def test_build_read_transformations(self):
primer_pair = clipper.PrimerPair(target_id="target_1",
chrom="chr42",
sense_primer_region=(100,102),
antisense_primer_region=(148,150))
read1 = MockRead(query_name="read1-sense",
is_positive_strand=True,
reference_name="chr42",
reference_start=100,
reference_end=150,
cigarstring="10M",
is_paired=True,
is_unmapped=False,
key=111)
read2 = MockRead(query_name="read2-antisense",
is_positive_strand=False,
reference_name="chr42",
reference_start=140,
reference_end=150,
cigarstring="10M",
is_paired=False,
is_unmapped=False,
key=222)
read3 = MockRead(query_name="read3",
is_positive_strand=True,
reference_name="chr42",
reference_start=333,
reference_end=343,
cigarstring="10M",
is_paired=True,
is_unmapped=False,
key=333)
filter_builder = lambda transform: []
read_iter = iter([read1, read2, read3])
actual_read_transforms = _build_read_transformations(read_iter,
filter_builder)
self.assertEquals(3, len(actual_read_transforms))
filter_builder=lambda x: []
transform1 = ReadTransformation(read1,
primer_pair,
MockCigarUtil(reference_start=102,
cigar="2S8M"),
filter_builder)
transform2 = ReadTransformation(read2,
primer_pair,
MockCigarUtil(reference_start=140,
cigar="8M2S"),
filter_builder)
transform3 = ReadTransformation(read3,
clipper.PrimerPair.NULL,
MockCigarUtil(reference_start=333,
cigar="10M"),
filter_builder)
self.assertEquals(transform1,
actual_read_transforms[111])
self.assertEquals(transform2,
actual_read_transforms[222])
self.assertEquals(transform3,
actual_read_transforms[333])
def test_build_read_transformations(self):
primer_pair = clipper.PrimerPair(target_id="target_1",
chrom="chr42",
sense_primer_region=(100, 102),
antisense_primer_region=(148, 150))
read1 = MockRead(query_name="read1-sense",
is_positive_strand=True,
reference_name="chr42",
reference_start=100,
reference_end=150,
cigarstring="10M",
is_paired=True,
is_unmapped=False,
key=111)
read2 = MockRead(query_name="read2-antisense",
is_positive_strand=False,
reference_name="chr42",
reference_start=140,
reference_end=150,
cigarstring="10M",
is_paired=False,
is_unmapped=False,
key=222)
read3 = MockRead(query_name="read3",
is_positive_strand=True,
reference_name="chr42",
reference_start=333,
reference_end=343,
cigarstring="10M",
is_paired=True,
is_unmapped=False,
key=333)
filter_builder = lambda transform: []
read_iter = iter([read1, read2, read3])
actual_read_transforms = _build_read_transformations(
read_iter, filter_builder)
self.assertEquals(3, len(actual_read_transforms))
filter_builder = lambda x: []
transform1 = ReadTransformation(
read1, primer_pair, MockCigarUtil(reference_start=102,
cigar="2S8M"), filter_builder)
transform2 = ReadTransformation(
read2, primer_pair, MockCigarUtil(reference_start=140,
cigar="8M2S"), filter_builder)
transform3 = ReadTransformation(
read3, clipper.PrimerPair.NULL,
MockCigarUtil(reference_start=333, cigar="10M"), filter_builder)
self.assertEquals(transform1, actual_read_transforms[111])
self.assertEquals(transform2, actual_read_transforms[222])
self.assertEquals(transform3, actual_read_transforms[333])
def test_build_read_transformations2_addsFilters(self):
clipper.PrimerPair(target_id="target_1",
chrom="chr42",
sense_primer_region=(100, 102),
antisense_primer_region=(148, 150))
clipper.PrimerPair(target_id="target_2",
chrom="chr42",
sense_primer_region=(200, 202),
antisense_primer_region=(248, 250))
read1 = MockRead(query_name="readA",
is_positive_strand=True,
reference_name="chr42",
reference_start=100,
reference_end=150,
cigarstring="50M",
is_paired=True,
is_unmapped=False,
key=111)
read2 = MockRead(query_name="readB",
is_positive_strand=False,
reference_name="chr42",
reference_start=200,
reference_end=250,
cigarstring="50M",
is_paired=False,
is_unmapped=False,
key=222)
read_iter = iter([read1, read2])
filter_builder = lambda transform: [
str(transform.reference_start), transform.primer_pair.target_id
]
actual_read_transforms = _build_read_transformations(
read_iter, filter_builder)
self.assertEquals(2, len(actual_read_transforms))
self.assertEquals(("102", "target_1"),
actual_read_transforms[111].filters)
self.assertEquals(("202", "target_2"),
actual_read_transforms[222].filters)
def test_build_read_transformations2_addsFilters(self):
clipper.PrimerPair(target_id="target_1",
chrom="chr42",
sense_primer_region=(100,102),
antisense_primer_region=(148,150))
clipper.PrimerPair(target_id="target_2",
chrom="chr42",
sense_primer_region=(200,202),
antisense_primer_region=(248,250))
read1 = MockRead(query_name="readA",
is_positive_strand=True,
reference_name="chr42",
reference_start=100,
reference_end=150,
cigarstring="50M",
is_paired=True,
is_unmapped=False,
key=111)
read2 = MockRead(query_name="readB",
is_positive_strand=False,
reference_name="chr42",
reference_start=200,
reference_end=250,
cigarstring="50M",
is_paired=False,
is_unmapped=False,
key=222)
read_iter = iter([read1, read2])
filter_builder = lambda transform: [str(transform.reference_start),
transform.primer_pair.target_id]
actual_read_transforms = _build_read_transformations(read_iter,
filter_builder)
self.assertEquals(2, len(actual_read_transforms))
self.assertEquals(("102", "target_1"),
actual_read_transforms[111].filters)
self.assertEquals(("202", "target_2"),
actual_read_transforms[222].filters)
