Phylo BioPython建筑树

Question

我试图建立与BioPython，Phylo模块一棵树。结果 我到目前为止所做的就是这一形象：

每个名字具有四位数字后跟 - 和一个数字：这个数目指的是序列表示的次数。这意味着1578 - 22，该节点应该代表22sequences

与所述序列文件对准：文件结果 随着距离的文件建立一个树：文件

所以，现在我知道如何到节点的每个尺寸改变。每个节点具有不同的尺寸，这是很容易做的不同的值的数组：

    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())

但是，阵列是任意的，我想放正确的节点尺寸为右节点，我试图这样：

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

但没有出现，当我使用if语句。

反正这样做的？

我真的很感激！

谢谢大家

Answer 1

我终于得到了这个工作。基本的前提是，你要使用labels/nodelist建立你node_sizes。这样，他们正确关联。我敢肯定，我错过了一些重要的选项，使树看起来100％，但它出现的节点尺寸是否正确显示出来。

#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()

产生的树