def test_calc_coverage_4():
"""If uniqueley_aligned_only is True skip any mapping of read
that are aligned to more than on location.
"""
coverage_calculator = CoverageCalculator(uniquely_aligned_only=True)
bam_file_4 = generate_bam_file(ccd.sam_content_3, ccd.sam_bam_prefix)
coverage_calculator._init_coverage_list(bam_file_4.lengths[0])
coverage_calculator._calc_coverage("chrom", bam_file_4)
assert (coverage_calculator._coverages["forward"][0:15]).all() == (
np.array([
3.0, 3.0, 3.0, 3.0, 3.0, 3.0, 3.0, 3.0, 3.0, 3.0, 0.0, 0.0, 0.0,
0.0, 0.0
])).all()
def test_calc_coverage_3():
"""If read_count_splitting is set to False then every
mapping is counted as one to each of the matching position
independent how often its read is mapped in in total.
"""
coverage_calculator = CoverageCalculator(read_count_splitting=False)
bam_file_3 = generate_bam_file(ccd.sam_content_2, ccd.sam_bam_prefix)
coverage_calculator._init_coverage_list(bam_file_3.lengths[0])
coverage_calculator._calc_coverage("chrom", bam_file_3)
assert (coverage_calculator._coverages["forward"][0:15]).all() == (
np.array([
1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 0.0, 0.0, 0.0,
0.0, 0.0
])).all()
def test_calc_coverage_5():
"""If first_base_only is True only the first nucleotide of a
mapping is considered.
"""
coverage_calculator = CoverageCalculator(coverage_style="first_base_only")
bam_file_5 = generate_bam_file(ccd.sam_content_1, ccd.sam_bam_prefix)
coverage_calculator._init_coverage_list(bam_file_5.lengths[0])
coverage_calculator._calc_coverage("chrom", bam_file_5)
assert (coverage_calculator._coverages["forward"][0:15]).all() == (
np.array([
5.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,
0.0, 0.0
])).all()
assert (coverage_calculator._coverages["reverse"][0:15]).all() == (
np.array([
0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, -5.0, 0.0, 0.0, 0.0,
0.0, 0.0
])).all()
class TestCoverageCalculator(unittest.TestCase):
def setUp(self):
self.coverage_calculator = CoverageCalculator()
self.example_data = ExampleData()
self._sam_bam_prefix = "dummy"
def tearDown(self):
for suffix in [".sam", ".bam", ".bam.bai"]:
if os.path.exists(self._sam_bam_prefix + suffix) is True:
os.remove(self._sam_bam_prefix + suffix)
def _generate_bam_file(self, sam_content, file_prefix):
sam_file = "%s.sam" % file_prefix
bam_file = "%s.bam" % file_prefix
sam_fh = open(sam_file, "w")
sam_fh.write(sam_content)
sam_fh.close()
pysam.view("-Sb", "-o%s" % bam_file, sam_file)
pysam.index(bam_file)
self._bam = pysam.Samfile(bam_file)
def test_init_coverage_list(self):
self.coverage_calculator._init_coverage_list(10)
self.assertListEqual(
sorted(self.coverage_calculator._coverages.keys()),
["forward", "reverse"])
self.assertListEqual(
self.coverage_calculator._coverages["forward"], [0.0] * 10)
self.assertListEqual(
self.coverage_calculator._coverages["reverse"], [0.0] * 10)
def test_calc_coverage_1(self):
"""Check correct start at first list element"""
self._generate_bam_file(
self.example_data.sam_content_1, self._sam_bam_prefix)
self.coverage_calculator._init_coverage_list(self._bam.lengths[0])
self.coverage_calculator._calc_coverage("chrom", self._bam)
self.assertEqual(
len(self.coverage_calculator._coverages["forward"]), 1500)
self.assertListEqual(
self.coverage_calculator._coverages["forward"][0:15],
[5.0, 5.0, 5.0, 5.0, 5.0, 5.0, 5.0, 5.0, 5.0, 5.0,
0.0, 0.0, 0.0, 0.0, 0.0])
self.assertListEqual(
self.coverage_calculator._coverages["reverse"][0:15],
[-5.0, -5.0, -5.0, -5.0, -5.0, -5.0, -5.0, -5.0, -5.0, -5.0,
0.0, 0.0, 0.0, 0.0, 0.0])
def test_calc_coverage_2(self):
"""Consider how often a read is mapped. Mappings of reads that
are aligned to several location contribute only fractions to
the counting.
"""
self._generate_bam_file(
self.example_data.sam_content_2, self._sam_bam_prefix)
self.coverage_calculator._init_coverage_list(self._bam.lengths[0])
self.coverage_calculator._calc_coverage("chrom", self._bam)
self.assertListEqual(
self.coverage_calculator._coverages[
"forward"][0:15],
[0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5,
0.0, 0.0, 0.0, 0.0, 0.0])
def test_calc_coverage_3(self):
"""If read_count_splitting is set to False then every
mapping is counted as one to each of the matching position
independent how often its read is mapped in in total.
"""
self.coverage_calculator = CoverageCalculator(
read_count_splitting=False)
self._generate_bam_file(
self.example_data.sam_content_2, self._sam_bam_prefix)
self.coverage_calculator._init_coverage_list(self._bam.lengths[0])
self.coverage_calculator._calc_coverage("chrom", self._bam)
self.assertListEqual(
self.coverage_calculator._coverages[
"forward"][0:15],
[1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0,
0.0, 0.0, 0.0, 0.0, 0.0])
def test_calc_coverage_4(self):
"""If uniqueley_aligned_only is True skip any mapping of read
that are aligned to more than on location.
"""
self.coverage_calculator = CoverageCalculator(
uniqueley_aligned_only=True)
self._generate_bam_file(
self.example_data.sam_content_3, self._sam_bam_prefix)
self.coverage_calculator._init_coverage_list(self._bam.lengths[0])
self.coverage_calculator._calc_coverage("chrom", self._bam)
self.assertListEqual(
self.coverage_calculator._coverages[
"forward"][0:15],
[3.0, 3.0, 3.0, 3.0, 3.0, 3.0, 3.0, 3.0, 3.0, 3.0,
0.0, 0.0, 0.0, 0.0, 0.0])
def test_calc_coverage_5(self):
"""If first_base_only is True only the first nucleotide of a
mapping is considered.
"""
self.coverage_calculator = CoverageCalculator(first_base_only=True)
self._generate_bam_file(
self.example_data.sam_content_1, self._sam_bam_prefix)
self.coverage_calculator._init_coverage_list(self._bam.lengths[0])
self.coverage_calculator._calc_coverage("chrom", self._bam)
self.assertListEqual(
self.coverage_calculator._coverages[
"forward"][0:15],
[5.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,
0.0, 0.0, 0.0, 0.0, 0.0])
self.assertListEqual(
self.coverage_calculator._coverages[
"reverse"][0:15],
[0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, -5.0,
0.0, 0.0, 0.0, 0.0, 0.0])
class TestCoverageCalculator(unittest.TestCase):
def setUp(self):
self.coverage_calculator = CoverageCalculator()
self.example_data = ExampleData()
self._sam_bam_prefix = "dummy"
def tearDown(self):
for suffix in [".sam", ".bam", ".bam.bai"]:
if os.path.exists(self._sam_bam_prefix + suffix) is True:
os.remove(self._sam_bam_prefix + suffix)
def _generate_bam_file(self, sam_content, file_prefix):
sam_file = "{}.sam".format(file_prefix)
bam_file = "{}.bam".format(file_prefix)
sam_fh = open(sam_file, "w")
sam_fh.write(sam_content)
sam_fh.close()
pysam.view("-Sb",
"-o{}".format(bam_file),
sam_file,
catch_stdout=False)
pysam.index(bam_file)
self._bam = pysam.Samfile(bam_file)
def test_init_coverage_list(self):
self.coverage_calculator._init_coverage_list(10)
self.assertListEqual(
sorted(self.coverage_calculator._coverages.keys()),
["forward", "reverse"],
)
self.assertListEqual(
self.coverage_calculator._coverages["forward"].tolist(),
[0.0] * 10)
self.assertListEqual(
self.coverage_calculator._coverages["reverse"].tolist(),
[0.0] * 10)
def test_calc_coverage_1(self):
"""Check correct start at first list element"""
self._generate_bam_file(self.example_data.sam_content_1,
self._sam_bam_prefix)
self.coverage_calculator._init_coverage_list(self._bam.lengths[0])
self.coverage_calculator._calc_coverage("chrom", self._bam)
self.assertEqual(len(self.coverage_calculator._coverages["forward"]),
1500)
self.assertListEqual(
self.coverage_calculator._coverages["forward"][0:15].tolist(),
[
5.0,
5.0,
5.0,
5.0,
5.0,
5.0,
5.0,
5.0,
5.0,
5.0,
0.0,
0.0,
0.0,
0.0,
0.0,
],
)
self.assertListEqual(
self.coverage_calculator._coverages["reverse"][0:15].tolist(),
[
-5.0,
-5.0,
-5.0,
-5.0,
-5.0,
-5.0,
-5.0,
-5.0,
-5.0,
-5.0,
0.0,
0.0,
0.0,
0.0,
0.0,
],
)
def test_calc_coverage_2(self):
"""Consider how often a read is mapped. Mappings of reads that
are aligned to several location contribute only fractions to
the counting.
"""
self._generate_bam_file(self.example_data.sam_content_2,
self._sam_bam_prefix)
self.coverage_calculator._init_coverage_list(self._bam.lengths[0])
self.coverage_calculator._calc_coverage("chrom", self._bam)
self.assertListEqual(
self.coverage_calculator._coverages["forward"][0:15].tolist(),
[
0.5,
0.5,
0.5,
0.5,
0.5,
0.5,
0.5,
0.5,
0.5,
0.5,
0.0,
0.0,
0.0,
0.0,
0.0,
],
)
def test_calc_coverage_3(self):
"""If read_count_splitting is set to False then every
mapping is counted as one to each of the matching position
independent how often its read is mapped in in total.
"""
self.coverage_calculator = CoverageCalculator(
read_count_splitting=False)
self._generate_bam_file(self.example_data.sam_content_2,
self._sam_bam_prefix)
self.coverage_calculator._init_coverage_list(self._bam.lengths[0])
self.coverage_calculator._calc_coverage("chrom", self._bam)
self.assertListEqual(
self.coverage_calculator._coverages["forward"][0:15].tolist(),
[
1.0,
1.0,
1.0,
1.0,
1.0,
1.0,
1.0,
1.0,
1.0,
1.0,
0.0,
0.0,
0.0,
0.0,
0.0,
],
)
def test_calc_coverage_4(self):
"""If uniqueley_aligned_only is True skip any mapping of read
that are aligned to more than on location.
"""
self.coverage_calculator = CoverageCalculator(
uniquely_aligned_only=True)
self._generate_bam_file(self.example_data.sam_content_3,
self._sam_bam_prefix)
self.coverage_calculator._init_coverage_list(self._bam.lengths[0])
self.coverage_calculator._calc_coverage("chrom", self._bam)
self.assertListEqual(
self.coverage_calculator._coverages["forward"][0:15].tolist(),
[
3.0,
3.0,
3.0,
3.0,
3.0,
3.0,
3.0,
3.0,
3.0,
3.0,
0.0,
0.0,
0.0,
0.0,
0.0,
],
)
def test_calc_coverage_5(self):
"""If first_base_only is True only the first nucleotide of a
mapping is considered.
"""
self.coverage_calculator = CoverageCalculator(
coverage_style="first_base_only")
self._generate_bam_file(self.example_data.sam_content_1,
self._sam_bam_prefix)
self.coverage_calculator._init_coverage_list(self._bam.lengths[0])
self.coverage_calculator._calc_coverage("chrom", self._bam)
self.assertListEqual(
self.coverage_calculator._coverages["forward"][0:15].tolist(),
[
5.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
],
)
self.assertListEqual(
self.coverage_calculator._coverages["reverse"][0:15].tolist(),
[
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
-5.0,
0.0,
0.0,
0.0,
0.0,
0.0,
],
)
