def test_filter_annotations1():
annotations = [
Annotation(start=1, end=10, bitscore=20),
Annotation(start=5, end=10, bitscore=30),
Annotation(start=9, end=15, bitscore=10),
Annotation(start=16, end=20, bitscore=30),
Annotation(start=16, end=20, bitscore=20),
Annotation(start=21, end=30, bitscore=40),
]
choose_func = None
assert filter_annotations(annotations, choose_func=choose_func) == \
set(
[
annotations[1],
annotations[2],
annotations[3],
annotations[5],
]
)
def test_filter_attr_num_ge_fail2():
a = Annotation()
assert not filter_attr_num(a, 'bitscore', 15, True)
a = Annotation(bitscore=10)
assert filter_attr_num(a, 'bitscore', 10, False)
def test_filter_attr_num_le_fail1():
a = Annotation(bitscore=10)
assert not filter_attr_num(a, 'bitscore', 5, False)
def test_filter_attr_num_le_fail2():
a = Annotation()
assert not filter_attr_num(a, 'bitscore', 5, False)
@pytest.mark.parametrize("annotation,attr,value,greater,result", [
(Annotation(bitscore=11), 'bitscore', 10, True, True),
(Annotation(bitscore=10), 'bitscore', 10, True, False),
(Annotation(bitscore=None), 'bitscore', 10, True, False),
(Annotation(bitscore=11), 'bitscore', 10, False, False),
(Annotation(bitscore=9), 'bitscore', 10, False, True),
])
def test_filter_attr_num_s(annotation, attr, value, greater, result):
assert filter_attr_num_s(annotation, attr, value, greater) == result
def test_filter_attr_str_eq_ok1():
a = Annotation(ec='1.1.1.1')
assert filter_attr_str(a, 'ec', '1.1.1.1', True)
def test_filter_attr_str_eq_fail1():
def test_choose_annotation_contained1():
# same size, better score
a = Annotation(start=1, end=10, bitscore=10)
b = Annotation(start=1, end=10, bitscore=15)
assert choose_annotation(a, b) == a
def test_choose_annotation_none2():
# overlap lower than the limits
a = Annotation(start=1, end=10, bitscore=10)
b = Annotation(start=9, end=12, bitscore=10)
assert choose_annotation(a, b, overlap=2) is None
def test_choose_annotation_overlap2():
# overlapping, same score, choose longer
a = Annotation(start=1, end=11, bitscore=10)
b = Annotation(start=5, end=11, bitscore=10)
assert choose_annotation(a, b, overlap=4) == b
def test_filter_attr_str_in_ok1():
a = Annotation(ec='1.1.1.1')
assert filter_attr_str(a, 'ec', '1.1.1.1', False)
def test_choose_annotation_overlap1():
# overlapping, better score
a = Annotation(start=1, end=10, bitscore=10)
b = Annotation(start=5, end=11, bitscore=15)
assert choose_annotation(a, b, overlap=4) == a
def test_filter_len_le_fail1():
a = Annotation(start=1, end=10)
assert not filter_len(a, 5, False)
def test_filter_len_ge_fail1():
a = Annotation(start=1, end=3)
assert not filter_len(a, 5, True)
def test_filter_len_le_ok2():
# lower
a = Annotation(start=1, end=3)
assert filter_len(a, 5, False)
def test_filter_len_ge_ok2():
# greater
a = Annotation(start=1, end=3)
assert filter_len(a, 2, True)
def test_filter_len_le_ok1():
# equal
a = Annotation(start=1, end=2)
assert filter_len(a, 2, False)
def test_filter_base_fail2():
a = Annotation(seq_id='seq1')
assert not filter_base(a, 'seqid', 'seq1')
def test_filter_attr_num_le_ok2():
a = Annotation(bitscore=10)
assert filter_attr_num(a, 'bitscore', 10, False)
def test_filter_attr_num_le_fail2():
a = Annotation()
assert not filter_attr_num(a, 'bitscore', 5, False)
def test_filter_base_num_ge_ok2():
a = Annotation(bitscore=10)
assert filter_base_num(a, 'bitscore', 10, True)
def test_filter_attr_str_eq_fail2():
a = Annotation(ec='1.1.1.1')
assert not filter_attr_str(a, 'ec', '1.1.1', True)
def test_filter_base_num_ge_fail1():
a = Annotation(bitscore=10)
assert not filter_base_num(a, 'bitscore', 15, True)
def test_filter_attr_str_in_fail2():
a = Annotation(ec='1.1.1.1')
assert not filter_attr_str(a, 'ec', '1.1.1.2', False)
def test_choose_annotation_contained2():
# same score, longer
a = Annotation(start=1, end=10, bitscore=10)
b = Annotation(start=5, end=10, bitscore=10)
assert choose_annotation(a, b) == b
def test_choose_annotation_none1():
# no overlap
a = Annotation(start=1, end=10, bitscore=10)
b = Annotation(start=11, end=12, bitscore=10)
assert choose_annotation(a, b, overlap=4) is None
def test_filter_base_num_le_ok1():
a = Annotation(bitscore=10)
assert filter_base_num(a, 'bitscore', 15, False)
def test_filter_base_num_le_fail1():
a = Annotation(bitscore=10)
assert not filter_base_num(a, 'bitscore', 5, False)
def test_filter_attr_num_ge_ok1():
a = Annotation(bitscore=10)
assert filter_attr_num(a, 'bitscore', 5, True)
def test_filter_base_ok1():
a = Annotation(seq_id='seq1')
assert filter_base(a, 'seq_id', 'seq1')
def annotations():
return [
Annotation(seq_id='1', start=0, end=100, strand='+', uid='u1'),
Annotation(seq_id='1', start=10, end=100, strand='-', uid='u2'),
Annotation(seq_id='2', start=0, end=100, strand='+', uid='u3'),
]