def testScaffoldLengthStats(self):
"""Verify computation of scaffold length statistics."""
binStats = BinStatistics(threads=1)
scaffolds = {
'S1': 'ACGT' + DefaultValues.CONTIG_BREAK + 'ACGT',
'S2': 'ACGTACGT',
'S3': 'TTtt'
}
scaffoldStats = defaultdict(dict)
maxScaffoldLen, maxContigLen, totalScaffoldBps, _, _, numContigs = binStats.calculateScaffoldLengthStats(
scaffolds, scaffoldStats)
self.assertAlmostEqual(scaffoldStats['S1']['Length'],
len(DefaultValues.CONTIG_BREAK) + 8)
self.assertAlmostEqual(scaffoldStats['S1']['Total contig length'], 8)
self.assertAlmostEqual(scaffoldStats['S1']['# contigs'], 2)
self.assertAlmostEqual(maxScaffoldLen,
len(DefaultValues.CONTIG_BREAK) + 8)
self.assertAlmostEqual(maxContigLen, 8)
self.assertAlmostEqual(totalScaffoldBps,
len(DefaultValues.CONTIG_BREAK) + 8 + 8 + 4)
self.assertAlmostEqual(numContigs, 4)
def testScaffoldLengthStats(self):
"""Verify computation of scaffold length statistics."""
binStats = BinStatistics(threads = 1)
scaffolds = {'S1':'ACGT' + DefaultValues.CONTIG_BREAK + 'ACGT', 'S2':'ACGTACGT', 'S3':'TTtt'}
scaffoldStats = defaultdict(dict)
maxScaffoldLen, maxContigLen, totalScaffoldBps, _, _, numContigs = binStats.calculateScaffoldLengthStats(scaffolds, scaffoldStats)
self.assertAlmostEqual(scaffoldStats['S1']['Length'], len(DefaultValues.CONTIG_BREAK) + 8)
self.assertAlmostEqual(scaffoldStats['S1']['Total contig length'], 8)
self.assertAlmostEqual(scaffoldStats['S1']['# contigs'], 2)
self.assertAlmostEqual(maxScaffoldLen, len(DefaultValues.CONTIG_BREAK) + 8)
self.assertAlmostEqual(maxContigLen, 8)
self.assertAlmostEqual(totalScaffoldBps, len(DefaultValues.CONTIG_BREAK) + 8 + 8 + 4)
self.assertAlmostEqual(numContigs, 4)
