def test_reframe(self):
'''Move bases around gaps to improve translation'''
read1 = 'GAAGCG---ACTACT' # Already in frame
assert LS.reframe(read1, 3) == read1
read2 = 'GAAGC---GACTACT' # Move one base <--
assert LS.reframe(read2, 3) == read1
read3 = 'GAAGCGA---CTACT' # Move one base -->
assert LS.reframe(read3, 3) == read1, LS.reframe(read3, 3)
def test_find_frame(self):
'''As in the name. Frame is 1 based'''
read = 'GTCGTCGTCCCATGTGTAAAATTAACCCCACTCTGTGTTAGTTTAAAGTGCACTGATTT'
assert LS.find_frame(read) == 1, read
read = 'AGTCGTCGTCCCATGTGTAAAATTAACCCCACTCTGTGTTAGTTTAAAGTGCACTGATTT'
assert LS.find_frame(read) == 2, read
read = 'TCGTCGTCCCATGTGTAAAATTAACCCCACTCTGTGTTAGTTTAAAGTGCACTGATTT'
assert LS.find_frame(read) == 3, read
def test_gap_translation(self):
'''Translation with gaps, frame dependent'''
assert LS.gap_translation('AAG') == 'K'
assert LS.gap_translation('AAG---') == 'K-'
assert LS.gap_translation('AAGAA') == 'K'
assert LS.gap_translation('CAAGA', frame=2) == 'K'