def testCodingBases(self):
"""Verify computation of coding bases."""
binStats = BinStatistics(threads = 1)
aaGenes = {'S1_C1':'ACGTACGT', 'S1_C2':'ACGTACGT', 'S3_C1':'TTtt'}
seqStats = defaultdict(dict)
codingBasePairs = binStats._BinStatistics__calculateCodingBases(aaGenes, seqStats)
self.assertAlmostEqual(seqStats['S1']['# ORFs'], 2)
self.assertAlmostEqual(seqStats['S1']['Coding bases'], len(aaGenes['S1_C1'])*3 + len(aaGenes['S1_C2'])*3)
self.assertAlmostEqual(codingBasePairs, len(aaGenes['S1_C1'])*3 + len(aaGenes['S1_C2'])*3 + len(aaGenes['S3_C1'])*3)
def testCodingBases(self):
"""Verify computation of coding bases."""
binStats = BinStatistics(threads=1)
aaGenes = {'S1_C1': 'ACGTACGT', 'S1_C2': 'ACGTACGT', 'S3_C1': 'TTtt'}
seqStats = defaultdict(dict)
codingBasePairs = binStats._BinStatistics__calculateCodingBases(
aaGenes, seqStats)
self.assertAlmostEqual(seqStats['S1']['# ORFs'], 2)
self.assertAlmostEqual(
seqStats['S1']['Coding bases'],
len(aaGenes['S1_C1']) * 3 + len(aaGenes['S1_C2']) * 3)
self.assertAlmostEqual(
codingBasePairs,
len(aaGenes['S1_C1']) * 3 + len(aaGenes['S1_C2']) * 3 +
len(aaGenes['S3_C1']) * 3)
