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-Updated hypermut test cases and test file
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-Fixes (#26)
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@kwade4
kwade4 committed Aug 27, 2019
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7 changes: 5 additions & 2 deletions poplars/hypermut.py
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Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,6 @@
Supplementary Materials.
"""

# TODO: Check that input sequences are the same length

import argparse
from poplars.common import convert_fasta
Expand Down Expand Up @@ -74,7 +73,6 @@ def make_results(seq, gees):
"""

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

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

# Check that sequences are aligned
length = len(fasta[0][1])
for h, s in fasta:
assert length == len(s), "Sequences are not aligned."

refseq = fasta[0][1] # First sequence is the reference sequence
gees = [i for i, nt in enumerate(refseq) if nt.upper() == 'G'] # Locate GRD motifs in reference sequence
results = []
Expand Down
55 changes: 55 additions & 0 deletions poplars/tests/fixtures/hypermut-test.fasta
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Original file line number Diff line number Diff line change
@@ -0,0 +1,55 @@
>seq1
CAACTGCTGTTAAATGGCAGTCTAGCAGAAGAAGAGGTAGTAATTAGATCTGAAAATTTCACGAATAATG
CTAAAATCATAATAGTACAGTTGAATGAATCTGTAAAAATTGATTGTATAAGACCCAACAACAATACAAG
AAAAAGTATACATATCGGACCAGGGAGAGCATTTTACACAACAGGAGAAATAATAGGAGATATAAGACAA
GCACATTGTAACATTAGTAAGAAAGATTGGAATAACGCTTTAAAACAGATAGTTATAAAATTAAGACAAC
AATTTAATAGAACAATAGCCTTTACTCGATCCTCAGGAGGGGACCCAGAAATTGTAATGCACAGTTTTAA
TTGTGGAGGGGAATTTTTCTACTGTAATACAACACAACTGTTTAATAGTACTTGGAATGTTAATAGTACT
TGGAATGTTACTGAAGGGTCAAATAACACTGAAGGAAATATCACACTTCCATGTAGAATAAAACAAATTA
TAAACATGTGGCAGGAAGTAGGAAAAGCAATGTATGCCCCTCCCATCAGAGGACAAATTAGATGTTCATC
AAATATTACAGGGCTATTATTAACAAGAGATGGTGGTAATAACAATGGGACCGATGGTAATAACAATGGG
ACCGAAATCTTCAGA
>seq2
CAACTGCTGTTAAATGGCAGTCTAGCAGAAGAAGAGGTAGTAACTAGATCTGAAAATTTCACGAATAATG
CTAAAATCATAATAGTACAGTTGAATGAATCTGTAAAAATTGATTGTATAAGACCCAACAACAATACAAG
AAAAAGTATACATATCGGACCAGGGAGAGCATTTTACACAACAGGAGAAATAATAGGAGATATAAGACAA
GCACATTGTAACATTAGTAAGAAAGATTGGAATAACGCTTTAAAACAGATAGTTATAAAATTAAGACAAC
AATTTAATAGAACAATAGCCTTTACTCGATCCTCAGGAGGGGACCCAGAAATTGTAATGCACAGTTTTAA
TTGTGGAGGGGAATTTTTCTACTGTAATACAACACAACTGTTTAATAGTACTTGGAATGTTAATAGTACT
TGGAATGTTACTGAAGGGTCAAATAACACTGAAGGAAATATCACACTTCCATGTAGAATAAAACAAATTA
TAAACATGTGGCAGGAAGTAGGAAAAGCAATGTATGCCCCTCCCATCAGAGGACAAATTAGATGTTCATC
AAATATTACAGGGCTATTATTAACAAGAGATGGTGGTAATAACAATGGGACCGATGGTAATAACAATGGG
ACCGAAATCTTCAGA
>seq5
CAACTGCTGTTAAATGGCAGTCTAGCAGAAGAAGAGGTAGTAATTAGATCTGAAAATTTCACGAATAATG
CTAAAATCATAATAGTACAGTTGAATGAATCTGTAAAAATTGATTGTATAAGACCCAACAACAATACAAG
AAAAAGTATACATATCGGACCAGGGAGAGCATTTTACACAACAGGAGAAATAATAGGAAATATAAGACAA
GCACATTGTAACATTAGTAAGAAAGAATGGAATAACGCTTTAAAACAGATAGTTATAAAATTAAGACAAC
AATTTAATAAAACAATAGTCTTTAATCATTCCTCAGGAGGGGACCCAGAAATTGTAATGCATAGTTTTAA
TTGTGGAGGGGAATTTTTCTACTGTGATACAACACAACTGTTTA------------------ATAGTACT
TGGAATGGTACTGAAGGGTCAAATAACACTGGAGGAAATATCACACTTCCATGTAGAATAAAACAAATTA
TAAACATGTGGCAGGAAGTAGGAAAAGCAATGTATGCCCCGCCCATCAGAGGACAAATTAGATGTTCATC
AAATATTACAGGGCTATTATTAACAAGAGATGGTGGTAATAACAATAGGACCGATGGTAATAACAATAGG
ACCGAAACCTTCAGA
>seq7
CAACTGCTGTTAAATGGCAGTCTAGCAGAAGAAGAAGTAGTAACTAGATCTAAAAATTTCACGAATAATG
CTAAAATCATAATAGTACAGTTAAATGAATCTGTAAAAATTAATTGTATAAGACCCAACAACAATACAAG
AAAAAGTATACATATCAGACCAGAGAGAGCATTTTACACAACAGGAGAAATAATAAGAGATATAAGACAA
GCACATTGTAACATTAGTAAGAAAGATTAAAATAACGCTTTAAAACAGATAGTTATAAAATTAAGACAAC
AATTTAATAGAACAATAGCCTTTACTCGATCCTCAGGAAAGGACCCAGAAATTGTAATGCACAGTTTTAA
TTGTAGAGAAGAATTTTTCTACTGTAATACAACACAACTGTTTAATAGTACTTAAAATGTTAATAGTACT
TAGAATGTTACTGAAAGGTCAAATAACACTGAAGGAAATATCACACTTCCATGTAGAATAAAACAAATTA
TAAACATGTGGCAAGAAGTAAGAAAAGCAATGTATGCCCCTCCCATCAGAGGACAAATTAGATGTTCATC
AAATATTACAAGGCTATTATTAACAAGAGATGGTAATAATAACAATAAGACCGATAGTAATAACAATAGG
ACCGAAATCTTCAGA
>seq14
CAACTGCTGTTAAATGGCAGTCTAGCAGAAGAAAAGGTAGTAATTAAATCTAAAAATTTCACAAATAATG
CTAAAATCATAATAGTACAGTTAAATAAATCTGTAAAAATTAATTGTATAAAACCCAACAACAATACAAA
AAAAAGTATACATATCGAACCAAGGAAAGCATTTTACACAACAGAAAAAATAATAGGAAATATAAAACAA
GCACATTGTAACATTAGTAAAAAAAATTAAAATAACGCTTTAAAACAGATAGTTATAAAATTAAAACAAC
AATTTAATAGAACAATAGCCTTTACTCAATCCTCAGAAAGAAACCCAGAAATTGTAATGCACAGTTTTAA
TTGTAAAGGGGAATTTTTCTACTGTAATACAACACAACTGTTTAATAGTACTTAAAATGTTAATAGTACT
TAAAATGTTACTAAAAAGTCAAATAACACTAAAAAAAATATCACACTTCCATGTAAAATAAAACAAATTA
TAAACATGTGGCAAAAAGTAGAAAAAGCAATGTATACCCCTCCCATCAAAAAACAAATTAAATGTTCATC
AAATATTACAGGGCTATTATTAACAAAAAATAGTAGTAATAACAATGAAACCAATAGTAATAACAATAGA
ACCGAAACCTTCAAA
243 changes: 149 additions & 94 deletions poplars/tests/test_hypermut.py
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Original file line number Diff line number Diff line change
@@ -1,108 +1,161 @@
import unittest
import os
import re
from poplars.common import convert_fasta
from poplars.hypermut import make_results
from poplars.hypermut import hypermut
from poplars.hypermut import rate_ratio
from poplars.hypermut import make_data_file
from poplars.hypermut import *

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

class HIVTestCase(unittest.TestCase):

class TestMakeResults(unittest.TestCase):
def setUp(self):
self.hiv_data = open(TEST_HIV)
self.data = open(TEST_DATA)

def testDSMotifs(self):
mut = re.compile('[AGCT](?=[AG][AGT])') # Matches potential mutation sites (GRD)
s = convert_fasta(self.hiv_data)[0][1]
result = [match.start() for match in mut.finditer(s)]
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,
63, 64, 76, 77, 80, 83, 84, 85, 96, 97, 98, 102, 103, 104, 105, 106, 109, 110, 111, 113, 120,
127, 128, 129, 131, 132, 139, 140, 144, 145, 150, 151, 154, 155, 159, 160, 161, 162, 163, 164,
165, 168, 169, 170, 171, 172, 173, 174, 178, 181, 182, 183, 184, 185, 186, 187, 188, 189, 190,
196, 201, 211, 213, 214, 221, 223, 224, 225, 226, 228, 229, 230, 232, 237, 238, 239, 240, 241,
242, 243, 244, 245, 246, 247, 249, 252, 253, 254, 255, 257, 258, 259, 260, 261, 265, 268, 276,
279, 284, 289, 291, 296, 297, 298, 299, 305, 309, 310, 311, 312, 319, 320, 321, 322, 329, 332,
335, 336, 346, 347]
self.assertEqual(expected, result)

def testCtrlMotifs(self):
ctrl = re.compile('[AGCT](?=[CT].|[AG]C)')
s = convert_fasta(self.hiv_data)[0][1]
result = [match.start() for match in ctrl.finditer(s)]
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,
44, 46, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 65, 66, 67, 68, 69, 70, 71, 72, 73,
74, 75, 78, 79, 81, 82, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 99, 100, 101, 107, 108, 112,
114, 115, 116, 117, 118, 119, 121, 122, 123, 124, 125, 126, 130, 133, 134, 135, 136, 137, 138,
141, 142, 143, 146, 147, 148, 149, 152, 153, 156, 157, 158, 166, 167, 175, 176, 177, 179, 180,
191, 192, 193, 194, 195, 197, 198, 199, 200, 202, 203, 204, 205, 206, 207, 208, 209, 210, 212,
215, 216, 217, 218, 219, 220, 222, 227, 231, 233, 234, 235, 236, 248, 250, 251, 256, 262, 263,
264, 266, 267, 269, 270, 271, 272, 273, 274, 275, 277, 278, 280, 281, 282, 283, 285, 286, 287,
288, 290, 292, 293, 294, 295, 300, 301, 302, 303, 304, 306, 307, 308, 313, 314, 315, 316, 317,
318, 323, 324, 325, 326, 327, 328, 330, 331, 333, 334, 337, 338, 339, 340, 341, 342, 343, 344, 345]
self.assertEqual(expected, result)

def test_alignmentA1(self):
fasta = convert_fasta(self.data)
refseq = fasta[0][1]
gees = [i for i, nt in enumerate(refseq) if nt.upper() == 'G']
seq = fasta[1]
output = make_results(seq, gees)

ex_num_muts = 47
self.assertEqual(ex_num_muts, output.num_muts)

ex_pot_muts = 1068
self.assertEqual(ex_pot_muts, output.pot_muts)

ex_ctrl_muts = 53
self.assertEqual(ex_ctrl_muts, output.ctrl_muts)

ex_pot_ctrl_muts = 986
self.assertEqual(ex_pot_ctrl_muts, output.potential_ctrls)

ex_rate_ratio = 0.82
self.assertEqual(ex_rate_ratio, round(output.rate_ratio, 2))

ex_p_value = 0.870295
self.assertEqual(ex_p_value, output.p_value)

ex_ctable = [[47, 1068], [53, 986]]
self.assertEqual(ex_ctable, output.ctable)

# ex_mut_sites = None
# ex_ctrl_sites = None

def tearDown(self):
self.hiv_data.close()
self.data.close()


class TestHypermut(unittest.TestCase):

def setUp(self):
self.hiv_data = open(TEST_HIV)

def testGees(self):
fasta = convert_fasta(self.hiv_data)
refseq = fasta[0][1] # Reference sequence is the first entry
result = [i for i, nt in enumerate(refseq) if nt.upper() == 'G']
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,
121, 128, 129, 132, 133, 135, 142, 146, 152, 155, 157, 161, 163, 166, 170, 173, 176, 185, 186,
188, 190, 198, 202, 212, 214, 216, 220, 224, 225, 229, 230, 233, 238, 239, 241, 243, 245, 248,
250, 254, 256, 258, 259, 261, 262, 266, 270, 273, 278, 292, 293, 297, 299, 301, 304, 310, 311,
313, 322, 327, 330, 336, 338, 342, 349]
self.assertEqual(expected, result)

def tearDown(self):
self.hiv_data.close()
genome_path = os.path.join(os.path.dirname(__file__), 'fixtures/hiv-test-genome.fasta')
infile_path = os.path.join(os.path.dirname(__file__), 'fixtures/aligned_HIV1_Mgroup.fasta')
test_data = os.path.join(os.path.dirname(__file__), 'fixtures/hypermut-test.fasta')

with open(genome_path) as handle, open(infile_path) as in_handle, open(test_data) as test_handle:
self.hiv_genome = handle.read()
self.hiv_data = in_handle.read()
self.simple_data = convert_fasta(test_handle.read().split())

self.mut = re.compile('[AGCT](?=[AG][AGT])') # Matches potential mutation sites (RD)
self.ctrl = re.compile('[AGCT](?=[CT].|[AG]C)') # Matches potential control sites (YN or RC)


class Hypermut(HIVTestCase):

maxDiff = None

def testSimpleData(self):

# Test potential mutation sites
test_matches = ['GAA', 'GAG', 'GAT', 'GGA', 'GGG', 'GGT', 'CGAA']
for s in test_matches:
self.assertTrue(self.mut.match(s))
test_mismatches = ['CTC', 'GTC', 'GGCGC']
for s in test_mismatches:
self.assertFalse(self.mut.match(s))

# Test potential control sites
test_matches = ['TAC', 'CCC', 'CAC', 'TTGC']
for s in test_matches:
self.assertTrue(self.ctrl.match(s))
test_mismatches = ['TAT', 'CGGC', 'CAA']
for s in test_mismatches:
self.assertFalse(self.ctrl.match(s))

# Test gees
refseq = self.simple_data[0][1] # Reference sequence is the first entry
res_gees = [i for i, nt in enumerate(refseq) if nt.upper() == 'G']
exp_gees = [5, 8, 15, 16, 19, 24, 27, 30, 33, 35, 36, 39, 46, 51, 62, 69, 84, 89, 92, 96, 102, 111,
115, 121, 139, 145, 156, 157, 162, 163, 164, 166, 168, 183, 184, 186, 195, 196, 198, 205,
210, 217, 226, 230, 234, 238, 239, 246, 257, 261, 274, 289, 297, 307, 315, 316, 318, 319,
320, 321, 327, 333, 338, 343, 352, 354, 355, 357, 358, 359, 360, 373, 389, 397, 403, 404,
408, 415, 421, 422, 426, 432, 435, 436, 437, 450, 453, 454, 472, 475, 497, 499, 500, 503,
504, 507, 510, 511, 516, 521, 525, 538, 540, 541, 550, 553, 570, 571, 572, 586, 588, 591,
592, 594, 595, 606, 607, 608, 612, 615, 616, 627, 628, 629, 633, 643]
self.assertEqual(exp_gees, res_gees)

query_seq = self.simple_data[1:]

outputs = []
for seq in query_seq:
outputs.append(make_results(seq, res_gees))

for i in range(len(outputs)):
ex_num_muts = [0, 4, 26, 48]
self.assertEqual(ex_num_muts[i], outputs[i].num_muts) # Test match sites

ex_pot_muts = [71, 69, 71, 71]
self.assertEqual(ex_pot_muts[i], outputs[i].pot_muts) # Test potential mutation sites

ex_ctrl_muts = [0, 1, 1, 9]
self.assertEqual(ex_ctrl_muts[i], outputs[i].ctrl_muts) # Test control mutations

ex_pot_ctrl_muts = [54, 52, 54, 54]
self.assertEqual(ex_pot_ctrl_muts[i], outputs[i].potential_ctrls) # Test potential controls

ex_rate_ratio = ['undef', 3.01, 19.77, 4.06]
if type(ex_rate_ratio) == str:
self.assertEqual(ex_rate_ratio[i], outputs[i].rate_ratio) # Test rate ratio
else:
self.assertAlmostEqual(ex_rate_ratio[i], outputs[i].rate_ratio, places=2)

ex_p_value = [1, 0.282669, 5.35061e-07, 8.26961e-09]
self.assertAlmostEqual(ex_p_value[i], outputs[i].p_value, places=2) # Test p-value

ex_ctable = [[[0, 71], [0, 54]], # Seq2

[[4, 65], [1, 51]], # Seq5

[[26, 45], [1, 53]], # Seq7

[[48, 23], [9, 45]]] # Seq14
self.assertEqual(ex_ctable[i], outputs[i].ctable) # Test contingency table

# Test mutation sites
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,
163: 0, 164: 0, 165: 0, 167: 0, 184: 0, 185: 0, 187: 0, 196: 0, 197: 0, 199: 0, 231: 0,
235: 0, 239: 0, 240: 0, 258: 0, 290: 0, 308: 0, 316: 0, 317: 0, 319: 0, 320: 0, 321: 0,
328: 0, 355: 0, 356: 0, 358: 0, 359: 0, 360: 0, 361: 0, 404: 0, 405: 0, 422: 0, 423: 0,
433: 0, 436: 0, 437: 0, 451: 0, 454: 0, 455: 0, 476: 0, 504: 0, 505: 0, 511: 0, 512: 0,
539: 0, 541: 0, 551: 0, 571: 0, 587: 0, 589: 0, 592: 0, 595: 0, 607: 0, 608: 0, 613: 0,
616: 0, 628: 0, 629: 0, 634: 0},

{28: 0, 31: 0, 34: 0, 36: 0, 47: 0, 52: 0, 63: 0, 93: 0, 97: 0, 112: 0, 140: 0, 157: 0,
163: 0, 164: 0, 165: 0, 167: 0, 184: 0, 185: 0, 187: 0, 196: 0, 197: 0, 199: 1, 231: 0,
235: 0, 239: 0, 240: 0, 258: 0, 290: 1, 316: 0, 317: 0, 319: 0, 320: 0, 321: 0, 328: 0,
355: 0, 356: 0, 358: 0, 359: 0, 360: 0, 361: 0, 422: 0, 423: 0, 427: 0, 433: 0, 436: 0,
437: 0, 451: 0, 454: 0, 455: 0, 476: 0, 504: 0, 505: 0, 511: 0, 512: 0, 539: 0, 541: 0,
551: 0, 571: 0, 587: 0, 589: 0, 592: 0, 595: 0, 607: 1, 608: 0, 613: 0, 616: 0, 628: 1,
629: 0, 634: 0},

{28: 0, 31: 0, 34: 0, 36: 1, 47: 0, 52: 1, 63: 0, 93: 1, 97: 0, 112: 1, 140: 0, 157: 1,
163: 0, 164: 1, 165: 0, 167: 0, 184: 0, 185: 0, 187: 0, 196: 1, 197: 0, 199: 0, 231: 0,
235: 0, 239: 1, 240: 1, 258: 0, 290: 0, 308: 0, 316: 0, 317: 0, 319: 1, 320: 1, 321: 0,
328: 0, 355: 1, 356: 0, 358: 0, 359: 1, 360: 1, 361: 0, 404: 1, 405: 1, 422: 1, 423: 0,
433: 0, 436: 1, 437: 0, 451: 0, 454: 0, 455: 0, 476: 0, 504: 1, 505: 0, 511: 1, 512: 0,
539: 0, 541: 0, 551: 0, 571: 1, 587: 0, 589: 0, 592: 0, 595: 1, 607: 1, 608: 1, 613: 0,
616: 1, 628: 1, 629: 0, 634: 0},

{28: 0, 31: 0, 34: 1, 36: 0, 47: 1, 52: 1, 63: 1, 93: 1, 97: 1, 112: 1, 140: 1, 157: 0,
163: 1, 164: 0, 165: 0, 167: 1, 184: 0, 185: 1, 187: 1, 196: 0, 197: 0, 199: 1, 231: 1,
235: 1, 239: 1, 240: 1, 258: 0, 290: 0, 308: 1, 316: 0, 317: 1, 319: 1, 320: 0, 321: 1,
328: 0, 355: 1, 356: 1, 358: 0, 359: 0, 360: 0, 361: 0, 404: 1, 405: 1, 422: 1, 423: 1,
433: 1, 436: 1, 437: 1, 451: 1, 454: 1, 455: 1, 476: 1, 504: 1, 505: 1, 511: 0, 512: 1,
539: 1, 541: 1, 551: 1, 571: 0, 587: 1, 589: 1, 592: 1, 595: 1, 607: 0, 608: 1, 613: 1,
616: 1, 628: 1, 629: 0, 634: 0}]

self.assertEqual(ex_mut_sites[i], outputs[i].mut_sites)

# Test control sites
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,
116: 0, 122: 0, 146: 0, 158: 0, 169: 0, 206: 0, 211: 0, 218: 0, 227: 0, 247: 0, 262: 0,
275: 0, 298: 0, 322: 0, 334: 0, 339: 0, 344: 0, 353: 0, 374: 0, 390: 0, 398: 0, 409: 0,
416: 0, 427: 0, 438: 0, 473: 0, 498: 0, 500: 0, 501: 0, 508: 0, 517: 0, 522: 0, 526: 0,
542: 0, 554: 0, 572: 0, 573: 0, 593: 0, 596: 0, 609: 0, 617: 0, 630: 0},

{6: 0, 9: 0, 16: 0, 17: 0, 20: 0, 25: 0, 37: 0, 40: 0, 70: 0, 85: 0, 90: 0, 103: 0,
116: 0, 122: 0, 146: 0, 158: 0, 169: 0, 206: 0, 211: 0, 218: 0, 227: 0, 247: 0, 262: 0,
275: 0, 298: 0, 308: 1, 322: 0, 334: 0, 339: 0, 344: 0, 353: 0, 374: 0, 390: 0, 416: 0,
438: 0, 473: 0, 498: 0, 500: 0, 501: 0, 508: 0, 517: 0, 522: 0, 526: 0, 542: 0, 554: 0,
572: 0, 573: 0, 593: 0, 596: 0, 609: 0, 617: 0, 630: 0},

{6: 0, 9: 0, 16: 0, 17: 0, 20: 0, 25: 0, 37: 0, 40: 0, 70: 0, 85: 0, 90: 0, 103: 0,
116: 0, 122: 0, 146: 0, 158: 0, 169: 0, 206: 0, 211: 0, 218: 0, 227: 0, 247: 0, 262: 0,
275: 0, 298: 0, 322: 0, 334: 0, 339: 0, 344: 0, 353: 0, 374: 0, 390: 0, 398: 0, 409: 0,
416: 0, 427: 0, 438: 0, 473: 0, 498: 0, 500: 0, 501: 0, 508: 0, 517: 0, 522: 0, 526: 0,
542: 0, 554: 0, 572: 0, 573: 0, 593: 0, 596: 1, 609: 0, 617: 0, 630: 0},

{6: 0, 9: 0, 16: 0, 17: 0, 20: 0, 25: 0, 37: 0, 40: 0, 70: 0, 85: 0, 90: 0, 103: 0,
116: 0, 122: 1, 146: 0, 158: 1, 169: 0, 206: 1, 211: 0, 218: 0, 227: 0, 247: 0, 262: 0,
275: 1, 298: 0, 322: 1, 334: 0, 339: 0, 344: 0, 353: 0, 374: 0, 390: 0, 398: 0, 409: 0,
416: 0, 427: 0, 438: 0, 473: 0, 498: 0, 500: 0, 501: 0, 508: 0, 517: 0, 522: 0, 526: 1,
542: 1, 554: 0, 572: 0, 573: 0, 593: 0, 596: 0, 609: 1, 617: 0, 630: 1}]
self.assertEqual(ex_ctrl_sites[i], outputs[i].ctrl_sites)


class TestRateRatio(unittest.TestCase):

def testRateRatio(self):
ctable = [[4, 17], [7, 33]]
expected = 1.1
Expand All @@ -123,3 +176,5 @@ def test2UndefinedRateRatio(self):
self.assertEqual(expected, result)


if __name__ == '__main__':
unittest.main()

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