def test_getRep(self):
'''getRep should return the desired number of sequences '''
aaUsage = tcrRepSim.readAaUsage(self.aaUsageFile)
codonUsage = tcrRepSim.readCodonUsage(self.codonUsageFile)
seqs = tcrRepSim.getUniqSeqRep(10, aaUsage[9], codonUsage)
tcrRepSim.getRep( seqs, 50, None )
total = sum([s.count for s in seqs])
self.assertTrue( total == 50 )
def test_getUniqSeqRep(self):
'''getUniqSeqRep should return the desired number of uniq sequences '''
aaUsage = tcrRepSim.readAaUsage(self.aaUsageFile)
codonUsage = tcrRepSim.readCodonUsage(self.codonUsageFile)
seqs = tcrRepSim.getUniqSeqRep(100, aaUsage[9], codonUsage)
self.assertTrue( len(seqs) == 100)
visited = []
for s in seqs:
self.assertTrue( s.nuc not in visited )
visited .append(s.nuc)
def test_sampling(self):
'''sampling should return the desired number of sequences '''
aaUsage = tcrRepSim.readAaUsage(self.aaUsageFile)
codonUsage = tcrRepSim.readCodonUsage(self.codonUsageFile)
seqs = tcrRepSim.getUniqSeqRep(10, aaUsage[9], codonUsage)
tcrRepSim.getRep( seqs, 50, None )
samseqs = tcrRepSim.sampling( seqs, 20 )
total = sum([s.count for s in samseqs])
self.assertTrue( len(samseqs) <= 10 )
self.assertTrue( total == 20 )
def test_readCodonUsage_goodInput(self):
'''readCodonUsage: usage of codon should add up to 1 for each a.a'''
aa2codons = tcrRepSim.readCodonUsage(self.goodEx)
self.assertTrue( len( aa2codons.keys() ) == 21 )
for aa, codons in aa2codons.iteritems():
self.assertTrue( abs(len(codons) - 100) <= 1 )
for c in codons:
for letter in c:
self.assertTrue( letter in "ACTG" )
codonsF = aa2codons['F']
c2c = {}
for c in codonsF:
if c in c2c:
c2c[c] += 1
else:
c2c[c] = 1
self.assertTrue( c2c['TTT'] == 45 )
self.assertTrue( c2c['TTC'] == 55 )