def test_extended_read_no_binning_extended_boundaries(self):
#0123456789012345[67]8901234567890123456789
#.....aaaaaAAAAAA[AA]AA....................
#...............b[bb]bbBBBBBBBBBB..........
#.....CCCCCCCCCCc[cc]cc.....DDDDDDDDDDddddd
peak_data = bam_parser._read_samfile_region(self.samfile, 'chr1', 16, 18, resolution=1, extend_to=15)
correct = np.array([3,3])
assert_array_equal(correct, peak_data)
#012345678901234567890123456789012345678[9012]
#.....aaaaaAAAAAAAAAA...................[....]
#...............bbbbbBBBBBBBBBB.........[....]
#.....CCCCCCCCCCccccc.....DDDDDDDDDDdddd[d...]
peak_data = bam_parser._read_samfile_region(self.samfile, 'chr1', 39, 43, resolution=1, extend_to=15)
correct = np.array([1,0,0,0])
assert_array_equal(correct, peak_data)
#01234567890123456789012345678901234567890[123]
#.....aaaaaAAAAAAAAAA.....................[...]
#...............bbbbbBBBBBBBBBB...........[...]
#.....CCCCCCCCCCccccc.....DDDDDDDDDDddddd[....]
peak_data = bam_parser._read_samfile_region(self.samfile, 'chr1', 41, 44, resolution=1, extend_to=15)
correct = np.array([0,0,0])
assert_array_equal(correct, peak_data)
def test_extended_reads_extended_boundaries_binning(self):
#012345678901234567[8901234|5678901|2345678]90123
#.....aaaaaAAAAAAAA[AA.....|.......|.......].....
#...............bbb[bbBBBBB|BBBBB..|.......].....
#.....CCCCCCCCCCccc[cc.....|DDDDDDD|DDDdddd]d....
peak_data = bam_parser._read_samfile_region(self.samfile, 'chr1', 18, 39, resolution=7, extend_to=15)
correct = np.array([3,2,1])
assert_array_equal(correct, peak_data)
def test_extended_read_no_binning_extended_boundaries_edge_case(self):
#[012345]67890123456789012345678901234567890123
#[.....a]aaaaAAAAAAAAAA........................
#[......].........bbbbbBBBBBBBBBB..............
#[.....C]CCCCCCCCCccccc.....DDDDDDDDDDddddd....
peak_data = bam_parser._read_samfile_region(self.samfile, 'chr1', 0, 6, resolution=1, extend_to=15)
correct = np.array([0,0,0,0,0,2])
assert_array_equal(correct, peak_data)
#[01234]567890123456789012345678901234567890123
#[.....]aaaaaAAAAAAAAAA........................
#[.....]..........bbbbbBBBBBBBBBB..............
#[.....]CCCCCCCCCCccccc.....DDDDDDDDDDddddd....
peak_data = bam_parser._read_samfile_region(self.samfile, 'chr1', 0, 5, resolution=1, extend_to=15)
correct = np.array([0,0,0,0,0])
assert_array_equal(correct, peak_data)
def test_extended_read_binning(self):
peak_data = bam_parser._read_samfile_region(self.samfile, 'chr1', 3, 43, resolution=5, extend_to=15)
#012[34567|89012|34567|89012|34567|89012|34567|89012]
#...[..aaa|aaAAA|AAAAA|AA...|.....|.....|.....|.....]
#...[.....|.....|..bbb|bbBBB|BBBBB|BB...|.....|.....]
#...[..CCC|CCCCC|CCccc|cc...|..DDD|DDDDD|DDddd|dd...]
correct = np.array([2,2,3,3,2,2,1,1])
assert_array_equal(correct, peak_data)
def test_extended_read_no_binning(self):
peak_data = bam_parser._read_samfile_region(self.samfile, 'chr1', 3, 40, resolution=1, extend_to=15)
#012|3456789012345678901234567890123456789|
#...|..aaaaaAAAAAAAAAA....................|
#...|............bbbbbBBBBBBBBBB..........|
#...|..CCCCCCCCCCccccc.....DDDDDDDDDDddddd|
correct = np.array([0,0,2,2,2,2,2,2,2,2,2,2,3,3,3,3,3,1,1,1,1,1,2,2,2,2,2,1,1,1,1,1,1,1,1,1,1])
assert_array_equal(correct, peak_data)
def test_non_extended_read_binning(self):
peak_data = bam_parser._read_samfile_region(self.samfile, 'chr1', 3, 43, resolution=5, extend_to=None)
correct = np.array([1,2,2,2,2,2,1,0])
assert_array_equal(correct, peak_data)