How to pass variable filename to python ete?

Question

I am trying load newick string from a file using following code:

filename = templist[1].lower().replace(" ","") + ".nwk"
tt = Tree(filename, format=1)

but getting following error:

 tt = Tree(filename, format=1) # Loads a tree structure from a newick string. The returned variable tt is the root node for the tree.
  File "/python2.7/dist-packages/ete2-2.2.1072-py2.7.egg/ete2/coretype/tree.py", line 225, in __init__
    read_newick(newick, root_node = self, format=format)
  File "/python2.7/dist-packages/ete2-2.2.1072-py2.7.egg/ete2/parser/newick.py", line 237, in read_newick
    'Unexisting tree file or Malformed newick tree structure.'
ete2.parser.newick.NewickError: Unexisting tree file or Malformed newick tree structure.

I have verified the file format, and it is Ok. I think I am passing the variable in wrong way, can you please guide me to pass filename as variable.

When I pass the filename as string without using variable it is working fine, but I need to use variable value to load tree.

Answer 1

Are you sure the format=1 is correct?

According to documentation -

for named internal nodes we will use format 1

Are you sure your newick tree has named internal nodes? If not, try without passing any value to the format argument.

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Also, please make sure that the filename is either absolute path to the file, or if its relative path , for example a.nwk , then make sure the file exists in the directory from which you are running the python script.