python - Phylo BioPython 构建树

Question

我正在尝试使用 BioPython、Phylo 模块构建一棵树。
到目前为止我所做的是这张图片:

每个名称都有一个四位数字，后跟 - 和一个数字:这个数字指的是该序列出现的次数。这意味着 1578 - 22，该节点应表示 22 个序列。

序列对齐的文件:file
构建树的距离文件:file

所以现在我知道如何更改节点的每个大小。每个节点都有不同的大小，这很容易做一个不同值的数组:

    fh = open(MEDIA_ROOT + "groupsnp.txt")    
    list_size = {}
    for line in fh:
        if '>' in line:
            labels = line.split('>')
            label = labels[-1]
            label = label.split()
            num = line.split('-')
            size = num[-1]
            size = size.split()
            for lab in label:
                for number in size:
                    list_size[lab] = int(number)

    a = array(list_size.values())

但数组是任意的，我想将正确的节点大小放入正确的节点中，我试过这个:

         for elem in list_size.keys():
             if labels == elem:
                 Phylo.draw_graphviz(tree_xml, prog="neato", node_size=a)

但是当我使用 if 语句时什么也没有出现。

无论如何都要这样做？

非常感谢!

谢谢大家

Answer 1

我终于搞定了。基本前提是您将使用 labels/nodelist 构建您的 node_sizes。这样它们就可以正确关联。我确定我遗漏了一些使树看起来 100% 的重要选项，但节点大小显示正确。

#basically a stripped down rewrite of Phylo.draw_graphviz
import networkx, pylab
from Bio import Phylo


#taken from draw_graphviz
def get_label_mapping(G, selection): 
    for node in G.nodes(): 
        if (selection is None) or (node in selection): 
            try: 
                label = str(node) 
                if label not in (None, node.__class__.__name__): 
                    yield (node, label) 
            except (LookupError, AttributeError, ValueError): 
                pass


kwargs={}
tree = Phylo.read('tree.dnd', 'newick')
G = Phylo.to_networkx(tree)
Gi = networkx.convert_node_labels_to_integers(G, discard_old_labels=False)

node_sizes = []
labels = dict(get_label_mapping(G, None))
kwargs['nodelist'] = labels.keys()

#create our node sizes based on our labels because the labels are used for the node_list
#this way they should be correct
for label in labels.keys():
    if str(label) != "Clade":
        num = label.name.split('-')
        #the times 50 is just a guess on what would look best
        size = int(num[-1]) * 50
        node_sizes.append(size)

kwargs['node_size'] = node_sizes
posi = networkx.pygraphviz_layout(Gi, 'neato', args='') 
posn = dict((n, posi[Gi.node_labels[n]]) for n in G) 

networkx.draw(G, posn, labels=labels, node_color='#c0deff', **kwargs)

pylab.show()

结果树