answer = aln.getBySequenceAnnotation('b', 'test_type')[0].todict()
self.assertEqual(answer, {'b': 'A--T', 'a': 'AAAT'})
if 0: # old, needs fixes
# Maps
a = Map([(10, 20)], parent_length=100)
for (desc, map, expected) in [
('a ', a, "Map([10:20] on base)"),
('i ', a.inverse(), "Map([-10-, 0:10, -80-] on Map([10:20] on base))"),
('1 ', a[5:], "Map([5:10] on Map([10:20] on base))"),
('1r', a[5:].relative_to(b), "Map([15:20] on base)"),
('2 ', a[:5], "Map([0:5] on Map([10:20] on base))"),
('2r', a[:5].relative_to(b), "Map([10:15] on base)"),
('r ', a.relative_to(a[5:]),
"Map([-5-, 0:5] on Map([5:10] on Map([10:20] on base)))"),
('r ', a[2:4].relative_to(a[2:6]),
"Map([0:2] on Map([2:6] on Map([10:20] on base)))"),
('r ', a[2:4].relative_to(a[2:6][0:3]),
"Map([0:2] on Map([0:3] on Map([2:6] on Map([10:20] on base))))")
]:
print(desc, repr(map), end=' ')
if repr(map) == expected:
print()
else:
print(' <--- ', expected)
bad = True
if __name__ == '__main__':
unittest.main()
b.addAnnotation(Feature, 'test_type', 'test_label', [(4,6)])
answer = aln.getBySequenceAnnotation('b', 'test_type')[0].todict()
self.assertEqual(answer, {'b':'A--T', 'a':'AAAT'})
if 0: # old, needs fixes
# Maps
a = Map([(10,20)], parent_length=100)
for (desc, map, expected) in [
('a ', a, "Map([10:20] on base)"),
('i ', a.inverse(), "Map([-10-, 0:10, -80-] on Map([10:20] on base))"),
('1 ', a[5:], "Map([5:10] on Map([10:20] on base))"),
('1r', a[5:].relative_to(b), "Map([15:20] on base)"),
('2 ', a[:5], "Map([0:5] on Map([10:20] on base))"),
('2r', a[:5].relative_to(b), "Map([10:15] on base)"),
('r ', a.relative_to(a[5:]), "Map([-5-, 0:5] on Map([5:10] on Map([10:20] on base)))"),
('r ', a[2:4].relative_to(a[2:6]), "Map([0:2] on Map([2:6] on Map([10:20] on base)))"),
('r ', a[2:4].relative_to(a[2:6][0:3]), "Map([0:2] on Map([0:3] on Map([2:6] on Map([10:20] on base))))")]:
print desc, repr(map),
if repr(map) == expected:
print
else:
print ' <--- ', expected
bad = True
if __name__ == '__main__':
unittest.main()
b.addAnnotation(Feature, 'test_type', 'test_label', [(4,6)])
answer = aln.getBySequenceAnnotation('b', 'test_type')[0].todict()
self.assertEqual(answer, {'b':'A--T', 'a':'AAAT'})
if 0: # old, needs fixes
# Maps
a = Map([(10,20)], parent_length=100)
for (desc, map, expected) in [
('a ', a, "Map([10:20] on base)"),
('i ', a.inverse(), "Map([-10-, 0:10, -80-] on Map([10:20] on base))"),
('1 ', a[5:], "Map([5:10] on Map([10:20] on base))"),
('1r', a[5:].relative_to(b), "Map([15:20] on base)"),
('2 ', a[:5], "Map([0:5] on Map([10:20] on base))"),
('2r', a[:5].relative_to(b), "Map([10:15] on base)"),
('r ', a.relative_to(a[5:]), "Map([-5-, 0:5] on Map([5:10] on Map([10:20] on base)))"),
('r ', a[2:4].relative_to(a[2:6]), "Map([0:2] on Map([2:6] on Map([10:20] on base)))"),
('r ', a[2:4].relative_to(a[2:6][0:3]), "Map([0:2] on Map([0:3] on Map([2:6] on Map([10:20] on base))))")]:
print desc, repr(map),
if repr(map) == expected:
print
else:
print ' <--- ', expected
bad = True
if __name__ == '__main__':
unittest.main()
