class TestDigest(object):
'''Test digest function.'''
def __init__(self):
# Contains NcoI site
self.dna = DNA('TGACCATGGAAA')
def test_not_found(self):
'''If site not found, should return input sequence in list.'''
ecorv = RestrictionSite(DNA('GATATC'), (3, 3), name='EcoRV')
assert_equal(self.dna, reaction.digest(self.dna, ecorv)[0])
def test_ncoi_cut(self):
'''Test standard TypeII cutter.'''
ncoi = RestrictionSite(DNA('CCATGG'), (1, 5), name='NcoI')
assert_equal(reaction.digest(self.dna, ncoi),
[DNA('TGAC----', bottom='CATGGTCA'),
DNA('CATGGAAA', bottom='TTTC----')])
assert_equal(reaction.digest(self.dna.circularize(), ncoi),
[DNA('CATGGAAATGAC----', bottom='CATGGTCATTTC----')])
def test_ecorv_cut(self):
'''Test blunt-end cutter.'''
ecorv = RestrictionSite(DNA('GATATC'), (3, 3), name='EcoRV')
assert_equal(reaction.digest(DNA('GATATC'), ecorv),
[DNA('GAT'), DNA('ATC')])
def test_psti_cut(self):
'''Test 3\' cutter.'''
psti = RestrictionSite(DNA('CTGCAG'), (5, 1), name='PstI')
assert_equal(reaction.digest(DNA('ACTGCAGA'), psti),
[DNA('ACTGCA', bottom='----GT'),
DNA('----GA', bottom='TCTGCA')])
class TestDigest(object):
'''Test digest function.'''
def __init__(self):
# Contains NcoI site
self.dna = DNA('TGACCATGGAAA')
def test_not_found(self):
'''If site not found, should return input sequence in list.'''
ecorv = RestrictionSite(DNA('GATATC'), (3, 3), name='EcoRV')
assert_equal(self.dna, reaction.digest(self.dna, ecorv)[0])
def test_ncoi_cut(self):
'''Test standard TypeII cutter.'''
ncoi = RestrictionSite(DNA('CCATGG'), (1, 5), name='NcoI')
assert_equal(reaction.digest(self.dna, ncoi), [
DNA('TGAC----', bottom='CATGGTCA'),
DNA('CATGGAAA', bottom='TTTC----')
])
assert_equal(reaction.digest(self.dna.circularize(), ncoi),
[DNA('CATGGAAATGAC----', bottom='CATGGTCATTTC----')])
def test_ecorv_cut(self):
'''Test blunt-end cutter.'''
ecorv = RestrictionSite(DNA('GATATC'), (3, 3), name='EcoRV')
assert_equal(reaction.digest(DNA('GATATC'), ecorv),
[DNA('GAT'), DNA('ATC')])
def test_psti_cut(self):
'''Test 3\' cutter.'''
psti = RestrictionSite(DNA('CTGCAG'), (5, 1), name='PstI')
assert_equal(
reaction.digest(DNA('ACTGCAGA'), psti),
[DNA('ACTGCA', bottom='----GT'),
DNA('----GA', bottom='TCTGCA')])
class TestDNA(object):
'''Testing class for DNA'''
def __init__(self):
self.test_dna = DNA('atgc')
def test_reverse_complement(self):
assert_equal(str(self.test_dna.reverse_complement()), 'GCAT')
def test_linearize(self):
circ_dna = self.test_dna.circularize()
assert_equal(str(circ_dna.linearize()), 'ATGC')
assert_equal(str(circ_dna.linearize(0)), 'ATGC')
assert_equal(str(circ_dna.linearize(1)), 'TGCA')
assert_equal(str(circ_dna.linearize(2)), 'GCAT')
assert_equal(str(circ_dna.linearize(3)), 'CATG')
assert_equal(str(circ_dna.linearize(-1)), 'CATG')
assert_raises(ValueError, circ_dna.linearize().linearize)
def test_to_ss_ds(self):
assert_equal(self.test_dna.to_ds(), self.test_dna)
ss_dna = self.test_dna.to_ss()
assert_equal(ss_dna.stranded, 'ss')
ds_dna = self.test_dna.to_ds()
assert_equal(ds_dna.stranded, 'ds')
assert_equal(ds_dna.top(), str(ss_dna))
ds_to_ss_to_ds = self.test_dna.to_ss().to_ds()
assert_equal(self.test_dna, ds_to_ss_to_ds)
empty_top = reaction.three_resect(self.test_dna, 400)
assert_equal(empty_top.to_ds(), self.test_dna)
def test_locate(self):
assert_equal(self.test_dna.locate('a'), [[0], [2]])
assert_equal(self.test_dna.locate('at'), [[0], [2]])
assert_equal(self.test_dna.locate('gc'), [[2], [0]])
assert_equal(self.test_dna.locate('atgg'), [[], []])
# Circular DNA tests
assert_equal(self.test_dna.circularize().locate('a'), [[0], [2]])
assert_equal(self.test_dna.circularize().locate('at'), [[0], [2]])
assert_equal(self.test_dna.circularize().locate('gc'), [[2], [0]])
assert_equal(self.test_dna.circularize().locate('atgg'), [[], []])
def test_copy(self):
assert_equal(self.test_dna, self.test_dna.copy())
def test_palindrome(self):
palindromic_seq_even = DNA('ATGCGCAT')
nonpalindromic_seq_even = DNA('ATGCGCAA')
almost_palindrome_odd = DNA('ATGCCAT')
assert_true(palindromic_seq_even.is_palindrome())
assert_false(nonpalindromic_seq_even.is_palindrome())
assert_false(almost_palindrome_odd.is_palindrome())
def test_getitem(self):
assert_equal(str(self.test_dna[0]), 'A')
assert_equal(str(self.test_dna[1]), 'T')
assert_equal(str(self.test_dna[2]), 'G')
assert_equal(str(self.test_dna[3]), 'C')
assert_equal(str(self.test_dna[-1]), 'C')
def test_delitem(self):
copy0 = self.test_dna.copy()
del copy0[0]
assert_equal(str(copy0), 'TGC')
copy1 = self.test_dna.copy()
del copy1[1]
assert_equal(str(copy1), 'AGC')
copy2 = self.test_dna.copy()
del copy2[2]
assert_equal(str(copy2), 'ATC')
copy3 = self.test_dna.copy()
del copy3[3]
assert_equal(str(copy3), 'ATG')
copy_1 = self.test_dna.copy()
del copy_1[-1]
assert_equal(str(copy_1), 'ATG')
def test_setitem(self):
copy0 = self.test_dna.copy()
copy0[0] = 't'
assert_equal(str(copy0), 'TTGC')
copy1 = self.test_dna.copy()
copy1[1] = 'a'
assert_equal(str(copy1), 'AAGC')
copy2 = self.test_dna.copy()
copy2[2] = 'a'
assert_equal(str(copy2), 'ATAC')
copy3 = self.test_dna.copy()
copy3[3] = 'a'
assert_equal(str(copy3), 'ATGA')
copy_1 = self.test_dna.copy()
copy_1[-1] = 'a'
assert_equal(str(copy_1), 'ATGA')
def set_gap(seq):
seq[2] = '-'
assert_raises(ValueError, set_gap, self.test_dna)
def test_repr(self):
expected_repr = 'linear dsDNA:\nATGC\nTACG'
assert_equal(repr(self.test_dna), expected_repr)
expected_circ_repr = 'circular dsDNA:\nATGC\nTACG'
assert_equal(repr(self.test_dna.circularize()), expected_circ_repr)
repr_1 = 'linear dsDNA:\nATGCATGCATGCATGCATGCATGCATGCATGCATGCATGC ... '
repr_2 = 'ATGCATGCATGCATGCATGCATGCATGCATGCATGCATGC\n'
repr_3 = 'TACGTACGTACGTACGTACGTACGTACGTACGTACGTACG ... '
repr_4 = 'TACGTACGTACGTACGTACGTACGTACGTACGTACGTACG'
expected_long_repr = repr_1 + repr_2 + repr_3 + repr_4
assert_equal(repr(self.test_dna * 50), expected_long_repr)
def test_str(self):
assert_equal(str(self.test_dna), 'ATGC')
def test_len(self):
assert_equal(len(self.test_dna), 4)
def test_add(self):
assert_equal(str(self.test_dna + self.test_dna), 'ATGCATGC')
assert_equal(str(self.test_dna.to_ss() + self.test_dna.to_ss()),
'ATGCATGC')
def test_radd(self):
assert_equal(str(sum([self.test_dna, self.test_dna])), 'ATGCATGC')
def radd_800(seq):
return 800 + seq
assert_raises(TypeError, radd_800, self.test_dna)
def test_mul(self):
assert_equal(str(self.test_dna * 4), 'ATGCATGCATGCATGC')
def mul_float(seq):
return seq * 7.56
assert_raises(TypeError, mul_float, self.test_dna)
# TODO: reimplement this test using manual sequence input
# def mul_incompatible(seq):
# return seq * 3
# incompatible_seq = self.test_dna.copy()
# incompatible_seq = incompatible_seq.five_resect(1)
# incompatible_seq = incompatible_seq.reverse_complement()
# incompatible_seq = incompatible_seq.five_resect(1)
# incompatible_seq = incompatible_seq.reverse_complement()
# assert_raises(Exception, mul_incompatible, incompatible_seq)
def test_eq(self):
assert_true(self.test_dna == DNA('atgc'))
def test_ne(self):
assert_true(self.test_dna != DNA('aagc'))
def test_contains(self):
assert_true('a' in self.test_dna)
assert_true('t' in self.test_dna)
assert_true('g' in self.test_dna)
assert_true('c' in self.test_dna)
assert_false('u' in self.test_dna)
def test_flip(self):
flipped = self.test_dna.flip()
assert_equal(str(self.test_dna), flipped._bottom)
assert_equal(self.test_dna._bottom, str(flipped))
class TestDNA(object):
'''Testing class for DNA'''
def __init__(self):
self.test_dna = DNA('atgc')
def test_reverse_complement(self):
assert_equal(str(self.test_dna.reverse_complement()), 'GCAT')
def test_linearize(self):
circ_dna = self.test_dna.circularize()
assert_equal(str(circ_dna.linearize()), 'ATGC')
assert_equal(str(circ_dna.linearize(0)), 'ATGC')
assert_equal(str(circ_dna.linearize(1)), 'TGCA')
assert_equal(str(circ_dna.linearize(2)), 'GCAT')
assert_equal(str(circ_dna.linearize(3)), 'CATG')
assert_equal(str(circ_dna.linearize(-1)), 'CATG')
assert_raises(ValueError, circ_dna.linearize().linearize)
def test_locate(self):
assert_equal(self.test_dna.locate('a'), [[0], [2]])
assert_equal(self.test_dna.locate('at'), [[0], [2]])
assert_equal(self.test_dna.locate('gc'), [[2], [0]])
assert_equal(self.test_dna.locate('atgg'), [[], []])
# Circular DNA tests
assert_equal(self.test_dna.circularize().locate('a'), [[0], [2]])
assert_equal(self.test_dna.circularize().locate('at'), [[0], [2]])
assert_equal(self.test_dna.circularize().locate('gc'), [[2], [0]])
assert_equal(self.test_dna.circularize().locate('atgg'), [[], []])
def test_copy(self):
assert_equal(self.test_dna, self.test_dna.copy())
def test_palindrome(self):
palindromic_seq_even = DNA('ATGCGCAT')
nonpalindromic_seq_even = DNA('ATGCGCAA')
almost_palindrome_odd = DNA('ATGCCAT')
assert_true(palindromic_seq_even.is_palindrome())
assert_false(nonpalindromic_seq_even.is_palindrome())
assert_false(almost_palindrome_odd.is_palindrome())
def test_getitem(self):
assert_equal(str(self.test_dna[0]), 'A')
assert_equal(str(self.test_dna[1]), 'T')
assert_equal(str(self.test_dna[2]), 'G')
assert_equal(str(self.test_dna[3]), 'C')
assert_equal(str(self.test_dna[-1]), 'C')
def test_delitem(self):
copy0 = self.test_dna.copy()
del copy0[0]
assert_equal(str(copy0), 'TGC')
copy1 = self.test_dna.copy()
del copy1[1]
assert_equal(str(copy1), 'AGC')
copy2 = self.test_dna.copy()
del copy2[2]
assert_equal(str(copy2), 'ATC')
copy3 = self.test_dna.copy()
del copy3[3]
assert_equal(str(copy3), 'ATG')
copy_1 = self.test_dna.copy()
del copy_1[-1]
assert_equal(str(copy_1), 'ATG')
def test_setitem(self):
copy0 = self.test_dna.copy()
copy0[0] = 't'
assert_equal(str(copy0), 'TTGC')
copy1 = self.test_dna.copy()
copy1[1] = 'a'
assert_equal(str(copy1), 'AAGC')
copy2 = self.test_dna.copy()
copy2[2] = 'a'
assert_equal(str(copy2), 'ATAC')
copy3 = self.test_dna.copy()
copy3[3] = 'a'
assert_equal(str(copy3), 'ATGA')
copy_1 = self.test_dna.copy()
copy_1[-1] = 'a'
assert_equal(str(copy_1), 'ATGA')
def set_gap(seq):
seq[2] = '-'
assert_raises(ValueError, set_gap, self.test_dna)
def test_repr(self):
expected_repr = 'ATGC\nTACG'
assert_equal(repr(self.test_dna), expected_repr)
expected_circ_repr = 'ATGC\nTACG'
assert_equal(repr(self.test_dna.circularize()), expected_circ_repr)
repr_1 = 'ATGCATGCATGCATGCATGCATGCATGCATGCATGCATGC ... '
repr_2 = 'ATGCATGCATGCATGCATGCATGCATGCATGCATGCATGC\n'
repr_3 = 'TACGTACGTACGTACGTACGTACGTACGTACGTACGTACG ... '
repr_4 = 'TACGTACGTACGTACGTACGTACGTACGTACGTACGTACG'
expected_long_repr = repr_1 + repr_2 + repr_3 + repr_4
assert_equal(repr(self.test_dna * 50), expected_long_repr)
def test_str(self):
assert_equal(str(self.test_dna), 'ATGC')
def test_len(self):
assert_equal(len(self.test_dna), 4)
def test_add(self):
assert_equal(str(self.test_dna + self.test_dna), 'ATGCATGC')
def test_radd(self):
assert_equal(str(sum([self.test_dna, self.test_dna])), 'ATGCATGC')
def radd_800(seq):
return 800 + seq
assert_raises(TypeError, radd_800, self.test_dna)
def test_mul(self):
assert_equal(str(self.test_dna * 4), 'ATGCATGCATGCATGC')
def mul_float(seq):
return seq * 7.56
assert_raises(TypeError, mul_float, self.test_dna)
# TODO: reimplement this test using manual sequence input
# def mul_incompatible(seq):
# return seq * 3
# incompatible_seq = self.test_dna.copy()
# incompatible_seq = incompatible_seq.five_resect(1)
# incompatible_seq = incompatible_seq.reverse_complement()
# incompatible_seq = incompatible_seq.five_resect(1)
# incompatible_seq = incompatible_seq.reverse_complement()
# assert_raises(Exception, mul_incompatible, incompatible_seq)
def test_eq(self):
assert_true(self.test_dna == DNA('atgc'))
def test_ne(self):
assert_true(self.test_dna != DNA('aagc'))
def test_contains(self):
assert_true('a' in self.test_dna)
assert_true('t' in self.test_dna)
assert_true('g' in self.test_dna)
assert_true('c' in self.test_dna)
assert_false('u' in self.test_dna)
def test_flip(self):
flipped = self.test_dna.flip()
assert_equal(str(self.test_dna), flipped.bottom)
assert_equal(self.test_dna.bottom, str(flipped))
class TestFeatures(object):
'''Test features model using DNA object.'''
def __init__(self):
self.dna = DNA('ATGC') * 50
self.apply_features()
def apply_features(self):
misc_feature = Feature('Misc Feature', 1, 20, 'misc_feature')
misc_1_feature = Feature('Misc Feature', 1, 20, 'misc_feature',
strand=1)
coding_feature = Feature('Coding Feature', 21, 40, 'CDS')
primer_feature = Feature('Primer Feature', 41, 60, 'primer_bind')
promoter_feature = Feature('Promoter Feature', 61, 80, 'promoter')
terminator_feature = Feature('Terminator Feature', 81, 100,
'terminator')
rbs_feature = Feature('RBS Feature', 101, 120, 'RBS')
origin_feature = Feature('Origin Feature', 121, 140, 'rep_origin')
utr3_feature = Feature("3'UTR Feature", 141, 160, "3'UTR")
origin_feature2 = Feature('Origin Feature', 161, 180, 'rep_origin')
input_features = [misc_feature, misc_1_feature, coding_feature,
primer_feature, promoter_feature, terminator_feature,
rbs_feature, origin_feature, utr3_feature,
origin_feature2]
self.dna.features = input_features
def test_good_features(self):
for feature in self.dna.features:
assert_true(feature.copy() in self.dna.features)
def test_rev_comp(self):
rev = self.dna.reverse_complement()
for feature, rev_feature in zip(self.dna.features, rev.features):
assert_not_equal(feature.strand, rev_feature.strand)
assert_equal(len(self.dna) - feature.start, rev_feature.stop)
assert_equal(len(self.dna) - feature.stop, rev_feature.start)
def test_extract(self):
test_utr3_feature = [feature for feature in self.dna.features if
feature.name == "3'UTR Feature"][0]
extracted = self.dna.extract(test_utr3_feature)
assert_equal(str(extracted), 'TGCATGCATGCATGCATGC')
def test_excise(self):
copy = self.dna.circularize()
feature = copy.select_features('Coding Feature')[0]
rotated = copy.rotate_to(feature.start)
expected = rotated[feature.stop - feature.start:]
backbone = copy.excise(feature)
assert_equal(expected, backbone)
def test_getitem(self):
subsequence = self.dna[30:100]
remaining_features = [Feature('Primer Feature', 11, 30, 'primer_bind'),
Feature('Promoter Feature', 31, 50, 'promoter'),
Feature('Terminator Feature', 51, 70,
'terminator')]
assert_equal(subsequence.features, remaining_features)
assert_false(self.dna[10].features)
new_seq = DNA('ATGC', features=[Feature('A', 0, 0, 'misc_feature')])
assert_equal(new_seq[0].features[0],
Feature('A', 0, 0, 'misc_feature'))
def test_ne(self):
'''Test != operator'''
assert_true(self.dna.features[0] != self.dna.features[4])
assert_false(self.dna.features[0] != self.dna.features[0])
