def testKSpectrumMM(self):
spec = nc.features.kSpectrumMM(5)
testSeq = nc.sequence('', 'GAGAGAGAGT')
motifs = set([ testSeq.seq[i:i+5] for i in range(len(testSeq)-4) ])
motifs = motifs | set( nc.getReverseComplementaryDNASequence(m) for m in motifs )
def getMM(m):
return set(
m[:i] + mut + m[i+1:]
for i in range(len(m))
for mut in [ 'A', 'C', 'G', 'T' ]
)
motifs = motifs | set( mm for m in motifs for mm in getMM(m) )
# Ensure that only the main motif and mismatches are registered
specmotifs = set(
k
for k, f in zip(
[ f.kmer for f in spec ],
spec.getAll(testSeq)
)
if f > 0
)
self.assertEqual(specmotifs, motifs)
# Ensure that application to the reverse complement yields an identical spectrum
specmotifsRC = set(
k
for k, f in zip(
[ f.kmer for f in spec ],
spec.getAll(nc.sequence('',
nc.getReverseComplementaryDNASequence(testSeq.seq)))
)
if f > 0
)
self.assertEqual(specmotifs, specmotifsRC)
def testKSpectrum(self):
spec = nc.features.kSpectrum(5)
testSeq = nc.sequence('', 'GAGAGAGAGT')
kmerFreq = {
k: v
for k, v in zip([f.kmer for f in spec], spec.getAll(testSeq))
}
self.assertEqual(kmerFreq['AGAGT'], 100.)
self.assertEqual(kmerFreq['ACTCT'], 100.)
self.assertEqual(kmerFreq['AGAGA'], 200.)
self.assertEqual(kmerFreq['TCTCT'], 200.)
self.assertEqual(kmerFreq['GAGAG'], 300.)
self.assertEqual(kmerFreq['CTCTC'], 300.)
self.assertEqual(
sum(kmerFreq[kmer] for kmer in kmerFreq.keys() if kmer not in
['AGAGT', 'ACTCT', 'AGAGA', 'TCTCT', 'GAGAG', 'CTCTC']), 0.)
# Ensure that application to the reverse complement yields an identical spectrum
specmotifs = set(k
for k, f in zip([f.kmer
for f in spec], spec.getAll(testSeq))
if f > 0)
specmotifsRC = set(k for k, f in zip(
[f.kmer for f in spec],
spec.getAll(
nc.sequence(
'', nc.getReverseComplementaryDNASequence(testSeq.seq))))
if f > 0)
self.assertEqual(specmotifs, specmotifsRC)