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.

filename = templist[1].lower().replace(" ","") - this is just computed from list, and gets a string with only a-z chars — AJINKYA, Jun 20 '15 at 05:22
Can you print out the filename and check if it does give you the result you want? — Anand S Kumar, Jun 20 '15 at 05:25
Yes i did, its working correctly, i even used the filename and checked if tree structure is fine. — AJINKYA, Jun 20 '15 at 05:26

Anand S Kumar · Accepted Answer · 2015-06-20T05:38:47.800

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.

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.

edited Jun 20 '15 at 05:38

answered Jun 20 '15 at 05:31

Anand S Kumar

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Yes, its all working fine with string. Pretty sure problem is with the way variable is being passed – AJINKYA Jun 20 '15 at 05:33
templist = ['00Outdoor', 'TENNIS'] filename = tennis.nwk – AJINKYA Jun 20 '15 at 05:36
1

are you sure it is in the same folder , from where you are running the script? – Anand S Kumar Jun 20 '15 at 05:38
Yes, thanks its working now, code was running in loop and one file was not in same folder. – AJINKYA Jun 20 '15 at 05:53

How to pass variable filename to python ete?

1 Answers1