def test_extract_region():
test_seqs = [
('AAAABBBBCCCC', (0, 12), (0, 12), 'AAAABBBBCCCC'),
('AAAABBBBCCCC', (0, 12), (4, 8), 'BBBB'),
('AAAABBBBCCCC', (4, 16), (3, 7), '-AAA'),
('AAAABBBBCCCC', (4, 16), (0, 4), '----'),
('AAAABBBBCCCC', (4, 16), (14, 18), 'CC--'),
]
for found_seq, (fs, fe), (rs, re), cor in test_seqs:
out = HIVTransTool.extract_region(found_seq, fs, fe, rs, re)
eq_(out, cor, '(%i, %i), (%i, %i)' % (fs, fe, rs, re))
