def test_example_20():
"""Wilson et al 2002 Example 20
Seq: AAAGACACCCCCCCCCCCCACA
Seq: AAAGACACCCCCCCCCCCCACA
rCRS: AAAGACACCCCCC------ACA
Sites: 573.1C 573.2C 573.3C 573.4C 573.5C 573.6C
"""
a = Polymorphism(573,1,'C')
b = Polymorphism(573,2,'C')
c = Polymorphism(573,3,'C')
d = Polymorphism(573,4,'C')
e = Polymorphism(573,5,'C')
f = Polymorphism(573,6,'C')
seq = 'AACCAAACCCCAAAGACACCCCCCCCCCCCACAGTTTATGTAGCTT'
result = seq2sites(seq)
assert len(result) == 6
assert a in result
assert b in result
assert c in result
assert d in result
assert e in result
assert f in result
def test_309_315_insertions():
a = Polymorphism(309,1,'C')
b = Polymorphism(315,1,'C')
seq = 'CATCATAACAAAAAATTTCCACCAAACCCCCCCCTCCCCCCGCTTCTGGCCACAGCACTT'
result = seq2sites(seq)
assert a in result
assert b in result
def test_315_insertion_316_substitution():
a = Polymorphism(315,1,'C')
b = Polymorphism(316,0,'A')
seq = 'CACCAAACCCCCCCTCCCCCCACTTCTGGCCACAGCACTTAAACACATCTCTGCCAAACCCCA'
result = seq2sites(seq)
assert a in result
assert b in result
def test_523_524_deletions():
a = Polymorphism(523,0,'-')
b = Polymorphism(524,0,'-')
seq = 'TCTCATCAATACAACCCCCGCCCATCCTACCCAGCACACACACCGCTGCTAACCCCAT'
result = seq2sites(seq)
assert a in result
assert b in result
def test_two_309_insertions():
a = Polymorphism(309,1,'C')
b = Polymorphism(309,2,'C')
seq = 'ATAACAAAAAATTTCCACCAAACCCCCCCCCTCCCCCGCTTCTGGCCACAGCACTTAAACA'
result = seq2sites(seq)
assert a in result
assert b in result
def test_example_21():
"""Wilson et al 2002 Example 21
Seq: CTGGAGCACCC
Seq: CTGGAGC------ACCC
rCRS: CTGGAGCCGGAGCACCC
Sites: 105d 106d 107d 108d 109d 110d
"""
a = Polymorphism(105,0,'-')
b = Polymorphism(106,0,'-')
c = Polymorphism(107,0,'-')
d = Polymorphism(108,0,'-')
e = Polymorphism(109,0,'-')
f = Polymorphism(110,0,'-')
seq = 'GCATTGCGAGACGCTGGAGCACCCTATGTCGCAGTATCT'
result = seq2sites(seq)
assert len(result) == 6
assert a in result
assert b in result
assert c in result
assert d in result
assert e in result
assert f in result
def test_example_22():
"""Wilson et al 2002 Example 22
Seq: AGATCCTGGAGCCCCC
Seq: AGATC-CTGGAGCC------CCC
rCRS: AGA-CGCTGGAGCCGGAGCACCC
Sites: 95.1T 97d 106d 107d 108d 109d 110d 111d
"""
a = Polymorphism(95,1,'T')
b = Polymorphism(97,0,'-')
c = Polymorphism(106,0,'-')
d = Polymorphism(107,0,'-')
e = Polymorphism(108,0,'-')
f = Polymorphism(109,0,'-')
g = Polymorphism(110,0,'-')
h = Polymorphism(111,0,'-')
seq = 'TCGTCTGGGGGGTATGCACGCGATAGCATTGCGAGATCCTGGAGCCCCCTATGTCGCAGTATCT'
result = seq2sites(seq)
print 'expected: %s' % [a,b,c,d,e,f,g,h]
print 'actual: %s' % result
assert len(result) == 8
assert a in result
assert b in result
assert c in result
assert d in result
assert e in result
assert f in result
assert g in result
assert h in result
def test_two_309_insertions_and_315_insertion():
a = Polymorphism(309,1,'C')
b = Polymorphism(309,2,'C')
c = Polymorphism(315,1,'C')
seq = 'AATTTCCACCAAACCCCCCCCCTCCCCCCGCTTCTGGCCACAGCACTTAAA'
result = seq2sites(seq)
assert len(result) == 3
assert a in result
assert b in result
assert c in result
def test_29InsATTCTCTGTTCTTT():
"""Properly identify 16029InsATTCTCTGTTCTTT
Seq: GATTCTAATTTAAACTATTCTCTGTTCTTTATTCTCTGTTCTTTCATGGGGAAGCAGATTTGGGT
Seq: GATTCTAATTTAAACTATTCTCTGTTCTTTATTCTCTGTTCTTTCATGGGGAAGCAGATTTGGGT
rCRS: GATTCTAATTTAAACTATTCTCTGTTCTTT--------------CATGGGGAAGCAGATTTGGGT
Sites: <None>
"""
seq = 'GATTCTAATTTAAACTATTCTCTGTTCTTTATTCTCTGTTCTTTCATGGGGAAGCAGATTTGGGT'
result = seq2sites(seq)
assert len(result) == 14
def test_example_3():
"""Wilson et al 2002 Example 3
Seq: ATTGATGTC
Seq: ATTGA-TGTC
rCRS: ATTGAATGTC
Sites: 249d
"""
a = Polymorphism(249,0,'-')
seq = 'TGCTTGTAGGACATAATAATAACAATTGATGTCTGCACAGCCACTTTCC'
result = seq2sites(seq)
assert len(result) == 1
assert a in result
def test_example_1():
"""Wilson et al 2002 Example 1
Seq: ATACAACCCCCACCCAT
Seq: ATACAACCCCCACCCAT
rCRS: ATACAACCCCCGCCCAT
Sites: 499A
"""
a = Polymorphism(499,0,'A')
seq = 'ATACTACTAATCTCATCAATACAACCCCCACCCATCCTACCCAGCACACACACACCGCTG'
result = seq2sites(seq)
assert len(result) == 1
assert a in result
def test_example_19():
"""Wilson et al 2002 Example 19
Seq: AAACCCCCCCTTCCCCCCGC
Seq: AAACCCCCCCTTCCCCCCGC
rCRS: AAACCCCCCCT-CCCCC-GC
Sites: 310.1T 315.1C
"""
a = Polymorphism(310,1,'T')
b = Polymorphism(315,1,'C')
seq = 'AATTTCCACCAAACCCCCCCTTCCCCCCGCTTCTGGCCACAGCACTT'
result = seq2sites(seq)
assert len(result) == 2
assert a in result
assert b in result
def test_example_13():
"""Wilson et al 2002 Example 13
Seq: AAAACCTCCCCCCATGCT
Seq: AAAACCTCC-CCCCATGCT
rCRS: AAAACCCCCTCCCCATGCT
Sites: 16186T 16189d
"""
a = Polymorphism(16186,0,'T')
b = Polymorphism(16189,0,'-')
seq = 'CCTGTAGTACATAAAAACCCAATCCACATCAAAACCTCCCCCCATGCTTACAAGCAAGT'
result = seq2sites(seq)
assert len(result) == 2
assert a in result
assert b in result
def test_example_2():
"""Wilson et al 2002 Example 2
Seq: ATACAACCCCACCCAT
Seq: ATACAACCCC-ACCCAT
rCRS: ATACAACCCCCGCCCAT
Sites: 489d 499A
"""
a = Polymorphism(498,0,'-')
b = Polymorphism(499,0,'A')
seq = 'ATACTACTAATCTCATCAATACAACCCCACCCATCCTACCCAGCACACACACACCGCTG'
result = seq2sites(seq)
assert len(result) == 2
assert a in result
assert b in result
def test_example_7():
"""Wilson et al 2002 Example 7
Seq: ACCCAACACACACACCGC
Seq: ACCCA--ACACACACACCGC
rCRS: ACCCAGCACACACACACCGC
Sites: 513d 514d
"""
a = Polymorphism(513,0,'-')
b = Polymorphism(514,0,'-')
seq = 'ACAACCCCCGCCCATCCTACCCAACACACACACCGCTGCTAACCCCATACCCC'
result = seq2sites(seq)
assert len(result) == 2
assert a in result
assert b in result
def test_example_5():
"""Wilson et al 2002 Example 5
Seq: ACCCAGCACACACACACACCGCTG
Seq: ACCCAGCACACACACACACCGCTG
rCRS: ACCCAGCACACACACAC--CGCTG
Sites: 524.1A 524.2C
"""
a = Polymorphism(524,1,'A')
b = Polymorphism(524,2,'C')
seq = 'ACAACCCCCGCCCATCCTACCCAGCACACACACACACCGCTGCTAACCCCATACCCC'
result = seq2sites(seq)
assert len(result) == 2
assert a in result
assert b in result
def test_example_4():
"""Wilson et al 2002 Example 4
Seq: CATAACAAAATTT
Seq: CATAACAAAA--TTT
rCRS: CATAACAAAAAATTT
Sites: 290d 291d
"""
a = Polymorphism(290,0,'-')
b = Polymorphism(291,0,'-')
seq = 'ACACAGACATCATAACAAAATTTCCACCAAACCCCCCC'
result = seq2sites(seq)
assert len(result) == 2
assert a in result
assert b in result
def test_example_9():
"""Wilson et al 2002 Example 9
Seq: AAACCCCCCCCTCCCATGCT
Seq: AAACCCCCCCCTCCCATGCT
rCRS: AAAACCCCCTC-CCCATGCT
Sites: 16183C 15189C 16190.1T
"""
a = Polymorphism(16183,0,'C')
b = Polymorphism(16189,0,'C')
c = Polymorphism(16190,1,'T')
seq = 'CCTGTAGTACATAAAAACCCAATCCACATCAAACCCCCCCCTCCCATGCTTACAAGCAAGT'
result = seq2sites(seq)
assert len(result) == 3
assert a in result
assert b in result
assert c in result
def test_example_14():
"""Wilson et al 2002 Example 14
Seq: AAACCCCCCCTCCCCCATGCT
Seq: AAACCCCCCCTCCCCCATGCT
rCRS: AAAACCCCC-TCCCC-ATGCT
Sites: 16183C 16188.1C 16193.1C
"""
a = Polymorphism(16183,0,'C')
b = Polymorphism(16188,1,'C')
c = Polymorphism(16193,1,'C')
seq = 'CCTGTAGTACATAAAAACCCAATCCACATCAAACCCCCCCTCCCCCATGCTTACAAGCAAGT'
result = seq2sites(seq)
assert len(result) == 3
assert a in result
assert b in result
assert c in result
def test_example_18():
"""Wilson et al 2002 Example 18
Seq: AAACCCCCCTCCCCCCGC
Seq: AAACCCCCC-TCCCCCCGC
rCRS: AAACCCCCCCTCCCCC-GC
Sites: 309d 315.1C
"""
a = Polymorphism(309,0,'-')
b = Polymorphism(315,1,'C')
seq = 'CATAACAAAAAATTTCCACCAAACCCCCCTCCCCCCGCTTCTGGCCACAGCACTT'
result = seq2sites(seq)
print 'expected: %s' % [a,b]
print 'actual: %s' % result
assert len(result) == 2
assert a in result
assert b in result
def test_example_8():
"""Wilson et al 2002 Example 8
Seq: ACCCAGTACACACACCG
Seq: ACCCAGTACACACAC--CG
rCRS: ACCCAGCACACACACACCG
Sites: 514T 523d 524d
"""
a = Polymorphism(514,0,'T')
b = Polymorphism(523,0,'-')
c = Polymorphism(524,0,'-')
seq = 'ACAACCCCCGCCCATCCTACCCAGTACACACACCGCTGCTAACCCCATACCCC'
result = seq2sites(seq)
assert len(result) == 3
assert a in result
assert b in result
assert c in result
def test_example_16():
"""Wilson et al 2002 Example 16
Seq: AAACCCCCTCCCCCCATGCT
Seq: AAA-CCCCCTCCCCCCATGCT
rCRS: AAAACCCCCTCCCC--ATGCT
Sites: 16183d 16193.1C 16193.2C
"""
a = Polymorphism(16183,0,'-')
b = Polymorphism(16193,1,'C')
c = Polymorphism(16193,2,'C')
seq = 'CCTGTAGTACATAAAAACCCAATCCACATCAAACCCCCTCCCCCCATGCTTACAAGCAAGT'
result = seq2sites(seq)
print 'expected: %s' % [a,b,c]
print 'actual: %s' % result
assert len(result) == 3
assert a in result
assert b in result
assert c in result
def test_example_17():
"""Wilson et al 2002 Example 17
Seq: AAACCCCCCCCCGC
Seq: AAACCCCCCC----CCGC
rCRS: AAACCCCCCCTCCCCCGC
Sites: 310d 311d 312d 313d
"""
a = Polymorphism(310,0,'-')
b = Polymorphism(311,0,'-')
c = Polymorphism(312,0,'-')
d = Polymorphism(313,0,'-')
seq = 'AATTTCCACCAAACCCCCCCCCGCTTCTGGCCACAGCACTT'
result = seq2sites(seq)
assert len(result) == 4
assert a in result
assert b in result
assert c in result
assert d in result
def test_example_6():
"""Wilson et al 2002 Example 6
Seq: ACCCAGCACACACCGCTGC
Seq: ACCCAGCACACAC----CGCTGC
rCRS: ACCCAGCACACACACACCGCTGC
Sites: 521d 522d 523d 524d
"""
a = Polymorphism(521,0,'-')
b = Polymorphism(522,0,'-')
c = Polymorphism(523,0,'-')
d = Polymorphism(524,0,'-')
seq = 'ACAACCCCCGCCCATCCTACCCAGCACACACCGCTGCTAACCCCATACCCC'
result = seq2sites(seq)
assert len(result) == 4
assert a in result
assert b in result
assert c in result
assert d in result
def test_example_12():
"""Wilson et al 2002 Example 12
Seq: TTAACCCCCTCCCCCATGCT
Seq: TTAA--CCCCCTCCCCCATGCT
rCRS: TCAAAACCCCCTCCCC-ATGCT
Sites: 16179T 16182d 16183d 16193.1C
"""
a = Polymorphism(16179,0,'T')
b = Polymorphism(16182,0,'-')
c = Polymorphism(16183,0,'-')
d = Polymorphism(16193,1,'C')
seq = 'CCTGTAGTACATAAAAACCCAATCCACATTAACCCCCTCCCCCATGCTTACAAGCAAGTACAGCAATCAACCCTCAACT'
result = seq2sites(seq)
print 'expected: %s' % [a,b,c,d]
print 'actual: %s' % result
assert len(result) == 4
assert a in result
assert b in result
assert c in result
assert d in result
def test_substitution_at_end():
a = Polymorphism(16566,0,'A')
seq = 'CATAAAGCCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACAATG'
result = seq2sites(seq)
assert len(result) == 1
assert a in result
def test_3_changes():
seq = 'GTACATAAAAACCCAATCCACATCAAACCTCCCCCCCATGCTTACAAGCAAGTA'
result = seq2sites(seq)
assert len(result) == 3
def test_12236_substitution():
a = Polymorphism(12236,0,'A')
seq = 'AAAGCTCACAAGAACTGCTAACTCATACCCCCATGTCTAACAACATGGCT'
result = seq2sites(seq)
assert len(result) == 1
assert a in result
def test_15511_substitution():
a = Polymorphism(15511,0,'C')
seq = 'TCACCAGACCTCCTAGGCGACCCAGACAACTATACCCTAGCCAACCCCTTAAA'
result = seq2sites(seq)
assert len(result) == 1
assert a in result
def test_insertion_at_beginning():
a = Polymorphism(10,0,'G')
seq = 'GATCACAGGGCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCAT'
result = seq2sites(seq)
assert len(result) == 1
assert a in result
