예제 #1
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 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
예제 #2
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 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
예제 #3
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 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)
예제 #4
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 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)