class LysineAbundanceFilter(BaseFilter):
""" Only allow gene which code for more than 76.6 lysines if scaled to a length of 1000 bases
"""
def __init__(self):
self.dnaa = DNAAnalyzer(strict=False)
def apply(self, record):
res = self.dnaa._count_codons(str(record.seq))
lysin = res['AAA'] + res['AAG']
norm = lysin * 1000 / len(record.seq)
return norm > 76.6
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)
def find_special_AAA_freqs(genes):
#id_filter = ['DDB0305421|DDB_G0276433', 'DDB0347990|DDB_G0289359', 'DDB0347948|DDB_G0270662', 'DDB0349097|DDB_G0279651', 'DDB0306784|DDB_G0293038', 'DDB0218505|DDB_G0283527', 'DDB0348150|DDB_G0285779', 'DDB0347690|DDB_G0286087'] # AAA=0
#id_filter = ['DDB0230164|DDB_G0293360', 'DDB0186263|DDB_G0284929', 'DDB0232396|DDB_G0282423', 'DDB0238636|DDB_G0269008', 'DDB0234236|DDB_G0289721', 'DDB0229439|DDB_G0270122'] # AAA=1
id_filter = ['DDB0348668|DDB_G0276223', 'DDB0307442|DDB_G0269954', 'DDB0307413|DDB_G0269350', 'DDB0308362|DDB_G0269090', 'DDB0216219|DDB_G0269132'] # long AAA=1
def get_record(gene_id):
for gene in genes:
if gene.id == gene_id:
return gene
return None
dnaa = DNAAnalyzer()
for gid in id_filter:
rec = get_record(gid)
if not rec is None:
print(rec.id)
print(' ', 'gene length:', len(rec.seq))
coco = dnaa._count_codons(str(rec.seq))
print(' ', 'AAA:', coco['AAA'])
print(' ', 'AAG:', coco['AAG'])
print()