def test_multi_read_dataset_insert():
cuckoo_tree = CuckooBitTree(0.5, 3, 10, 8, 4, 500)
read_1 = Read('a.fastq', 'a', None, 'GCGT', 'IIII')
read_2 = Read('a.fastq', 'b', None, 'AAAG', 'IIII')
cuckoo_tree.insert([read_1, read_2])
assert cuckoo_tree.root is not None
assert cuckoo_tree.root.parent is None
assert cuckoo_tree.root.children == []
assert cuckoo_tree.root.dataset_id == 'a.fastq'
assert cuckoo_tree.root.filter.contains('GCG')
assert cuckoo_tree.root.filter.contains('CGT')
assert cuckoo_tree.root.filter.contains('AAA')
assert cuckoo_tree.root.filter.contains('AAG')
def test_single_read():
"""
Ensures the cuckoo tree can
1. create the new node and set it as root
2. insert all 3-mers from dataset into the filter
3. set the dataset_id of the leaf
"""
cuckoo_tree = CuckooBitTree(0.5, 3, 10, 8, 4, 500)
read_1 = Read('a.fastq', 'a', None, 'GCGT', 'IIII')
cuckoo_tree.insert([read_1])
assert cuckoo_tree.root is not None
assert cuckoo_tree.root.parent is None
assert cuckoo_tree.root.children == []
assert cuckoo_tree.root.dataset_id == 'a.fastq'
assert cuckoo_tree.root.filter.contains('GCG')
assert cuckoo_tree.root.filter.contains('CGT')
def test_construction():
""" Ensures the cuckoo Tree is constructed as we would expect """
cuckoo_tree = CuckooBitTree(0.5, 3, 10, 8, 4, 500)
assert cuckoo_tree.num_buckets == 10
assert cuckoo_tree.fp_size == 8
assert cuckoo_tree.root is None
assert cuckoo_tree.theta == 0.5
assert cuckoo_tree.k == 3
def test_single_read_queries():
"""
Ensures that we can query a single leaf/single node tree
"""
cuckoo_tree = CuckooBitTree(0.5, 3, 10, 8, 4, 500)
read_1 = Read('a.fastq', 'a', None, 'GCGT', 'IIII')
cuckoo_tree.insert([read_1])
assert cuckoo_tree.query('AAAA') == []
assert cuckoo_tree.query('GCGT') == ['a.fastq']
assert cuckoo_tree.query('ACGT') == ['a.fastq']
assert cuckoo_tree.query('GCGA') == ['a.fastq']
cuckoo_tree.theta = 0.6
assert cuckoo_tree.query('AAAA') == []
assert cuckoo_tree.query('GCGT') == ['a.fastq']
assert cuckoo_tree.query('ACGT') == []
assert cuckoo_tree.query('GCGA') == []
def test_best_child_selection():
cuckoo_tree = CuckooBitTree(0.5, 3, 10, 8, 4, 500)
read_1 = Read('a.fastq', 'a', None, 'ABCD', 'IIII')
read_2 = Read('b.fastq', 'b', None, 'EFGH', 'IIII')
read_3 = Read('c.fastq', 'c', None, 'ZABC', 'IIII')
read_4 = Read('d.fastq', 'd', None, 'ABCD', 'IIII')
cuckoo_tree.insert([read_1])
cuckoo_tree.insert([read_2])
cuckoo_tree.insert([read_3])
cuckoo_tree.insert([read_4])
# b shares no kmers with other side
assert cuckoo_tree.root.children[1].dataset_id == 'b.fastq'
assert cuckoo_tree.root.children[1].children == []
assert cuckoo_tree.root.children[1].parent == cuckoo_tree.root
# read c has 1 different kmer than a and d
left_subtree = cuckoo_tree.root.children[0]
assert left_subtree.dataset_id is None
assert left_subtree.num_children() == 2
assert left_subtree.children[1].dataset_id == 'c.fastq'
# a and d should have same parent since they have same info
left_left_subtree = left_subtree.children[0]
assert left_left_subtree.dataset_id is None
assert left_left_subtree.filter.num_items_in_filter == 2
assert left_left_subtree.children[0].dataset_id == 'a.fastq'
assert left_left_subtree.children[1].dataset_id == 'd.fastq'
def test_create_internal_node():
"""
Ensure that cuckoo tree can
1. create an internal node
2. set 2 datasets as children of internal node
2. put kmer info of both datasets into internal node
3. internal node has no dataset_id
"""
cuckoo_tree = CuckooBitTree(0.5, 3, 10, 8, 4, 500)
read_1 = Read('a.fastq', 'a', None, 'ABCD', 'IIII')
read_2 = Read('b.fastq', 'b', None, 'EFGH', 'IIII')
cuckoo_tree.insert([read_1])
read_1_leaf = cuckoo_tree.root
cuckoo_tree.insert([read_2])
internal_node = cuckoo_tree.root
idx = internal_node.children.index(read_1_leaf)
read_2_leaf = internal_node.children[(idx + 1) % 2]
assert internal_node.dataset_id is None
assert internal_node.num_children() == 2
assert internal_node.parent is None
assert read_1_leaf in internal_node.children
assert read_2_leaf in internal_node.children
assert read_1_leaf.parent == internal_node
assert read_2_leaf.parent == internal_node
assert read_1_leaf.children == []
assert read_2_leaf.children == []
assert read_1_leaf.dataset_id == 'a.fastq'
assert read_2_leaf.dataset_id == 'b.fastq'
assert internal_node.filter.contains('ABC')
assert internal_node.filter.contains('BCD')
assert internal_node.filter.contains('EFG')
assert internal_node.filter.contains('FGH')
assert not read_1_leaf.filter.contains('EFG')
assert not read_1_leaf.filter.contains('FGH')
assert not read_2_leaf.filter.contains('ABC')
assert not read_2_leaf.filter.contains('BCD')
def test_two_internal_nodes():
cuckoo_tree = CuckooBitTree(0.5, 3, 10, 8, 4, 500)
read_1 = Read('a.fastq', 'a', None, 'ABCD', 'IIII')
read_2 = Read('b.fastq', 'b', None, 'EFGH', 'IIII')
read_3 = Read('c.fastq', 'c', None, 'ZABC', 'IIII')
cuckoo_tree.insert([read_1])
cuckoo_tree.insert([read_2])
cuckoo_tree.insert([read_3])
root = cuckoo_tree.root
assert root.parent is None
assert root.num_children() == 2
assert root.dataset_id is None
left_internal = root.children[0]
assert left_internal.dataset_id is None
assert left_internal.num_children() == 2
assert left_internal.filter.num_items_in_filter == 3
right_leaf = root.children[1]
assert right_leaf.dataset_id == 'b.fastq'
left_most_read = left_internal.children[0]
right_read = left_internal.children[1]
assert left_most_read.parent == left_internal
assert left_most_read.children == []
assert right_read.parent == left_internal
assert right_read.children == []
def test_two_read_queries():
"""
Ensures that we can query correctly through an internal node
and that changing theta works accordingly
"""
cuckoo_tree = CuckooBitTree(0.3, 3, 10, 8, 4, 500)
# note: have 1 3mer in common
read_1 = Read('a.fastq', 'a', None, 'ABCDE', 'IIII')
read_2 = Read('b.fastq', 'b', None, 'CDEFG', 'IIII')
cuckoo_tree.insert([read_1])
cuckoo_tree.insert([read_2])
assert cuckoo_tree.query('AAAAA') == []
assert cuckoo_tree.query('BCDEF') == ['a.fastq', 'b.fastq']
assert cuckoo_tree.query('CDEFG') == ['a.fastq', 'b.fastq']
assert cuckoo_tree.query('ABCDE') == ['a.fastq', 'b.fastq']
cuckoo_tree.theta = 0.6
assert cuckoo_tree.query('AAAAA') == []
assert cuckoo_tree.query('BCDEF') == ['a.fastq', 'b.fastq']
assert cuckoo_tree.query('CDEFG') == ['b.fastq']
assert cuckoo_tree.query('ABCDE') == ['a.fastq']
cuckoo_tree.theta = 0.9
assert cuckoo_tree.query('AAAAA') == []
assert cuckoo_tree.query('BCDEF') == []
assert cuckoo_tree.query('CDEFG') == ['b.fastq']
assert cuckoo_tree.query('ABCDE') == ['a.fastq']