Convert newick tree to png or jpg image file

[Amine]

Dear,
How can I save newick tree into png or jpg image file using ete
toolkit.
thanks

[Jaime Huerta Cepas]

In short:

from ete2 import Tree
tree = Tree("((a,b),c);")
tree.render("/tmp/my_tree_image.png")

But, there are plenty of more options which are explained in detail in the ETE tutorial and examples (http://ete.cgenomics.org/documentation)

Jaime

[monkey79]

Hi Jaime,

I tried to run the script using the following newick file (see file 1) but does not print my tree into a png image format. Instead the script returns something like in the file 2.

any helps, please?

[Jaime Huerta Cepas]

Hi Barbara, 

the render() function returns a pixel map of the png image. This is what you see in file2 (just ignore it). 

The PNG file will be written into a file, whose name corresponds to the one you provided to the render method. For instance: 

my_img_map = tree.render("myFileName.png")

cheers, 

Jaime

[monkey79]

Hey Jaime, 

sorry again, but the PNG file does not includes my bootstrap values.

how I can include those in my image, please?

thanks

barbara

[monkey79]

I do have one more problem. If I run my script for more than two input files and I ask to print put as PNG, it returns files (see attached files) that I cant open. Strangely if I used t.render ("pdf") it works and I can open the same files without problem.

So at the end what I need to do is produce more than 300 PNG files with bootstrap values.

many thanks

barbara

[Jaime Huerta Cepas]

Hi Barbara,

Your PNG files are empty (0 bytes). Please, attach your script so we can see where is the problem.
Regarding the bootstrap values, see this example: http://packages.python.org/ete2/tutorial/tutorial_drawing.html#show-leaf-node-names-branch-length-and-branch-support

Jaime

[monkey79]

Hi Jaime,

yes I know. Please attached you will find my script (branch_values.py) and my input files(OG2 and OG9). Basically I want to  be able to process my files and save the output as different PNG images for each input, including my bootstrap values.

thank you very much,

barbara

[Salvador Capella]

Hi Barbara,

Let me suggest some changes that could make your script works.

You could format your output filename before calling to the render function. I have modified it as well the name of the output file to include ".png" instead of "_png", on this way the render knows which format you are asking for. Finally, you shall use "tree_style" argument to have the .png similar to the picture you see when you invoke show() method.

    output_filename = os.path.join(output_directory, filename_base+'.tree.png')
    t.render(output_filename, units="px", tree_style = ts)

I hope this helps you.

S

[Jaime Huerta Cepas]

The render() method autodetects image format based on filename extension. As Salva suggests (thanks salva), by making your filename to end as ".png", you will solve the problem.
I take note of this issue, so I can add some warnings when render is not called correctly.

[Jaime Huerta Cepas]

Wait, I have just realized that your problem is not in the render method. You are indeed creating a png file called "files.png", but I don't know why you create an empty file by the end of the script.....
Forget about the "open" line. Use the example that Salva provided.

[monkey79]

Hey there,

thanks so much to both. I changed the script, but I still having the same problem.  I cant open the output file, its saying:"Couldn’t open the file. It may be corrupt or a file format that Preview doesn’t recognize" 

Sorry I do not know how solve it!

thanks

B

[monkey79]

Sorry guys....script fixed!

thanks so much for prompt suggestions and helps, as always!

cheers

B