Python locate Examples

Example #1

def test_wildcards_in_adapter():
    r = 'CATCTGTCC' + WILDCARD_SEQUENCES[0] + 'GCCAGGGTTGATTCGGCTGATCTGGCCG'
    for a in WILDCARD_SEQUENCES:
        result = locate(a, r, 0.0, BACK, wildcard_ref=True)
        assert result == (0, 10, 9, 19, 10, 0), result
    a = 'CCCXTTXATC'
    result = locate(a, r, 0.0, BACK, wildcard_ref=True)
    assert result is None

Example #2

File: test_align.py Project: jdidion/atropos

def test_wildcards_in_adapter():
    r = 'CATCTGTCC' + WILDCARD_SEQUENCES[0] + 'GCCAGGGTTGATTCGGCTGATCTGGCCG'
    for a in WILDCARD_SEQUENCES:
        result = locate(a, r, 0.0, BACK, wildcard_ref=True)
        assert result == (0, 10, 9, 19, 10, 0), result

    a = 'CCCXTTXATC'
    result = locate(a, r, 0.0, BACK, wildcard_ref=True)
    assert result is None

Example #3

File: test_align.py Project: jdidion/atropos

def test_wildcards_in_both():
    for a in WILDCARD_SEQUENCES:
        for s in WILDCARD_SEQUENCES:
            if 'X' in s or 'X' in a:
                continue
            r = 'CATCTGTCC' + s + 'GCCAGGGTTGATTCGGCTGATCTGGCCG'
            result = locate(a, r, 0.0, BACK, wildcard_ref=True, wildcard_query=True)
            assert result == (0, 10, 9, 19, 10, 0), result

Example #4

File: test_align.py Project: llllaaaa/atropos

def test_wildcards_in_both():
    for a in WILDCARD_SEQUENCES:
        for s in WILDCARD_SEQUENCES:
            if 'X' in s or 'X' in a:
                continue
            r = 'CATCTGTCC' + s + 'GCCAGGGTTGATTCGGCTGATCTGGCCG'
            result = locate(a, r, 0.0, BACK, wildcard_ref=True, wildcard_query=True)
            assert result == (0, 10, 9, 19, 10, 0), result

Example #5

def test_wildcards_in_read():
    a = WILDCARD_SEQUENCES[0]
    for s in WILDCARD_SEQUENCES:
        r = 'CATCTGTCC' + s + 'GCCAGGGTTGATTCGGCTGATCTGGCCG'
        result = locate(a, r, 0.0, BACK, wildcard_query=True)
        if 'X' in s:
            assert result is None
        else:
            assert result == (0, 10, 9, 19, 10, 0), result

Example #6

File: test_align.py Project: jdidion/atropos

def test_wildcards_in_read():
    a = WILDCARD_SEQUENCES[0]
    for s in WILDCARD_SEQUENCES:
        r = 'CATCTGTCC' + s + 'GCCAGGGTTGATTCGGCTGATCTGGCCG'
        result = locate(a, r, 0.0, BACK, wildcard_query=True)
        if 'X' in s:
            assert result is None
        else:
            assert result == (0, 10, 9, 19, 10, 0), result

Example #7

def test_polya():
    s = 'AAAAAAAAAAAAAAAAA'
    t = 'ACAGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA'
    result = locate(s, t, 0.0, BACK)
    # start_s, stop_s, start_t, stop_t, matches, cost = result
    assert result == (0, len(s), 4, 4 + len(s), len(s), 0)

Example #8

def test_no_match():
    a = locate('CTGATCTGGCCG', 'AAAAGGG', 0.1, BACK)
    assert a is None, a

Example #9

File: test_align.py Project: jdidion/atropos

def test_polya():
    s = 'AAAAAAAAAAAAAAAAA'
    t = 'ACAGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA'
    result = locate(s, t, 0.0, BACK)
    #start_s, stop_s, start_t, stop_t, matches, cost = result
    assert result == (0, len(s), 4, 4 + len(s), len(s), 0)

Example #10

File: test_align.py Project: jdidion/atropos

def test_no_match():
    a = locate('CTGATCTGGCCG', 'AAAAGGG', 0.1, BACK)
    assert a is None, a