def calculateSeqStats(self, scaffolds, scaffoldsStats):
"""Calculate scaffold length statistics (min length, max length, total length, N50, # contigs)."""
scaffoldLens = []
contigLens = []
numAmbiguousBases = 0
for scaffoldId, scaffold in scaffolds.iteritems():
scaffoldLen = len(scaffold)
scaffoldLens.append(scaffoldLen)
splitScaffold = scaffold.split(DefaultValues.CONTIG_BREAK)
lenContigsInScaffold = []
for contig in splitScaffold:
contigLen = len(contig.replace('N', ''))
if contigLen > 0:
lenContigsInScaffold.append(contigLen)
contigLens += lenContigsInScaffold
scaffoldsStats[scaffoldId]['Length'] = scaffoldLen
scaffoldsStats[scaffoldId]['Total contig length'] = sum(lenContigsInScaffold)
scaffoldsStats[scaffoldId]['# contigs'] = len(lenContigsInScaffold)
numAmbiguousBases += scaffold.count('N') + scaffold.count('n')
scaffold_N50 = calculateN50(scaffoldLens)
contig_N50 = calculateN50(contigLens)
return max(scaffoldLens), max(contigLens), sum(scaffoldLens), scaffold_N50, contig_N50, len(contigLens), numAmbiguousBases
def calculateSeqStats(self, scaffolds, seqStats=None):
"""Calculate scaffold length statistics (min length, max length, total length, N50, # contigs)."""
scaffoldLens = []
contigLens = []
numAmbiguousBases = 0
for scaffoldId, scaffold in scaffolds.items():
scaffoldLen = len(scaffold)
scaffoldLens.append(scaffoldLen)
splitScaffold = scaffold.split(DefaultValues.CONTIG_BREAK)
lenContigsInScaffold = []
for contig in splitScaffold:
contigLen = len(contig.replace('N', ''))
if contigLen > 0:
lenContigsInScaffold.append(contigLen)
contigLens += lenContigsInScaffold
if seqStats:
seqStats[scaffoldId]['Length'] = scaffoldLen
seqStats[scaffoldId]['Total contig length'] = sum(
lenContigsInScaffold)
seqStats[scaffoldId]['# contigs'] = len(lenContigsInScaffold)
numAmbiguousBases += scaffold.count('N') + scaffold.count('n')
scaffold_N50 = calculateN50(scaffoldLens)
contig_N50 = calculateN50(contigLens)
return max(scaffoldLens), max(contigLens), sum(
scaffoldLens), scaffold_N50, contig_N50, mean(scaffoldLens), mean(
contigLens), len(contigLens), numAmbiguousBases
def testScaffoldLengthStats(self):
"""Verify computation of N50."""
n50 = calculateN50([1, 1, 2, 2, 2, 2, 10])
self.assertEqual(n50, 10)
