def test_multiple_references(self):
ref1 = Sequence('TGCGATGACGCGTGAGGTGTATGAAGCAAAGGCAGCGAAAAAAAAAGGTGGTGGGAGTATGACGAAAATAAACCAGCGAAAATTAACCGCGCGGACTATTTACTCCCACCACCTTTTTTTTTCCGTCACATCAAGTCGTCCATTAGGAGTAG')
ref2 = Sequence('TATAAGATTATGAACGTGAGGTGTATGAAGCAAAGGCAGCAATCAAGCTAATATGGAGATGGATTTCAGAAGGTTTTGTTTATAGCGAAAAACAAGAAACTGACTTATATGAGCTCGGTAAGAAGTACTTCAATGAGCTAGTAAATAGAAGTATGATACAGCCAATTGGTATTGATGATGGAGAAGATAAACAAGCGTGTCGTGTACATGACATGGTGCTTGATATCCTATGCT')
primer = Primer('CGTGAGGTGTATGAAGCAAAGGCAGC', span=(10, 36), strand=1)
sites = binding_sites([ref1, ref2], primer)
expected = [(10, 36), (14, 40)]
self.assertEqual(expected, [site.span() for site in sites])
def test_self_contig_complementary_score_2(self):
"""
AATT
||||
TTAA
"""
seq = Sequence('AATT')
primer = Primer(seq, 0, 0, 0)
self.assertEqual(primer.complementary_score, 4)
def test_self_complementary_3(self):
"""
GGGATGGGGGG
||
GGGGGGTAGGG
"""
seq = Sequence('GGGATGGGGGG')
primer = Primer(seq, 0, 0, 0)
self.assertEqual(primer.complementary_score, 2)
def test_rev_comp_binding_sites(self):
# TGACGGAAAAAAAAAGGTGGTGGGAGTA
# Reverse Complement:
# TACTCCCACCACCTTTTTTTTTCCGTCA
ref = Sequence('TGCGATGACGGAAAAAAAAAGGTGGTGGGAGTATGACGAAAATAAACCAGCGAAAATTAACCGCGCGGACTATTTACTCCCACCACCTTTTTTTTTCCGTCACATCAAGTCGTCCATTAGGAGTAG')
primer = Primer('TGACGGAAAAAAAAAGGTGGTGGGAGTA', span=(5, 33), strand=1)
sites = binding_sites([ref], primer)
expected = [(5, 33), (74, 102)]
self.assertEqual(expected, [site.span() for site in sites])
def test_fuzzy_binding_sites(self):
# ACGGAAAAAAAAAGGTGGTGGGAGTATGACGAAAAT
# |||| |||||||| |||||| ||||||||||||||
# ACGGTTAAAAAAAGATGGTGGCAGTATGACGAAAAT
ref = Sequence('TGCGATGACGGAAAAAAAAAGGTGGTGGGAGTATGACGAAAATAAACCAGCGAAAATTAACCGCGCGGACTATTCATCAAGTCGTCCATTAGGAGTAGAGACGGAAAAAAAAAGGTGGTGGGAGTATGACGGACGGTTAAAAAAAGATGGTGGCAGTATGACGAAAATATTTTCACAACCCAATTTGCCTATTTTATTTATTCATTGGAAAACTTGAAGAATGGAAATTTTGTGGTGCGATAATAGCATATTGTGTTGATGTTGTC')
primer = Primer('ACGGAAAAAAAAAGGTGGTGGGAGTATGACGAAAAT', span=(6, 38), strand=1)
sites = binding_sites([ref], primer)
expected = [(7, 43), (132, 168)]
self.assertEqual(expected, [site.span() for site in sites])
def test_self_complementary_2(self):
"""
AAAGGGGGT
| |
TGGGGGAAA
"""
seq = Sequence('AAAGGGGGT')
primer = Primer(seq, 0, 0, 0)
self.assertEqual(primer.complementary_score, 2)
def test_self_complementary(self):
seq = Sequence('AATT')
primer = Primer(seq, 0, 0, 0)
self.assertEqual(primer.complementary_score, 4)
def test_no_binding_sites(self):
ref = Sequence('GTAGCATGCGATCGTCTATCGTATGACGCTGCACGCAT')
primer = Primer('TGACGGAAAAAAA', span=(13, 26), strand=1)
sites = binding_sites([ref], primer)
expected = []
self.assertEqual(expected, [site.span() for site in sites])
def test_multiple_binding_sites(self):
ref = Sequence('TGCGATGACGGAAAAAAAAAGGTGGTGGGAGTATGACGAAAATAAACCAGCGAAAATTAACCGCGCGGACTATTCATCAAGTCGTCCATTAGGAGTAGAGACGGAAAAAAAAAGGTGGTGGGAGTATGACGGATTTTCACAACCCAATTTGCCTATTTTATTTATTCATTGGAAAACTTGAAGAATGGAAATTTTGTGGTGCGATAATAGCATATTGTGTTGATGTTGTC')
primer = Primer('GACGGAAAAAAAAAGGTGGTGGGAGTATGACG', span=(6, 38), strand=1)
sites = binding_sites([ref], primer)
expected = [(6, 38), (99, 131)]
self.assertEqual(expected, [site.span() for site in sites])
def test_single_binding_site(self):
ref = Sequence('TGCGATGACGGAAAAAAAAAGGTGGTGGGAGTATGACGAAAATAAACCAGCGAAAATTAACCGCGCGGACTATTCATCAAGTCGTCCATTAGGAGTAGAGATTTTCACAACCCAATTTGCCTATTTTATTTATTCATTGGAAAACTTGAAGAATGGAAATTTTGTGGTGCGATAATAGCATATTGTGTTGATGTTGTCAAATTTCTTCCCACCAACCGTGCCCTCCTCCAGTTGATTGTATGCACAAGCGTGCCACCCCATGACGGTAGGAAACGAGCACAACTGCACCATTGTTTAAATCATCTCGTCAGAGCTTCATCAGTTTATAATGGCATATGTTTGTCCACAAGCGCATCACCGGCCCCGGTGCGCCAAATATATTTTGTAACCACCCTTATCCTTTCAATCAACCATCACGAGGAAATAGTCTGAGAAGTTCGCAGCCACATTGTCGTTGTGGAGTCTATATCAACCACCATTCTTAAAATTAGCTACGTGTGATCAACTTGGTCCACCACCTACGCAAGGAGGTGCGTGGTGCGGAAGTTGATTAATCCAACCAAACGTGCCTGCTTGTCTCTAGATAATACAAACTAAGATGTCTAACTAAACTAATGCATCTGCTCAAAGGCATCAATCGCATCGGCGCAAGCGTTCAGAGGTCAGACGACCATTGGCAAGCACCAAAGGACGGGGCCATACGCTTAGAGACACCTACATGGCCGGGTATTAATTACTAGAGTGTTGCAACGCGTTCGCAAAGTCAGCACACGGAGATTGGTGC')
primer = Primer('CAGTTGATTGTATGCACAAGCGTGCCACCCCATGA', span=(228, 263), strand=1)
sites = binding_sites([ref], primer)
expected = [(228, 263)]
self.assertEqual(expected, [site.span() for site in sites])