def test_find_crispr_target_does_not_find_target_with_part_of_pam(self):
s1 = 'agaaggtctggtagcgatgtagtcgatct'
s2 = 'gactaggtacgtagtcgtcaggtcagtca'
pam = 'cgc'
g = self.build_genome(False, s1 + pam + s2)
guide = s1[-20:]
t = find_crispr_target(g, guide, 'ngg')
self.assertEquals(len(t), 0)
def test_find_crispr_target_does_not_find_target_with_part_of_pam(self):
s1 = 'agaaggtctggtagcgatgtagtcgatct'
s2 = 'gactaggtacgtagtcgtcaggtcagtca'
pam = 'cgc'
g = self.build_genome(False, s1 + pam + s2)
guide = s1[-20:]
t = find_crispr_target(g, guide, 'ngg')
self.assertEquals(len(t), 0)
def test_find_crispr_target_only_finds_perfect_match_to_guide(self):
s1 = 'agaaggtctggtagcgatgtagtcgatct'
s2 = 'gactaggtacgtagtcgtcaggtcagtca'
pam = 'cgg'
g = self.build_genome(False, s1 + pam + s2)
guide = 'aaaaa' + s1[-15:]
t = find_crispr_target(g, guide, 'ngg')
self.assertEquals(len(t), 0)
def test_find_crispr_target_only_finds_perfect_match_to_guide(self):
s1 = 'agaaggtctggtagcgatgtagtcgatct'
s2 = 'gactaggtacgtagtcgtcaggtcagtca'
pam = 'cgg'
g = self.build_genome(False, s1 + pam + s2)
guide = 'aaaaa' + s1[-15:]
t = find_crispr_target(g, guide, 'ngg')
self.assertEquals(len(t), 0)
def test_find_crispr_target_finds_target_on_reverse_strand(self):
s1 = 'agaaggtctggtagcgatgtagtcgatct'
s2 = 'gactaggtacgtagtcgtcaggtcagtca'
pam = 'cgg'
g = self.build_genome(False, str(Seq(s1 + pam + s2).reverse_complement()))
guide = s1[-20:]
t = find_crispr_target(g, guide, 'ngg')
self.assertEquals(len(t), 1)
self.assertEquals(t[0].fragment_id, g.fragments.all()[0].id)
self.assertEquals(t[0].fragment_name, g.fragments.all()[0].name)
self.assertEquals(t[0].subject_end, len(s2) + 3 + 1)
self.assertEquals(t[0].subject_start, len(s2) + 3 + 1 + 20 - 1)
self.assertEquals(t[0].pam, 'ngg')
def test_find_crispr_target_finds_target_on_forward_strand(self):
s1 = 'agaaggtctggtagcgatgtagtcgatct'
s2 = 'gactaggtacgtagtcgtcaggtcagtca'
pam = 'cgg'
g = self.build_genome(False, s1 + pam + s2)
guide = s1[-20:]
t = find_crispr_target(g, guide, 'ngg')
self.assertEquals(len(t), 1)
self.assertEquals(t[0].fragment_id, g.fragments.all()[0].id)
self.assertEquals(t[0].fragment_name, g.fragments.all()[0].name)
self.assertEquals(t[0].subject_start, s1.index(guide) + 1)
self.assertEquals(t[0].subject_end, len(s1))
self.assertEquals(t[0].pam, 'ngg')
def test_find_crispr_target_finds_target_on_forward_strand(self):
s1 = 'agaaggtctggtagcgatgtagtcgatct'
s2 = 'gactaggtacgtagtcgtcaggtcagtca'
pam = 'cgg'
g = self.build_genome(False, s1 + pam + s2)
guide = s1[-20:]
t = find_crispr_target(g, guide, 'ngg')
self.assertEquals(len(t), 1)
self.assertEquals(t[0].fragment_id, g.fragments.all()[0].id)
self.assertEquals(t[0].fragment_name, g.fragments.all()[0].name)
self.assertEquals(t[0].subject_start, s1.index(guide) + 1)
self.assertEquals(t[0].subject_end, len(s1))
self.assertEquals(t[0].pam, 'ngg')
def test_find_crispr_target_finds_target_across_circular_boundary(self):
s1 = 'agaaggtctggtagcgatgtagtcgatct'
s2 = 'gactaggtacgtagtcgtcaggtcagtca'
pam = 'cgg'
s = s1[10:] + pam + s2 + s1[0:10]
g = self.build_genome(True, s)
guide = s1[-20:]
t = find_crispr_target(g, guide, 'ngg')
self.assertEquals(len(t), 1)
self.assertEquals(t[0].fragment_id, g.fragments.all()[0].id)
self.assertEquals(t[0].fragment_name, g.fragments.all()[0].name)
self.assertEquals(t[0].subject_start, (s1.index(guide) + 1 - 10 - 1) % len(s) + 1)
self.assertEquals(t[0].subject_end, (len(s1) - 10 - 1) % len(s) + 1)
self.assertEquals(t[0].pam, 'ngg')
def test_find_crispr_target_finds_reverse_complement_with_pam_across_circular_boundary(self):
s1 = 'agaaggtctggtagcgatgtagtcgatct'
s2 = 'gactaggtacgtagtcgtcaggtcagtca'
pam = 'cgg'
s = pam[1:] + s2 + s1 + pam[:1]
g = self.build_genome(True, str(Seq(s).reverse_complement()))
guide = s1[-20:]
t = find_crispr_target(g, guide, 'ngg')
self.assertEquals(len(t), 1)
self.assertEquals(t[0].fragment_id, g.fragments.all()[0].id)
self.assertEquals(t[0].fragment_name, g.fragments.all()[0].name)
self.assertEquals(t[0].subject_end, 2)
self.assertEquals(t[0].subject_start, 2 + len(guide) - 1)
self.assertEquals(t[0].pam, 'ngg')
def test_find_crispr_target_finds_target_on_reverse_strand(self):
s1 = 'agaaggtctggtagcgatgtagtcgatct'
s2 = 'gactaggtacgtagtcgtcaggtcagtca'
pam = 'cgg'
g = self.build_genome(False,
str(Seq(s1 + pam + s2).reverse_complement()))
guide = s1[-20:]
t = find_crispr_target(g, guide, 'ngg')
self.assertEquals(len(t), 1)
self.assertEquals(t[0].fragment_id, g.fragments.all()[0].id)
self.assertEquals(t[0].fragment_name, g.fragments.all()[0].name)
self.assertEquals(t[0].subject_end, len(s2) + 3 + 1)
self.assertEquals(t[0].subject_start, len(s2) + 3 + 1 + 20 - 1)
self.assertEquals(t[0].pam, 'ngg')
def test_find_crispr_target_finds_reverse_complement_with_pam_across_circular_boundary(
self):
s1 = 'agaaggtctggtagcgatgtagtcgatct'
s2 = 'gactaggtacgtagtcgtcaggtcagtca'
pam = 'cgg'
s = pam[1:] + s2 + s1 + pam[:1]
g = self.build_genome(True, str(Seq(s).reverse_complement()))
guide = s1[-20:]
t = find_crispr_target(g, guide, 'ngg')
self.assertEquals(len(t), 1)
self.assertEquals(t[0].fragment_id, g.fragments.all()[0].id)
self.assertEquals(t[0].fragment_name, g.fragments.all()[0].name)
self.assertEquals(t[0].subject_end, 2)
self.assertEquals(t[0].subject_start, 2 + len(guide) - 1)
self.assertEquals(t[0].pam, 'ngg')
def test_find_crispr_target_finds_target_across_circular_boundary(self):
s1 = 'agaaggtctggtagcgatgtagtcgatct'
s2 = 'gactaggtacgtagtcgtcaggtcagtca'
pam = 'cgg'
s = s1[10:] + pam + s2 + s1[0:10]
g = self.build_genome(True, s)
guide = s1[-20:]
t = find_crispr_target(g, guide, 'ngg')
self.assertEquals(len(t), 1)
self.assertEquals(t[0].fragment_id, g.fragments.all()[0].id)
self.assertEquals(t[0].fragment_name, g.fragments.all()[0].name)
self.assertEquals(t[0].subject_start,
(s1.index(guide) + 1 - 10 - 1) % len(s) + 1)
self.assertEquals(t[0].subject_end, (len(s1) - 10 - 1) % len(s) + 1)
self.assertEquals(t[0].pam, 'ngg')