Example #1
0
def test_sw_positives_data():
    start, end, bestScore, matchedA, matchedB = sw(testa, testb, blosum50, -10,
                                                   -1)
    assert start == (29, 39)
    assert end == (76, 100)
    assert bestScore == 35.0
    assert matchedA == "NSNQIKILGNQGSFLTKG-PSKLNDRADSRRSLW--------DQGNFPLIIK------NLKI"
    assert matchedB == "NCSTFYVVKEDGTIVYTGTATSMFD-NDTKETVYIADFSSVNEEGTYYLAVPGVGKSVNFKI"
Example #2
0
def test_sw_Gap_beginB():
    assert sw("EFGACD", "ACD", blosum50, -3, -1)[3:] == ("ACD", "ACD")
Example #3
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def test_sw_trace_indelA():
    assert sw("LARN", "LAREN", blosum50, -3, -1)[3:] == ('LAR-N', 'LAREN')
Example #4
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def test_sw_trace_indelB():
    assert sw("LAREN", "LARN", blosum50, -3,
              -1)[3:] == ('LAREN', 'LAR-N')  #sadly i'm missing U
Example #5
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def test_sw_trace_mismatch():
    assert sw("ACDAFG", "ACDEFG", blosum50, -3,
              -1)[2:] == (41.0, 'ACDAFG', 'ACDEFG'
                          )  #make sure the score is right
Example #6
0
def test_sw_Gap_endB():
    assert sw("ACDEFG", "ACD", blosum50, -3, -1)[3:] == ("ACD", "ACD")