예제 #1
0
파일: 20080129b.py 프로젝트: BIGtigr/xgcode
def simulate_branch_path(tree, node):
    """
    Simulate the nucleotide history on the path between a node and its parent.
    This simulated path is conditional on known values at each node.
    Purines are red; pyrimidines are blue.
    A and T are brighter; G and C are darker.
    @param tree: a SpatialTree with simulated nucleotides at each node
    @param node: the node that defines the branch on which to simulate a history
    """
    nucleotide_to_color = {
        'A': 'FF4444',
        'G': 'FF8888',
        'T': '4444FF',
        'C': '8888FF'
    }
    node.branch_color = nucleotide_to_color[node.state]
    rate_matrix = RateMatrix.get_jukes_cantor_rate_matrix()
    initial_state = node.parent.state
    terminal_state = node.state
    states = 'ACGT'
    events = None
    while events is None:
        events = PathSampler.get_nielsen_sample(initial_state, terminal_state,
                                                states, node.blen, rate_matrix)
    parent = node.parent
    last_t = 0
    for t, state in events:
        new = SpatialTree.SpatialTreeNode()
        new.name = node.name
        new.state = state
        new.branch_color = nucleotide_to_color[parent.state]
        tree.insert_node(new, parent, node, (t - last_t) / float(node.blen))
        last_t = t
        parent = new
예제 #2
0
def simulate_branch_path(tree, node):
    """
    Simulate the nucleotide history on the path between a node and its parent.
    This simulated path is conditional on known values at each node.
    Purines are red; pyrimidines are blue.
    A and T are brighter; G and C are darker.
    @param tree: a SpatialTree with simulated nucleotides at each node
    @param node: the node that defines the branch on which to simulate a history
    """
    nucleotide_to_color = {
            'A':'FF4444', 'G':'FF8888', 'T':'4444FF', 'C':'8888FF'}
    node.branch_color = nucleotide_to_color[node.state]
    rate_matrix = RateMatrix.get_jukes_cantor_rate_matrix()
    initial_state = node.parent.state
    terminal_state = node.state
    states = 'ACGT'
    events = None
    while events is None:
        events = PathSampler.get_nielsen_sample(
                initial_state, terminal_state, states, node.blen, rate_matrix)
    parent = node.parent
    last_t = 0
    for t, state in events:
        new = SpatialTree.SpatialTreeNode()
        new.name = node.name
        new.state = state
        new.branch_color = nucleotide_to_color[parent.state]
        tree.insert_node(new, parent, node, (t - last_t) / float(node.blen))
        last_t = t
        parent = new
예제 #3
0
def simulate_branch_path(tree, node, rate_matrix_object):
    # purines are red; pyrimidines are blue
    # A and T are brighter, G and C are darker
    nt_to_color = {'A':'ff4444', 'G':'ffaaaa', 'T':'4444ff', 'C':'aaaaff'}
    node.branch_color = nt_to_color[node.state]
    rate_matrix = rate_matrix_object.dictionary_rate_matrix
    initial_state = node.parent.state
    terminal_state = node.state
    states = 'ACGT'
    events = None
    while events is None:
        events = PathSampler.get_nielsen_sample(
                initial_state, terminal_state, states, node.blen, rate_matrix)
    parent = node.parent
    last_t = 0
    for t, state in events:
        new = SpatialTree.SpatialTreeNode()
        new.name = node.name
        new.state = state
        new.branch_color = nt_to_color[parent.state]
        tree.insert_node(new, parent, node, (t - last_t) / float(node.blen))
        last_t = t
        parent = new