def test_011_lorenz_03(self):
# everything covered, is at least covered even densely
# x x x x x
# x x x x x
# - - - - - - - - - - - - - -
test_id = 'blc_011'
input_file_sam = TEST_DIR + "test_" + test_id + ".sam"
input_file_bam = T_TEST_DIR + "test_" + test_id + ".bam"
sam_to_sorted_bam(input_file_sam, input_file_bam)
b = bamlorenzcoverage()
idx, n = b.bam_file_to_idx(input_file_bam)
lc = b.estimate_lorenz_curves(idx)
# print(idx, file=sys.stderr)
# denote that it only considers the (size of the) sequences described in the SAM header
self.assertDictEqual(idx, {0: 6, 1: 6, 2: 2})
# print(idx, file=sys.stderr)
# denote that it only considers the (size of the) sequences described in the SAM header
self.assertListEqual(lc['fraction_genome'], [0.0, 1.0 * 2 / 8, 1.0])
self.assertListEqual(lc['fraction_reads'], [0.0, 1.0 * 4 / 10, 1.0])
# additional stats
self.assertEqual(n, 14) # sam header say reference size is 14
self.assertEqual(lc['roc'], 0.425)
self.assertEqual(lc['total_sequenced_bases'], 10)
self.assertEqual(lc['total_covered_positions_of_genome'], 8)
def test_005_deletion(self):
test_id = 'blc_005'
input_file_sam = TEST_DIR + "test_" + test_id + ".sam"
input_file_bam = T_TEST_DIR + "test_" + test_id + ".bam"
sam_to_sorted_bam(input_file_sam, input_file_bam)
b = bamlorenzcoverage()
idx, n = b.bam_file_to_idx(input_file_bam)
# denote that it only considers the (size of the) sequences described in the SAM header
self.assertDictEqual(idx, {0: 392, 1: 108})
def test_008_lorenz_01(self):
# x x x x
# - - - - - - - - - -
idx = {0: 6, 1: 4}
b = bamlorenzcoverage()
lc = b.estimate_lorenz_curves(idx)
# print(idx, file=sys.stderr)
# denote that it only considers the (size of the) sequences described in the SAM header
self.assertListEqual(lc['fraction_genome'], [0.0, 1.0])
self.assertListEqual(lc['fraction_reads'], [0.0, 1.0])
# additional stats
self.assertEqual(lc['roc'], 0.5)
def test_007_stacking(self):
test_id = 'blc_007'
input_file_sam = TEST_DIR + "test_" + test_id + ".sam"
input_file_bam = T_TEST_DIR + "test_" + test_id + ".bam"
sam_to_sorted_bam(input_file_sam, input_file_bam)
b = bamlorenzcoverage()
idx, n = b.bam_file_to_idx(input_file_bam)
# denote that it only considers the (size of the) sequences described in the SAM header
self.assertDictEqual(idx, {0: 372, 1: 48, 2: 80})
# additional stats
self.assertEqual(n, 500)
def test_010_lorenz_03(self):
# everything covered, is at least covered even densely
# x x x x x
# x x x x x
# - - - - - - - - - -
idx = {0: 6, 1: 6, 2: 2}
b = bamlorenzcoverage()
lc = b.estimate_lorenz_curves(idx)
# print(idx, file=sys.stderr)
self.assertListEqual(lc['fraction_genome'], [0.0, 1.0 * 2 / 8, 1.0])
self.assertListEqual(lc['fraction_reads'], [0.0, 1.0 * 4 / 10, 1.0])
# additional stats
self.assertEqual(lc['roc'], 0.425)
def test_013_bed(self):
# everything covered, is at least covered even densely
# x x x x x
# x x x x x
# - - - - - - - - - - - - - -
test_id = 'blc_013'
input_file_sam = TEST_DIR + "test_" + test_id + ".sam"
input_file_bed = TEST_DIR + "test_" + test_id + ".bed"
input_file_bam = T_TEST_DIR + "test_" + test_id + ".bam"
sam_to_sorted_bam(input_file_sam, input_file_bam)
b = bamlorenzcoverage()
idx, n = b.bam_file_to_idx(input_file_bam, None, input_file_bed)
self.assertEqual(n, 12)
def test_012_region(self):
# everything covered, is at least covered even densely
# x x x x x
# x x x x x
# - - - - - - - - - - - - - -
test_id = 'blc_012'
input_file_sam = TEST_DIR + "test_" + test_id + ".sam"
input_file_bam = T_TEST_DIR + "test_" + test_id + ".bam"
sam_to_sorted_bam(input_file_sam, input_file_bam)
b = bamlorenzcoverage()
idx, n = b.bam_file_to_idx(input_file_bam, 'chr1:2-14')
self.assertEqual(
n, 13
) # sam header say reference size is 14, but we start at 2nd position
def test_002_estimate_idx_from_bam(self):
# x x x x x
# x x x x x
# x x x x x
# - - - - - - - - - - - - - - -
# pct covered [ 0 read ] = 15 / 15 = 100.0%
# pct covered [ 1+ read ] = 5 / 15 = 33.3%
# pct covered [ 2+ read ] = 5 / 15 = 33.3%
# pct covered [ 3+ read ] = 5 / 15 = 33.3%
idx = {0: 10, 3: 5}
b = bamlorenzcoverage()
cc = b.estimate_cumulative_coverage_curves(idx)
# import sys
# print(cc, file=sys.stderr)
self.assertDictEqual(
cc, {
'minimum_coverage_depth': [0, 3],
'percentage_genome_covered': [100.0, 100.0 * 1.0 / 3.0]
})