def test_find_ssrs_with_motif3(self):
result = find_ssrs(self.seq, motif="TAT")
expect = [
RepData(11,
21,
3,
rep_seq="(TAT)_{3}",
motif="TAT",
motif_class="AAT")
]
self.assertEqual(result, expect)
def test_find_ssrs_with_motif2(self):
result = find_ssrs(self.seq, motif="TTA")
expect = [
RepData(10,
23,
4,
rep_seq="(TTA)_{4}",
motif="TTA",
motif_class="AAT")
]
self.assertEqual(result, expect)
def test_find_ssrs_with_motif4(self):
result = find_ssrs(self.seq, motif=["GC", "TTA"])
expect = [
RepData(0, 10, 3, rep_seq="(GC)_{3}", motif="GC",
motif_class="CG"),
RepData(10,
23,
4,
rep_seq="(TTA)_{4}",
motif="TTA",
motif_class="AAT"),
]
self.assertEqual(result, expect)
def test_find_ssrs_with_max_interrupt2(self):
result = find_ssrs(self.seq, motif="TTA", max_interrupt=3)
expect = [
RepData(
10,
34,
7,
rep_seq="(TTA)_{4}CC(TTA)_{1}CCC(TTA)_{1}",
motif="TTA",
motif_class="AAT",
)
]
self.assertEqual(result, expect)
def test_find_ssrs_with_motif1(self):
result = find_ssrs(self.seq, motif="GC")
expect = [
RepData(0, 10, 3, rep_seq="(GC)_{3}", motif="GC", motif_class="CG")
]
self.assertEqual(result, expect)
def test_find_ssrs_with_motif5(self):
result = find_ssrs(self.seq, motif="AT")
self.assertEqual(result, [])