def test_single_contig_2(self):
contigs_2 = ['ATCGCTGATT', 'ATCCCTCATT', 'ATCGCTCATT', 'ATCCCTGATT']
reads_2 = {\
'ATCC':[[0,0,0.5]],'TCGC':[[0,1,0.5]],'CCCT':[[0,2,0.5]],'GCTC':[[0,3,0.5]],\
'TTCA':[[0,4,0.5]],'TGAT':[[0,5,0.5]],'GATT':[[0,6,0.5]]}
freq = cs.consensus_sequence(reads_2)
self.assertTrue(cs.compute_new_contigs(freq)[0] in contigs_2)
def test_single_contig_1(self):
contigs_1 = ['ATCGCTGATT']
reads_1 = {\
'ATCG':[[0,0,0.5]],'TCGC':[[0,1,0.5]],'CCCT':[[0,2,0.5]],'GCTG':[[0,3,0.5]],\
'TTCA':[[0,4,0.5]],'TGAT':[[0,5,0.5]],'GATT':[[0,6,0.5]]}
freq = cs.consensus_sequence(reads_1)
self.assertEqual(contigs_1, cs.compute_new_contigs(freq))
def test_multiple_contigs_1(self):
contigs_3 = ['ATCGCTGATT', 'TTTACGATGC']
reads_3 = {\
'ATCG':[[0,0,0.5]],'TCGC':[[0,1,0.5]],'CCCT':[[0,2,0.5]],'GCTG':[[0,3,0.5]],\
'TTCA':[[0,4,0.5]],'TGAT':[[0,5,0.5]],'GATT':[[0,6,0.5]],\
'TTAA':[[1,0,0.5]],'TTAC':[[1,1,0.5]],'TGCG':[[1,2,0.5]],'ACGA':[[1,3,0.5]],\
'AGAT':[[1,4,0.5]],'GTTG':[[1,5,0.5]],'AAGC':[[1,6,0.5]]}
freq = cs.consensus_sequence(reads_3)
self.assertEqual(contigs_3, cs.compute_new_contigs(freq))
def test_multiple_contigs_2(self):
contigs_4 = ['ATCGCTGATT','ATCCCTCATT','ATCGCTCATT','ATCCCTGATT',\
'TTTACGATGC','TTTAAGATGC']
reads_4 = {\
'ATCG':[[0,0,0.5]],'TCGC':[[0,1,0.5]],'CCCT':[[0,2,0.5]],'GCTG':[[0,3,0.5]],\
'TTCA':[[0,4,0.5]],'TGAT':[[0,5,0.5]],'GATT':[[0,6,0.5]],\
'TTAA':[[1,0,0.5],[1,1,0.5]],'TGCG':[[1,2,0.5]],'CCGA':[[1,3,0.5]],\
'AGAT':[[1,4,0.5]],'GTTG':[[1,5,0.5]],'AAGC':[[1,6,0.5]]}
freq = cs.consensus_sequence(reads_4)
self.assertTrue(cs.compute_new_contigs(freq)[0] in contigs_4\
and cs.compute_new_contigs(freq)[1] in contigs_4)
def test_single_contig_2(self):
contigs_2 = ["ATCGCTGATT", "ATCCCTCATT", "ATCGCTCATT", "ATCCCTGATT"]
reads_2 = {
"ATCC": [[0, 0, 0.5]],
"TCGC": [[0, 1, 0.5]],
"CCCT": [[0, 2, 0.5]],
"GCTC": [[0, 3, 0.5]],
"TTCA": [[0, 4, 0.5]],
"TGAT": [[0, 5, 0.5]],
"GATT": [[0, 6, 0.5]],
}
freq = cs.consensus_sequence(reads_2)
self.assertTrue(cs.compute_new_contigs(freq)[0] in contigs_2)
def test_single_contig_1(self):
contigs_1 = ["ATCGCTGATT"]
reads_1 = {
"ATCG": [[0, 0, 0.5]],
"TCGC": [[0, 1, 0.5]],
"CCCT": [[0, 2, 0.5]],
"GCTG": [[0, 3, 0.5]],
"TTCA": [[0, 4, 0.5]],
"TGAT": [[0, 5, 0.5]],
"GATT": [[0, 6, 0.5]],
}
freq = cs.consensus_sequence(reads_1)
self.assertEqual(contigs_1, cs.compute_new_contigs(freq))
def test_multiple_contigs_2(self):
contigs_4 = ["ATCGCTGATT", "ATCCCTCATT", "ATCGCTCATT", "ATCCCTGATT", "TTTACGATGC", "TTTAAGATGC"]
reads_4 = {
"ATCG": [[0, 0, 0.5]],
"TCGC": [[0, 1, 0.5]],
"CCCT": [[0, 2, 0.5]],
"GCTG": [[0, 3, 0.5]],
"TTCA": [[0, 4, 0.5]],
"TGAT": [[0, 5, 0.5]],
"GATT": [[0, 6, 0.5]],
"TTAA": [[1, 0, 0.5], [1, 1, 0.5]],
"TGCG": [[1, 2, 0.5]],
"CCGA": [[1, 3, 0.5]],
"AGAT": [[1, 4, 0.5]],
"GTTG": [[1, 5, 0.5]],
"AAGC": [[1, 6, 0.5]],
}
freq = cs.consensus_sequence(reads_4)
self.assertTrue(cs.compute_new_contigs(freq)[0] in contigs_4 and cs.compute_new_contigs(freq)[1] in contigs_4)
def test_multiple_contigs_1(self):
contigs_3 = ["ATCGCTGATT", "TTTACGATGC"]
reads_3 = {
"ATCG": [[0, 0, 0.5]],
"TCGC": [[0, 1, 0.5]],
"CCCT": [[0, 2, 0.5]],
"GCTG": [[0, 3, 0.5]],
"TTCA": [[0, 4, 0.5]],
"TGAT": [[0, 5, 0.5]],
"GATT": [[0, 6, 0.5]],
"TTAA": [[1, 0, 0.5]],
"TTAC": [[1, 1, 0.5]],
"TGCG": [[1, 2, 0.5]],
"ACGA": [[1, 3, 0.5]],
"AGAT": [[1, 4, 0.5]],
"GTTG": [[1, 5, 0.5]],
"AAGC": [[1, 6, 0.5]],
}
freq = cs.consensus_sequence(reads_3)
self.assertEqual(contigs_3, cs.compute_new_contigs(freq))
