python ete2从树中删除节点

时间:2013-08-03 03:59:15

标签: regex python-2.7 tree treenode etetoolkit

我正在尝试从给定的树文件中删除一组节点。

Input : tree file+ txt file contains the name of nodes that should only exists in the tree.

这是我的代码:`

def find_id(file,id):

    f= open(file) 
    s = open(file).read()
    if re.search(id,s,re.MULTILINE):
        found= True
    else: 
        found= False
    return found

def remove_nodes(treeFile,idFile):  
        t= Tree(treeFile,format=8)
        removed=[]
        for node in t: 
              #print node.name
              if not find_id(idFile,'^'+node.name+'\s') and node.is_leaf():
                   n= node.delete()
                   removed.append(n)
        print removed
        t.write(format=1, outfile="newtree.nw")

    remove_nodes('arthropods.nw','taxidMap.txt')`

arthropods.nw是一个新的树文件,这是一个摘录:

((260574)58772(874683,874682,874681,874680,874685,874684,1096898,874676,874677,874678,874679)89902(((((61988,390855,109756,62003,374072,244964,146864,251422,388540,438507,681530)61987,(244997,1068629,485196,681527,126872,111303,58784,134582,89817,231264)58783)109754,((289475,390856,118505)118504)118506)61986(((((756952,756950,756951,171369,1053728,231396)171368,(980235)980234,(118484)118483,(126927)126926,(1147029,863609,89974,1255757...

taxidMap.txt:

135631 NC_015190
29137 NC_003314
29139 NC_003322
...

问题是当我打印列表“已删除”时,它给出了一个无列表,我意识到树中的节点数仍然是>输入文件中的名称数量 有什么建议吗? 提前致谢

1 个答案:

答案 0 :(得分:2)

我不确定代码的其余部分是否正常工作,找不到输入文件的例子。 但我发现了这一点,可能会改变:

- removed.append(n)  
+ removed.append(node)

n实际上等于None,因为delete函数不返回任何内容。

pd:顺便提一下@houdini,使用的Tree类记录在那里:http://pythonhosted.org/ete2/reference/reference_tree.html

编辑:

好的,根据你输入的文件,我会改变你的代码:

from ete2 import Tree
import re

def find_id(file,id):

    f= open(file) 
    s = open(file).read()
    if re.search(id,s,re.MULTILINE):
        found= True
    else: 
        found= False
    return found

def remove_nodes(treeFile,idFile):  

    t= Tree(treeFile,format=8)
    print t.get_ascii()
    removed=[]
    for node in t.iter_descendants():
        # print node.name
        if not find_id(idFile,'^'+node.name+'\s'):
            node.delete(prevent_nondicotomic=False)
            removed.append(node)

    print [n.name for n in removed]
    print t.get_ascii()
    t.write(format=1, outfile="newtree.nw")

remove_nodes('arthropods.nw','taxidMap.txt')

我的树文件是:

(58772,89902,((61988,390855)29139,((62003,374072)244964,146864,251422)388540,29137)61987);

和我的ids文件列表:

29137 NC_003314
29139 NC_003322
62003 NC_004444

这里输出:

      /-58772
     |
     |--89902
     |
     |          /-61988
-NoName    /29139
     |    |     \-390855
     |    |
     |    |            /-62003
     |    |      /244964
      \61987    |      \-374072
          |-388540
          |     |--146864
          |     |
          |      \-251422
          |
           \-29137
['58772', '89902', '61987', '388540', '61988', '390855', '244964', '146864', '251422', '374072']

      /-29139
     |
-NoName-29137
     |
      \-62003

EDIT2:

要仅移除树叶,只需删除iter_descendants,就像您一样:

def remove_nodes(treeFile,idFile):

    t= Tree(treeFile,format=8)
    print t
    removed=[]
    for node in t:
        # print node.name
        if not find_id(idFile,'^'+node.name+'\s'):
            node.delete(prevent_nondicotomic=False)
            removed.append(node)

    print [n.name for n in removed]
    print t
    t.write(format=1, outfile="newtree.nw")

然而,在我使用的例子中,结果很糟糕:S ...也许有更多的节点来保持它会更好。

   /-58772
  |
  |--89902
  |
  |      /-61988
--|   /-|
  |  |   \-390855
  |  |
  |  |      /-62003
  |  |   /-|
   \-|  |   \-374072
     |--|
     |  |--146864
     |  |
     |   \-251422
     |
      \-29137
['58772', '89902', '61988', '390855', '374072', '146864', '251422']

      /-29139
     |
-- /-|-- /- /-62003
     |
      \-29137