0.333)
self.assertEqual(round(avg_cod_freqs['AAG'], 3), 0.167)
self.assertEqual(round(avg_cod_freqs['TTT'], 3), 0.25)
self.assertEqual(round(avg_cod_freqs['TTC'], 3), 0.25)