ipyrad/analysis/tetrad2.py
def build_trees(fclade_counts, namedict):
    """ 
    A subfunc of consensus_tree(). Build an unrooted consensus tree 
    from filtered clade counts. 
    """

    ## storage
    nodes = {}
    idxarr = np.arange(len(fclade_counts[0][0]))
    queue = []

    ## create dict of clade counts and set keys
    countdict = defaultdict(int)
    for clade, count in fclade_counts:
        mask = np.int_(list(clade)).astype(np.bool)
        ccx = idxarr[mask]
        queue.append((len(ccx), frozenset(ccx)))
        countdict[frozenset(ccx)] = count

    while queue:
        queue.sort()
        (clade_size, clade) = queue.pop(0)
        new_queue = []
    
        # search for ancestors of clade
        for (_, ancestor) in queue:
            if clade.issubset(ancestor):
                # update ancestor such that, in the following example:
                # ancestor == {1, 2, 3, 4}
                # clade == {2, 3}
                # new_ancestor == {1, {2, 3}, 4}
                new_ancestor = (ancestor - clade) | frozenset([clade])          
                countdict[new_ancestor] = countdict.pop(ancestor)
                ancestor = new_ancestor
            
            new_queue.append((len(ancestor), ancestor))
   
        # if the clade is a tip, then we have a name
        if clade_size == 1:
            name = list(clade)[0]
            name = namedict[name]
        else:
            name = None 
        
        # the clade will not be in nodes if it is a tip
        children = [nodes.pop(c) for c in clade if c in nodes]
        node = ete3.Tree(name=name)    
        #node = toytree.tree(name=name).tree
        for child in children:
            node.add_child(child)
        if not node.is_leaf():
            node.dist = int(round(100*countdict[clade]))
            node.support = int(round(100*countdict[clade]))
        else:
            node.dist = int(100) 
            node.support = int(100)
        
        nodes[clade] = node
        queue = new_queue
    tre = nodes.values()[0]
    tre.unroot()
    ## return the tree and other trees if present
    return tre, list(nodes.values())
def build_trees(fclade_counts, namedict):
    """ 
    A subfunc of consensus_tree(). Build an unrooted consensus tree 
    from filtered clade counts. 
    """

    ## storage
    nodes = {}
    idxarr = np.arange(len(fclade_counts[0][0]))
    queue = []

    ## create dict of clade counts and set keys
    countdict = defaultdict(int)
    for clade, count in fclade_counts:
        mask = np.int_(list(clade)).astype(np.bool)
        ccx = idxarr[mask]
        queue.append((len(ccx), frozenset(ccx)))
        countdict[frozenset(ccx)] = count

    while queue:
        queue.sort()
        (clade_size, clade) = queue.pop(0)
        new_queue = []
    
        # search for ancestors of clade
        for (_, ancestor) in queue:
            if clade.issubset(ancestor):
                # update ancestor such that, in the following example:
                # ancestor == {1, 2, 3, 4}
                # clade == {2, 3}
                # new_ancestor == {1, {2, 3}, 4}
                new_ancestor = (ancestor - clade) | frozenset([clade])          
                countdict[new_ancestor] = countdict.pop(ancestor)
                ancestor = new_ancestor
            
            new_queue.append((len(ancestor), ancestor))
   
        # if the clade is a tip, then we have a name
        if clade_size == 1:
            name = list(clade)[0]
            name = namedict[name]
        else:
            name = None 
        
        # the clade will not be in nodes if it is a tip
        children = [nodes.pop(c) for c in clade if c in nodes]
        node = ete3.Tree(name=name)    
        #node = toytree.tree(name=name).tree
        for child in children:
            node.add_child(child)
        if not node.is_leaf():
            node.dist = int(round(100*countdict[clade]))
            node.support = int(round(100*countdict[clade]))
        else:
            node.dist = int(100) 
            node.support = int(100)
        
        nodes[clade] = node
        queue = new_queue
    tre = nodes.values()[0]
    tre.unroot()
    ## return the tree and other trees if present
    return tre, list(nodes.values())
def build_trees ( fclade_counts , namedict ) : ## storage nodes = { } idxarr = np . arange ( len ( fclade_counts [ 0 ] [ 0 ] ) ) queue = [ ] ## create dict of clade counts and set keys countdict = defaultdict ( int ) for clade , count in fclade_counts : mask = np . int_ ( list ( clade ) ) . astype ( np . bool ) ccx = idxarr [ mask ] queue . append ( ( len ( ccx ) , frozenset ( ccx ) ) ) countdict [ frozenset ( ccx ) ] = count while queue : queue . sort ( ) ( clade_size , clade ) = queue . pop ( 0 ) new_queue = [ ] # search for ancestors of clade for ( _ , ancestor ) in queue : if clade . issubset ( ancestor ) : # update ancestor such that, in the following example: # ancestor == {1, 2, 3, 4} # clade == {2, 3} # new_ancestor == {1, {2, 3}, 4} new_ancestor = ( ancestor - clade ) | frozenset ( [ clade ] ) countdict [ new_ancestor ] = countdict . pop ( ancestor ) ancestor = new_ancestor new_queue . append ( ( len ( ancestor ) , ancestor ) ) # if the clade is a tip, then we have a name if clade_size == 1 : name = list ( clade ) [ 0 ] name = namedict [ name ] else : name = None # the clade will not be in nodes if it is a tip children = [ nodes . pop ( c ) for c in clade if c in nodes ] node = ete3 . Tree ( name = name ) #node = toytree.tree(name=name).tree for child in children : node . add_child ( child ) if not node . is_leaf ( ) : node . dist = int ( round ( 100 * countdict [ clade ] ) ) node . support = int ( round ( 100 * countdict [ clade ] ) ) else : node . dist = int ( 100 ) node . support = int ( 100 ) nodes [ clade ] = node queue = new_queue tre = nodes . values ( ) [ 0 ] tre . unroot ( ) ## return the tree and other trees if present return tre , list ( nodes . values ( ) )
A subfunc of consensus_tree(). Build an unrooted consensus tree 
    from filtered clade counts.
A subfunc of consensus_tree () . Build an unrooted consensus tree from filtered clade counts .