Example of running mothur within an IPython notebook.

All code available at https://github.com/SchlossLab/ipython-mothurmagic

Prerequisites

mothur must be installed on your system and either in your path or in the directory where IPython is running. See http://www.mothur.org/wiki/Download_mothur to download a copy of mothur.

Installation



In [1]:

    
%install_ext https://raw.githubusercontent.com/SchlossLab/ipython-mothurmagic/master/mothurmagic.py









    



Installed mothurmagic.py. To use it, type:
  %load_ext mothurmagic

Load the extention



In [2]:

    
%load_ext mothurmagic

Running mothur commands

Example using data from http://www.mothur.org/w/images/3/37/AmazonData.zip A unique log file will be generated each time a %%mothur cell is executed.



In [3]:

    
%%mothur
cluster(phylip=AmazonData/98_sq_phylip_amazon.dist, cutoff=0.1)
collect.single()
rarefaction.single()









    



mothur > cluster(phylip=AmazonData/98_sq_phylip_amazon.dist, cutoff=0.1)
********************#****#****#****#****#****#****#****#****#****#****#
Reading matrix:     |||||||||||||||||||||||||||||||||||||||||||||||||||
***********************************************************************
changed cutoff to 0.069234

Output File Names:
AmazonData/98_sq_phylip_amazon.an.sabund
AmazonData/98_sq_phylip_amazon.an.rabund
AmazonData/98_sq_phylip_amazon.an.list

It took 0 seconds to cluster

mothur > collect.single()
Using AmazonData/98_sq_phylip_amazon.an.list as input file for the list parameter.
unique
0.01
0.02
0.03
0.04
0.05
0.06

Output File Names:
AmazonData/98_sq_phylip_amazon.an.sobs
AmazonData/98_sq_phylip_amazon.an.chao
AmazonData/98_sq_phylip_amazon.an.ace
AmazonData/98_sq_phylip_amazon.an.jack
AmazonData/98_sq_phylip_amazon.an.shannon
AmazonData/98_sq_phylip_amazon.an.npshannon
AmazonData/98_sq_phylip_amazon.an.simpson


mothur > rarefaction.single()
Using AmazonData/98_sq_phylip_amazon.an.list as input file for the list parameter.

Using 1 processors.
unique
0.01
0.02
0.03
0.04
0.05
0.06

Output File Names:
AmazonData/98_sq_phylip_amazon.an.rarefaction


mothur > quit()



In [3]: