I'm trying to remove a set of nodes from a given tree file.
Input : tree file+ txt file contains the name of nodes that should only exists in the tree.
this is my code: `
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 is a newick tree file this is an extract:
((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
...
the problem is when I print the list "removed" it gives me a list of none, and I realise that the number of nodes in the tree is still > of the number of names in the input file any suggestion ? Thanks in advance
I am not sure if the rest of the code is working find whithout examples of the input files. But I found this, that may be changed:
- removed.append(n)
+ removed.append(node)
n is actually equal to None, as the delete function does not return anything.
pd: by the way for @houdini , the Tree class used is documented there: http://pythonhosted.org/ete2/reference/reference_tree.html
EDIT:
Ok, according to you input files, I would change your codelike this:
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')
my tree file is:
(58772,89902,((61988,390855)29139,((62003,374072)244964,146864,251422)388540,29137)61987);
and my list of ids file:
29137 NC_003314
29139 NC_003322
62003 NC_004444
And here the output:
/-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:
To remove only leaves, just remove the iter_descendants, part, just as you were doing:
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")
However in the example I am using the result is quite uggly :S ... perhaps with more nodes to keep it would be nicer.
/-58772
|
|--89902
|
| /-61988
--| /-|
| | \-390855
| |
| | /-62003
| | /-|
\-| | \-374072
|--|
| |--146864
| |
| \-251422
|
\-29137
['58772', '89902', '61988', '390855', '374072', '146864', '251422']
/-29139
|
-- /-|-- /- /-62003
|
\-29137