Using Mothur in an IPython Notebook

Hi Forum,

I’m new here, so I hope that this the right place to put this. I am also new to Mother, but I have been using IPython for a while now. I saw this tweet the tweet:

I downloaded the software from here:

But, I can’t seem to get it working.
When I try to execute a command, for example:

%%mothur cluster(help)

I get the error message:

"Can’t open mothur: Permission denied”

However, the command ls -l indicates that I have full permission:

-rwxr-xr-x@ 1 USER staff 17728780 Apr 5 11:31 mother

Does anyone know what I need to do so that I can use this magic?

Is your executable mother (as written in the output) or mothur? We expect mothur :slight_smile:

Haha, it should have said “Mothur”. My browser still autocorrects mothur to mother. I bet you guys get that a lot.
The corrected line:
drwxr-xr-x@ 9 sanglab staff 306 Apr 17 12:12 mothur

Thank you for your reply by the way.

Can you execute mothur from the command line outside of the notebook fine? All that ipython-mothurmagic does is issue a system subprocess call so if you can open mothur from the command line then the notebook should also be able to open it… ipython-mothurmagic expects mothur to either be in your path or in the directory that you are running the notebook from.

Also, for when you do get it working, ipython-mothurmagic does cell magic not line magic. So:

%%mothur mothur.command(help)

That won’t work, but:


That will work. Also note mothur’s current variables won’t persist across notebook cells or sessions. If you want current variables to persist you can use my fork available here.

I had moved the Mothur directory into the folder with my notebooks, that was the problem :roll: . I just now made a new notebook inside the Mothur folder and it worked perfectly. Thanks for your help and for your reply. I think Mothur is a great product and I will recommend it to all of my friends (who do this kind of work). :geek:

Glad you got it working! :smiley: