def test_yield_greatest_overlaps_ecoli(self):
self.complexSetUp()
expected = [sub.parse_alignment(self.raw_reads[-2]), sub.parse_alignment(self.raw_reads[4])]
for seq in expected:
seq.pick()
result = list(self.matrix.yield_greatest_overlaps(3, 2))
self.assertEquals(expected, result)
#expected = self.matrix.seq_matrix[2][0]
pass
def test_yield_greatest_overlaps_ecoli(self):
self.complexSetUp()
expected = [
sub.parse_alignment(self.raw_reads[-2]),
sub.parse_alignment(self.raw_reads[4])
]
for seq in expected:
seq.pick()
result = list(self.matrix.yield_greatest_overlaps(3, 2))
self.assertEquals(expected, result)
#expected = self.matrix.seq_matrix[2][0]
pass
def test_parse_alignment(self):
expected = Alignment(
self.raw_reads[0],
"gi|110640213|ref|NC_008253.1|_2_451_1:0:0_1:0:0_12b/1", 0, "GCT",
0)
result = sub.parse_alignment(self.raw_reads[0])
self.assertEquals(expected, result)
def test_parse_alignment(self):
expected = Alignment(self.raw_reads[0], "gi|110640213|ref|NC_008253.1|_2_451_1:0:0_1:0:0_12b/1", 0, "GCT", 0)
result = sub.parse_alignment(self.raw_reads[0])
self.assertEquals(expected, result)