def test_all_primers(self):
primer_pair1 = util.PrimerPair(target_id="target_1",
chrom="chr42",
sense_primer_region=(100, 108),
antisense_primer_region=(145, 150))
primer_pair2 = util.PrimerPair(target_id="target_1",
chrom="chr42",
sense_primer_region=(200, 208),
antisense_primer_region=(245, 250))
actual_primers = util.PrimerPair._all_primers
self.assertEquals(primer_pair1, actual_primers[('chr42', 100, True)])
self.assertEquals(primer_pair1, actual_primers[('chr42', 150, False)])
self.assertEquals(primer_pair2, actual_primers[('chr42', 200, True)])
self.assertEquals(primer_pair2, actual_primers[('chr42', 250, False)])
self.assertEquals(4, len(actual_primers))
def test_init(self):
primer_pair = util.PrimerPair(target_id="target_1",
chrom="chr42",
sense_primer_region=(100, 110),
antisense_primer_region=(140, 150))
self.assertEquals("target_1", primer_pair.target_id)
self.assertEquals("chr42", primer_pair.chrom)
self.assertEquals(100, primer_pair.sense_start)
self.assertEquals(110, primer_pair._query_region_start)
self.assertEquals(140, primer_pair._query_region_end)
self.assertEquals(False, primer_pair.is_unmatched)
def test_softclip_primers(self):
primer_pair = util.PrimerPair(target_id="target_1",
chrom="chr42",
sense_primer_region=(100, 110),
antisense_primer_region=(140, 150))
expect_clipped_cigar = MockCigarUtil(reference_start=42, cigar="75X")
mock_cigar = MockCigarUtil(
_softclip_target_return=expect_clipped_cigar)
actual_clipped_cigar = primer_pair.softclip_primers(mock_cigar)
self.assertEquals([(110, 140)], mock_cigar._softclip_targets_calls)
self.assertEquals(expect_clipped_cigar, actual_clipped_cigar)
def test_get_primer_pair_noMatch(self):
util.PrimerPair._all_primers = {}
util.PrimerPair(target_id="target_1",
chrom="chr42",
sense_primer_region=(100, 110),
antisense_primer_region=(140, 150))
read = MockRead(reference_name="chrX",
is_positive_strand=True,
reference_start=42,
reference_end=142,
cigarstring="75M")
actual_primer_pair = util.PrimerPair.get_primer_pair(read)
self.assertIsInstance(actual_primer_pair, util._NullPrimerPair)
def test_get_primer_pair_matchNegativeStrand(self):
util.PrimerPair._all_primers = {}
util.PrimerPair(target_id="target_2",
chrom="chr42",
sense_primer_region=(100, 110),
antisense_primer_region=(140, 150))
read = MockRead(reference_name="chr42",
is_positive_strand=False,
reference_start=42,
reference_end=150,
cigarstring="75M")
actual_primer_pair = util.PrimerPair.get_primer_pair(read)
self.assertEquals("target_2", actual_primer_pair.target_id)