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_getOverlap_zeroOverlap(self):
'''Two repertoires with zero overlap should return zero overlap'''
samseqs1 = self.samseqs
#create another repertoire with totally different length
seqs2 = tcrRepSim.getUniqSeqRep(10, self.aaUsage[11], self.codonUsage)
tcrRepSim.getRep( seqs2, 50, None )
samseqs2 = tcrRepSim.sampling( seqs2, 20 )
reads1, reads2, clones1, clones2, stats1, stats2 = tcrRepSim.getOverlap(samseqs1, samseqs2, [0, 0.01, 10, 20, 100])
for i in xrange(5):
self.assertTrue( stats1["oclones"][i] == 0 )
self.assertTrue( stats2["oclones"][i] == 0 )
self.assertTrue( stats1["oreads"][i] == 0 )
self.assertTrue( stats2["oreads"][i] == 0 )