def test_end(self):
xlink_pos = 1
report_by = 'end'
by_bc = {
'AAAAA': [
# (middle_pos, end_pos, read_len, num_mapped, cigar, second_start)
(1, 10, 10, 1, 0),
(1, 10, 10, 1, 0),
(1, 80, 80, 8, 0),
],
'CCCCC': [
(1, 10, 10, 1, 0),
(15, 20, 10, 10, 0),
],
}
# Multimax = 1
result1 = xlsites._collapse(xlink_pos, by_bc, report_by, multimax=1)
expected1 = {10: (2.0, 3)}
self.assertEqual(result1, expected1)
# Multimax = 10
result2 = xlsites._collapse(xlink_pos, by_bc, report_by, multimax=10)
expected2 = {10: (0.7, 3), 80: (0.1, 1), 20: (0.05, 1)}
self.assertEqual(result2, expected2)
def test_middle(self):
xlink_pos = 1
report_by = 'middle'
by_bc = {
'AAAAA': [
# (middle_pos, end_pos, read_len, num_mapped, cigar, second_start)
(5, 10, 10, 1, 0),
(5, 10, 10, 1, 0),
(40, 80, 80, 8, 0)
],
'CCCCC': [(5, 10, 10, 1, 0), (25, 30, 10, 10, 0)]
}
# Multimax = 1
result1 = xlsites._collapse(xlink_pos, by_bc, report_by, multimax=1)
expected1 = {5: (2.0, 3)}
self.assertEqual(result1, expected1)
# Multimax = 10
result2 = xlsites._collapse(xlink_pos, by_bc, report_by, multimax=10)
expected2 = {5: (0.7, 3), 40: (0.1, 1), 25: (0.05, 1)}
self.assertEqual(result2, expected2)
def test_start_2(self):
"""
Two barcodes, multimax case.
"""
by_bc = {
'AAAAA': [
# (middle_pos, end_pos, read_len, num_mapped, cigar, second_start)
(5, 10, 10, 1, 0),
(5, 10, 10, 1, 0),
(15, 30, 20, 2, 0),
],
'CCCCC': [
(5, 10, 10, 1, 0),
(5, 10, 10, 100, 0), # Excluded becouse of multimax
],
}
result1 = xlsites._collapse(1, by_bc, 'start', multimax=10)
expected1 = {1: (1.75, 4)}
self.assertEqual(result1, expected1)
def test_start_1(self):
"""
Two barcodes, one with two second_start groups.
No multimax situation yet.
"""
by_bc = {
'AAAAA': [
# (middle_pos, end_pos, read_len, num_mapped, cigar, second_start)
(5, 10, 10, 1, 0),
(5, 10, 10, 1, 0),
(5, 30, 20, 1, 20),
],
'CCCCC': [
(5, 10, 10, 1, 0),
(5, 10, 10, 1, 0),
],
}
result1 = xlsites._collapse(1, by_bc, 'start', multimax=1)
expected1 = {1: (3.0, 5)}
self.assertEqual(result1, expected1)