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-Updated hypermut test cases and test file
-Fixes (#26)
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-96
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+209
-96
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Diff for: ‎poplars/hypermut.py

+5-2
Original file line numberDiff line numberDiff line change
@@ -4,7 +4,6 @@
44
Supplementary Materials.
55
"""
66

7-
# TODO: Check that input sequences are the same length
87

98
import argparse
109
from poplars.common import convert_fasta
@@ -74,7 +73,6 @@ def make_results(seq, gees):
7473
"""
7574

7675
# FIXME: Regexes do not catch all potential mutation/ control sites
77-
#
7876
mut = re.compile('[AGCT](?=[AG][AGT])') # Matches potential mutation sites (GRD)
7977
ctrl = re.compile('[AGCT](?=[CT].|[AG]C)') # Matches control sites (YN|RC)
8078

@@ -144,6 +142,11 @@ def hypermut(infile, skip=None):
144142
print("skipping first {} records".format(skip))
145143
fasta = fasta[int(skip):]
146144

145+
# Check that sequences are aligned
146+
length = len(fasta[0][1])
147+
for h, s in fasta:
148+
assert length == len(s), "Sequences are not aligned."
149+
147150
refseq = fasta[0][1] # First sequence is the reference sequence
148151
gees = [i for i, nt in enumerate(refseq) if nt.upper() == 'G'] # Locate GRD motifs in reference sequence
149152
results = []

Diff for: ‎poplars/tests/fixtures/hypermut-test.fasta

+55
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,55 @@
1+
>seq1
2+
CAACTGCTGTTAAATGGCAGTCTAGCAGAAGAAGAGGTAGTAATTAGATCTGAAAATTTCACGAATAATG
3+
CTAAAATCATAATAGTACAGTTGAATGAATCTGTAAAAATTGATTGTATAAGACCCAACAACAATACAAG
4+
AAAAAGTATACATATCGGACCAGGGAGAGCATTTTACACAACAGGAGAAATAATAGGAGATATAAGACAA
5+
GCACATTGTAACATTAGTAAGAAAGATTGGAATAACGCTTTAAAACAGATAGTTATAAAATTAAGACAAC
6+
AATTTAATAGAACAATAGCCTTTACTCGATCCTCAGGAGGGGACCCAGAAATTGTAATGCACAGTTTTAA
7+
TTGTGGAGGGGAATTTTTCTACTGTAATACAACACAACTGTTTAATAGTACTTGGAATGTTAATAGTACT
8+
TGGAATGTTACTGAAGGGTCAAATAACACTGAAGGAAATATCACACTTCCATGTAGAATAAAACAAATTA
9+
TAAACATGTGGCAGGAAGTAGGAAAAGCAATGTATGCCCCTCCCATCAGAGGACAAATTAGATGTTCATC
10+
AAATATTACAGGGCTATTATTAACAAGAGATGGTGGTAATAACAATGGGACCGATGGTAATAACAATGGG
11+
ACCGAAATCTTCAGA
12+
>seq2
13+
CAACTGCTGTTAAATGGCAGTCTAGCAGAAGAAGAGGTAGTAACTAGATCTGAAAATTTCACGAATAATG
14+
CTAAAATCATAATAGTACAGTTGAATGAATCTGTAAAAATTGATTGTATAAGACCCAACAACAATACAAG
15+
AAAAAGTATACATATCGGACCAGGGAGAGCATTTTACACAACAGGAGAAATAATAGGAGATATAAGACAA
16+
GCACATTGTAACATTAGTAAGAAAGATTGGAATAACGCTTTAAAACAGATAGTTATAAAATTAAGACAAC
17+
AATTTAATAGAACAATAGCCTTTACTCGATCCTCAGGAGGGGACCCAGAAATTGTAATGCACAGTTTTAA
18+
TTGTGGAGGGGAATTTTTCTACTGTAATACAACACAACTGTTTAATAGTACTTGGAATGTTAATAGTACT
19+
TGGAATGTTACTGAAGGGTCAAATAACACTGAAGGAAATATCACACTTCCATGTAGAATAAAACAAATTA
20+
TAAACATGTGGCAGGAAGTAGGAAAAGCAATGTATGCCCCTCCCATCAGAGGACAAATTAGATGTTCATC
21+
AAATATTACAGGGCTATTATTAACAAGAGATGGTGGTAATAACAATGGGACCGATGGTAATAACAATGGG
22+
ACCGAAATCTTCAGA
23+
>seq5
24+
CAACTGCTGTTAAATGGCAGTCTAGCAGAAGAAGAGGTAGTAATTAGATCTGAAAATTTCACGAATAATG
25+
CTAAAATCATAATAGTACAGTTGAATGAATCTGTAAAAATTGATTGTATAAGACCCAACAACAATACAAG
26+
AAAAAGTATACATATCGGACCAGGGAGAGCATTTTACACAACAGGAGAAATAATAGGAAATATAAGACAA
27+
GCACATTGTAACATTAGTAAGAAAGAATGGAATAACGCTTTAAAACAGATAGTTATAAAATTAAGACAAC
28+
AATTTAATAAAACAATAGTCTTTAATCATTCCTCAGGAGGGGACCCAGAAATTGTAATGCATAGTTTTAA
29+
TTGTGGAGGGGAATTTTTCTACTGTGATACAACACAACTGTTTA------------------ATAGTACT
30+
TGGAATGGTACTGAAGGGTCAAATAACACTGGAGGAAATATCACACTTCCATGTAGAATAAAACAAATTA
31+
TAAACATGTGGCAGGAAGTAGGAAAAGCAATGTATGCCCCGCCCATCAGAGGACAAATTAGATGTTCATC
32+
AAATATTACAGGGCTATTATTAACAAGAGATGGTGGTAATAACAATAGGACCGATGGTAATAACAATAGG
33+
ACCGAAACCTTCAGA
34+
>seq7
35+
CAACTGCTGTTAAATGGCAGTCTAGCAGAAGAAGAAGTAGTAACTAGATCTAAAAATTTCACGAATAATG
36+
CTAAAATCATAATAGTACAGTTAAATGAATCTGTAAAAATTAATTGTATAAGACCCAACAACAATACAAG
37+
AAAAAGTATACATATCAGACCAGAGAGAGCATTTTACACAACAGGAGAAATAATAAGAGATATAAGACAA
38+
GCACATTGTAACATTAGTAAGAAAGATTAAAATAACGCTTTAAAACAGATAGTTATAAAATTAAGACAAC
39+
AATTTAATAGAACAATAGCCTTTACTCGATCCTCAGGAAAGGACCCAGAAATTGTAATGCACAGTTTTAA
40+
TTGTAGAGAAGAATTTTTCTACTGTAATACAACACAACTGTTTAATAGTACTTAAAATGTTAATAGTACT
41+
TAGAATGTTACTGAAAGGTCAAATAACACTGAAGGAAATATCACACTTCCATGTAGAATAAAACAAATTA
42+
TAAACATGTGGCAAGAAGTAAGAAAAGCAATGTATGCCCCTCCCATCAGAGGACAAATTAGATGTTCATC
43+
AAATATTACAAGGCTATTATTAACAAGAGATGGTAATAATAACAATAAGACCGATAGTAATAACAATAGG
44+
ACCGAAATCTTCAGA
45+
>seq14
46+
CAACTGCTGTTAAATGGCAGTCTAGCAGAAGAAAAGGTAGTAATTAAATCTAAAAATTTCACAAATAATG
47+
CTAAAATCATAATAGTACAGTTAAATAAATCTGTAAAAATTAATTGTATAAAACCCAACAACAATACAAA
48+
AAAAAGTATACATATCGAACCAAGGAAAGCATTTTACACAACAGAAAAAATAATAGGAAATATAAAACAA
49+
GCACATTGTAACATTAGTAAAAAAAATTAAAATAACGCTTTAAAACAGATAGTTATAAAATTAAAACAAC
50+
AATTTAATAGAACAATAGCCTTTACTCAATCCTCAGAAAGAAACCCAGAAATTGTAATGCACAGTTTTAA
51+
TTGTAAAGGGGAATTTTTCTACTGTAATACAACACAACTGTTTAATAGTACTTAAAATGTTAATAGTACT
52+
TAAAATGTTACTAAAAAGTCAAATAACACTAAAAAAAATATCACACTTCCATGTAAAATAAAACAAATTA
53+
TAAACATGTGGCAAAAAGTAGAAAAAGCAATGTATACCCCTCCCATCAAAAAACAAATTAAATGTTCATC
54+
AAATATTACAGGGCTATTATTAACAAAAAATAGTAGTAATAACAATGAAACCAATAGTAATAACAATAGA
55+
ACCGAAACCTTCAAA

Diff for: ‎poplars/tests/test_hypermut.py

+149-94
Original file line numberDiff line numberDiff line change
@@ -1,108 +1,161 @@
11
import unittest
22
import os
3-
import re
43
from poplars.common import convert_fasta
5-
from poplars.hypermut import make_results
6-
from poplars.hypermut import hypermut
7-
from poplars.hypermut import rate_ratio
8-
from poplars.hypermut import make_data_file
4+
from poplars.hypermut import *
95

10-
TEST_HIV = os.path.join(os.path.dirname(__file__), 'fixtures/hiv-test-genome.fasta')
11-
TEST_DATA = os.path.join(os.path.dirname(__file__), 'fixtures/aligned_HIV1_Mgroup.fasta')
126

7+
class HIVTestCase(unittest.TestCase):
138

14-
class TestMakeResults(unittest.TestCase):
159
def setUp(self):
16-
self.hiv_data = open(TEST_HIV)
17-
self.data = open(TEST_DATA)
18-
19-
def testDSMotifs(self):
20-
mut = re.compile('[AGCT](?=[AG][AGT])') # Matches potential mutation sites (GRD)
21-
s = convert_fasta(self.hiv_data)[0][1]
22-
result = [match.start() for match in mut.finditer(s)]
23-
expected = [0, 1, 2, 3, 4, 5, 9, 10, 20, 23, 24, 25, 26, 29, 30, 31, 32, 34, 40, 41, 45, 47, 48, 49, 62,
24-
63, 64, 76, 77, 80, 83, 84, 85, 96, 97, 98, 102, 103, 104, 105, 106, 109, 110, 111, 113, 120,
25-
127, 128, 129, 131, 132, 139, 140, 144, 145, 150, 151, 154, 155, 159, 160, 161, 162, 163, 164,
26-
165, 168, 169, 170, 171, 172, 173, 174, 178, 181, 182, 183, 184, 185, 186, 187, 188, 189, 190,
27-
196, 201, 211, 213, 214, 221, 223, 224, 225, 226, 228, 229, 230, 232, 237, 238, 239, 240, 241,
28-
242, 243, 244, 245, 246, 247, 249, 252, 253, 254, 255, 257, 258, 259, 260, 261, 265, 268, 276,
29-
279, 284, 289, 291, 296, 297, 298, 299, 305, 309, 310, 311, 312, 319, 320, 321, 322, 329, 332,
30-
335, 336, 346, 347]
31-
self.assertEqual(expected, result)
32-
33-
def testCtrlMotifs(self):
34-
ctrl = re.compile('[AGCT](?=[CT].|[AG]C)')
35-
s = convert_fasta(self.hiv_data)[0][1]
36-
result = [match.start() for match in ctrl.finditer(s)]
37-
expected = [6, 7, 8, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 27, 28, 33, 35, 36, 37, 38, 39, 42, 43,
38-
44, 46, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 65, 66, 67, 68, 69, 70, 71, 72, 73,
39-
74, 75, 78, 79, 81, 82, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 99, 100, 101, 107, 108, 112,
40-
114, 115, 116, 117, 118, 119, 121, 122, 123, 124, 125, 126, 130, 133, 134, 135, 136, 137, 138,
41-
141, 142, 143, 146, 147, 148, 149, 152, 153, 156, 157, 158, 166, 167, 175, 176, 177, 179, 180,
42-
191, 192, 193, 194, 195, 197, 198, 199, 200, 202, 203, 204, 205, 206, 207, 208, 209, 210, 212,
43-
215, 216, 217, 218, 219, 220, 222, 227, 231, 233, 234, 235, 236, 248, 250, 251, 256, 262, 263,
44-
264, 266, 267, 269, 270, 271, 272, 273, 274, 275, 277, 278, 280, 281, 282, 283, 285, 286, 287,
45-
288, 290, 292, 293, 294, 295, 300, 301, 302, 303, 304, 306, 307, 308, 313, 314, 315, 316, 317,
46-
318, 323, 324, 325, 326, 327, 328, 330, 331, 333, 334, 337, 338, 339, 340, 341, 342, 343, 344, 345]
47-
self.assertEqual(expected, result)
48-
49-
def test_alignmentA1(self):
50-
fasta = convert_fasta(self.data)
51-
refseq = fasta[0][1]
52-
gees = [i for i, nt in enumerate(refseq) if nt.upper() == 'G']
53-
seq = fasta[1]
54-
output = make_results(seq, gees)
55-
56-
ex_num_muts = 47
57-
self.assertEqual(ex_num_muts, output.num_muts)
58-
59-
ex_pot_muts = 1068
60-
self.assertEqual(ex_pot_muts, output.pot_muts)
61-
62-
ex_ctrl_muts = 53
63-
self.assertEqual(ex_ctrl_muts, output.ctrl_muts)
64-
65-
ex_pot_ctrl_muts = 986
66-
self.assertEqual(ex_pot_ctrl_muts, output.potential_ctrls)
67-
68-
ex_rate_ratio = 0.82
69-
self.assertEqual(ex_rate_ratio, round(output.rate_ratio, 2))
70-
71-
ex_p_value = 0.870295
72-
self.assertEqual(ex_p_value, output.p_value)
7310

74-
ex_ctable = [[47, 1068], [53, 986]]
75-
self.assertEqual(ex_ctable, output.ctable)
76-
77-
# ex_mut_sites = None
78-
# ex_ctrl_sites = None
79-
80-
def tearDown(self):
81-
self.hiv_data.close()
82-
self.data.close()
83-
84-
85-
class TestHypermut(unittest.TestCase):
86-
87-
def setUp(self):
88-
self.hiv_data = open(TEST_HIV)
89-
90-
def testGees(self):
91-
fasta = convert_fasta(self.hiv_data)
92-
refseq = fasta[0][1] # Reference sequence is the first entry
93-
result = [i for i, nt in enumerate(refseq) if nt.upper() == 'G']
94-
expected = [1, 2, 5, 6, 7, 24, 27, 32, 41, 46, 48, 49, 65, 66, 77, 82, 85, 98, 99, 100, 104, 105, 106, 111,
95-
121, 128, 129, 132, 133, 135, 142, 146, 152, 155, 157, 161, 163, 166, 170, 173, 176, 185, 186,
96-
188, 190, 198, 202, 212, 214, 216, 220, 224, 225, 229, 230, 233, 238, 239, 241, 243, 245, 248,
97-
250, 254, 256, 258, 259, 261, 262, 266, 270, 273, 278, 292, 293, 297, 299, 301, 304, 310, 311,
98-
313, 322, 327, 330, 336, 338, 342, 349]
99-
self.assertEqual(expected, result)
100-
101-
def tearDown(self):
102-
self.hiv_data.close()
11+
genome_path = os.path.join(os.path.dirname(__file__), 'fixtures/hiv-test-genome.fasta')
12+
infile_path = os.path.join(os.path.dirname(__file__), 'fixtures/aligned_HIV1_Mgroup.fasta')
13+
test_data = os.path.join(os.path.dirname(__file__), 'fixtures/hypermut-test.fasta')
14+
15+
with open(genome_path) as handle, open(infile_path) as in_handle, open(test_data) as test_handle:
16+
self.hiv_genome = handle.read()
17+
self.hiv_data = in_handle.read()
18+
self.simple_data = convert_fasta(test_handle.read().split())
19+
20+
self.mut = re.compile('[AGCT](?=[AG][AGT])') # Matches potential mutation sites (RD)
21+
self.ctrl = re.compile('[AGCT](?=[CT].|[AG]C)') # Matches potential control sites (YN or RC)
22+
23+
24+
class Hypermut(HIVTestCase):
25+
26+
maxDiff = None
27+
28+
def testSimpleData(self):
29+
30+
# Test potential mutation sites
31+
test_matches = ['GAA', 'GAG', 'GAT', 'GGA', 'GGG', 'GGT', 'CGAA']
32+
for s in test_matches:
33+
self.assertTrue(self.mut.match(s))
34+
test_mismatches = ['CTC', 'GTC', 'GGCGC']
35+
for s in test_mismatches:
36+
self.assertFalse(self.mut.match(s))
37+
38+
# Test potential control sites
39+
test_matches = ['TAC', 'CCC', 'CAC', 'TTGC']
40+
for s in test_matches:
41+
self.assertTrue(self.ctrl.match(s))
42+
test_mismatches = ['TAT', 'CGGC', 'CAA']
43+
for s in test_mismatches:
44+
self.assertFalse(self.ctrl.match(s))
45+
46+
# Test gees
47+
refseq = self.simple_data[0][1] # Reference sequence is the first entry
48+
res_gees = [i for i, nt in enumerate(refseq) if nt.upper() == 'G']
49+
exp_gees = [5, 8, 15, 16, 19, 24, 27, 30, 33, 35, 36, 39, 46, 51, 62, 69, 84, 89, 92, 96, 102, 111,
50+
115, 121, 139, 145, 156, 157, 162, 163, 164, 166, 168, 183, 184, 186, 195, 196, 198, 205,
51+
210, 217, 226, 230, 234, 238, 239, 246, 257, 261, 274, 289, 297, 307, 315, 316, 318, 319,
52+
320, 321, 327, 333, 338, 343, 352, 354, 355, 357, 358, 359, 360, 373, 389, 397, 403, 404,
53+
408, 415, 421, 422, 426, 432, 435, 436, 437, 450, 453, 454, 472, 475, 497, 499, 500, 503,
54+
504, 507, 510, 511, 516, 521, 525, 538, 540, 541, 550, 553, 570, 571, 572, 586, 588, 591,
55+
592, 594, 595, 606, 607, 608, 612, 615, 616, 627, 628, 629, 633, 643]
56+
self.assertEqual(exp_gees, res_gees)
57+
58+
query_seq = self.simple_data[1:]
59+
60+
outputs = []
61+
for seq in query_seq:
62+
outputs.append(make_results(seq, res_gees))
63+
64+
for i in range(len(outputs)):
65+
ex_num_muts = [0, 4, 26, 48]
66+
self.assertEqual(ex_num_muts[i], outputs[i].num_muts) # Test match sites
67+
68+
ex_pot_muts = [71, 69, 71, 71]
69+
self.assertEqual(ex_pot_muts[i], outputs[i].pot_muts) # Test potential mutation sites
70+
71+
ex_ctrl_muts = [0, 1, 1, 9]
72+
self.assertEqual(ex_ctrl_muts[i], outputs[i].ctrl_muts) # Test control mutations
73+
74+
ex_pot_ctrl_muts = [54, 52, 54, 54]
75+
self.assertEqual(ex_pot_ctrl_muts[i], outputs[i].potential_ctrls) # Test potential controls
76+
77+
ex_rate_ratio = ['undef', 3.01, 19.77, 4.06]
78+
if type(ex_rate_ratio) == str:
79+
self.assertEqual(ex_rate_ratio[i], outputs[i].rate_ratio) # Test rate ratio
80+
else:
81+
self.assertAlmostEqual(ex_rate_ratio[i], outputs[i].rate_ratio, places=2)
82+
83+
ex_p_value = [1, 0.282669, 5.35061e-07, 8.26961e-09]
84+
self.assertAlmostEqual(ex_p_value[i], outputs[i].p_value, places=2) # Test p-value
85+
86+
ex_ctable = [[[0, 71], [0, 54]], # Seq2
87+
88+
[[4, 65], [1, 51]], # Seq5
89+
90+
[[26, 45], [1, 53]], # Seq7
91+
92+
[[48, 23], [9, 45]]] # Seq14
93+
self.assertEqual(ex_ctable[i], outputs[i].ctable) # Test contingency table
94+
95+
# Test mutation sites
96+
ex_mut_sites = [{28: 0, 31: 0, 34: 0, 36: 0, 47: 0, 52: 0, 63: 0, 93: 0, 97: 0, 112: 0, 140: 0, 157: 0,
97+
163: 0, 164: 0, 165: 0, 167: 0, 184: 0, 185: 0, 187: 0, 196: 0, 197: 0, 199: 0, 231: 0,
98+
235: 0, 239: 0, 240: 0, 258: 0, 290: 0, 308: 0, 316: 0, 317: 0, 319: 0, 320: 0, 321: 0,
99+
328: 0, 355: 0, 356: 0, 358: 0, 359: 0, 360: 0, 361: 0, 404: 0, 405: 0, 422: 0, 423: 0,
100+
433: 0, 436: 0, 437: 0, 451: 0, 454: 0, 455: 0, 476: 0, 504: 0, 505: 0, 511: 0, 512: 0,
101+
539: 0, 541: 0, 551: 0, 571: 0, 587: 0, 589: 0, 592: 0, 595: 0, 607: 0, 608: 0, 613: 0,
102+
616: 0, 628: 0, 629: 0, 634: 0},
103+
104+
{28: 0, 31: 0, 34: 0, 36: 0, 47: 0, 52: 0, 63: 0, 93: 0, 97: 0, 112: 0, 140: 0, 157: 0,
105+
163: 0, 164: 0, 165: 0, 167: 0, 184: 0, 185: 0, 187: 0, 196: 0, 197: 0, 199: 1, 231: 0,
106+
235: 0, 239: 0, 240: 0, 258: 0, 290: 1, 316: 0, 317: 0, 319: 0, 320: 0, 321: 0, 328: 0,
107+
355: 0, 356: 0, 358: 0, 359: 0, 360: 0, 361: 0, 422: 0, 423: 0, 427: 0, 433: 0, 436: 0,
108+
437: 0, 451: 0, 454: 0, 455: 0, 476: 0, 504: 0, 505: 0, 511: 0, 512: 0, 539: 0, 541: 0,
109+
551: 0, 571: 0, 587: 0, 589: 0, 592: 0, 595: 0, 607: 1, 608: 0, 613: 0, 616: 0, 628: 1,
110+
629: 0, 634: 0},
111+
112+
{28: 0, 31: 0, 34: 0, 36: 1, 47: 0, 52: 1, 63: 0, 93: 1, 97: 0, 112: 1, 140: 0, 157: 1,
113+
163: 0, 164: 1, 165: 0, 167: 0, 184: 0, 185: 0, 187: 0, 196: 1, 197: 0, 199: 0, 231: 0,
114+
235: 0, 239: 1, 240: 1, 258: 0, 290: 0, 308: 0, 316: 0, 317: 0, 319: 1, 320: 1, 321: 0,
115+
328: 0, 355: 1, 356: 0, 358: 0, 359: 1, 360: 1, 361: 0, 404: 1, 405: 1, 422: 1, 423: 0,
116+
433: 0, 436: 1, 437: 0, 451: 0, 454: 0, 455: 0, 476: 0, 504: 1, 505: 0, 511: 1, 512: 0,
117+
539: 0, 541: 0, 551: 0, 571: 1, 587: 0, 589: 0, 592: 0, 595: 1, 607: 1, 608: 1, 613: 0,
118+
616: 1, 628: 1, 629: 0, 634: 0},
119+
120+
{28: 0, 31: 0, 34: 1, 36: 0, 47: 1, 52: 1, 63: 1, 93: 1, 97: 1, 112: 1, 140: 1, 157: 0,
121+
163: 1, 164: 0, 165: 0, 167: 1, 184: 0, 185: 1, 187: 1, 196: 0, 197: 0, 199: 1, 231: 1,
122+
235: 1, 239: 1, 240: 1, 258: 0, 290: 0, 308: 1, 316: 0, 317: 1, 319: 1, 320: 0, 321: 1,
123+
328: 0, 355: 1, 356: 1, 358: 0, 359: 0, 360: 0, 361: 0, 404: 1, 405: 1, 422: 1, 423: 1,
124+
433: 1, 436: 1, 437: 1, 451: 1, 454: 1, 455: 1, 476: 1, 504: 1, 505: 1, 511: 0, 512: 1,
125+
539: 1, 541: 1, 551: 1, 571: 0, 587: 1, 589: 1, 592: 1, 595: 1, 607: 0, 608: 1, 613: 1,
126+
616: 1, 628: 1, 629: 0, 634: 0}]
127+
128+
self.assertEqual(ex_mut_sites[i], outputs[i].mut_sites)
129+
130+
# Test control sites
131+
ex_ctrl_sites = [{6: 0, 9: 0, 16: 0, 17: 0, 20: 0, 25: 0, 37: 0, 40: 0, 70: 0, 85: 0, 90: 0, 103: 0,
132+
116: 0, 122: 0, 146: 0, 158: 0, 169: 0, 206: 0, 211: 0, 218: 0, 227: 0, 247: 0, 262: 0,
133+
275: 0, 298: 0, 322: 0, 334: 0, 339: 0, 344: 0, 353: 0, 374: 0, 390: 0, 398: 0, 409: 0,
134+
416: 0, 427: 0, 438: 0, 473: 0, 498: 0, 500: 0, 501: 0, 508: 0, 517: 0, 522: 0, 526: 0,
135+
542: 0, 554: 0, 572: 0, 573: 0, 593: 0, 596: 0, 609: 0, 617: 0, 630: 0},
136+
137+
{6: 0, 9: 0, 16: 0, 17: 0, 20: 0, 25: 0, 37: 0, 40: 0, 70: 0, 85: 0, 90: 0, 103: 0,
138+
116: 0, 122: 0, 146: 0, 158: 0, 169: 0, 206: 0, 211: 0, 218: 0, 227: 0, 247: 0, 262: 0,
139+
275: 0, 298: 0, 308: 1, 322: 0, 334: 0, 339: 0, 344: 0, 353: 0, 374: 0, 390: 0, 416: 0,
140+
438: 0, 473: 0, 498: 0, 500: 0, 501: 0, 508: 0, 517: 0, 522: 0, 526: 0, 542: 0, 554: 0,
141+
572: 0, 573: 0, 593: 0, 596: 0, 609: 0, 617: 0, 630: 0},
142+
143+
{6: 0, 9: 0, 16: 0, 17: 0, 20: 0, 25: 0, 37: 0, 40: 0, 70: 0, 85: 0, 90: 0, 103: 0,
144+
116: 0, 122: 0, 146: 0, 158: 0, 169: 0, 206: 0, 211: 0, 218: 0, 227: 0, 247: 0, 262: 0,
145+
275: 0, 298: 0, 322: 0, 334: 0, 339: 0, 344: 0, 353: 0, 374: 0, 390: 0, 398: 0, 409: 0,
146+
416: 0, 427: 0, 438: 0, 473: 0, 498: 0, 500: 0, 501: 0, 508: 0, 517: 0, 522: 0, 526: 0,
147+
542: 0, 554: 0, 572: 0, 573: 0, 593: 0, 596: 1, 609: 0, 617: 0, 630: 0},
148+
149+
{6: 0, 9: 0, 16: 0, 17: 0, 20: 0, 25: 0, 37: 0, 40: 0, 70: 0, 85: 0, 90: 0, 103: 0,
150+
116: 0, 122: 1, 146: 0, 158: 1, 169: 0, 206: 1, 211: 0, 218: 0, 227: 0, 247: 0, 262: 0,
151+
275: 1, 298: 0, 322: 1, 334: 0, 339: 0, 344: 0, 353: 0, 374: 0, 390: 0, 398: 0, 409: 0,
152+
416: 0, 427: 0, 438: 0, 473: 0, 498: 0, 500: 0, 501: 0, 508: 0, 517: 0, 522: 0, 526: 1,
153+
542: 1, 554: 0, 572: 0, 573: 0, 593: 0, 596: 0, 609: 1, 617: 0, 630: 1}]
154+
self.assertEqual(ex_ctrl_sites[i], outputs[i].ctrl_sites)
103155

104156

105157
class TestRateRatio(unittest.TestCase):
158+
106159
def testRateRatio(self):
107160
ctable = [[4, 17], [7, 33]]
108161
expected = 1.1
@@ -123,3 +176,5 @@ def test2UndefinedRateRatio(self):
123176
self.assertEqual(expected, result)
124177

125178

179+
if __name__ == '__main__':
180+
unittest.main()

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