PERMANOVA analysis in Jupyter notebook

[malenaamer (Malena)]

Hello,

I'm new to programing but Jupyter notebook is helping me keep track.

Is there a way to obtain the beta diversity PERMANOVA results different from the .qzv file using Python?

I tried using:

from skbio.stats.distance import DistanceMatrix
from skbio.stats.ordination import permanova

however, it seems that the permanova function is no longer supported, is this true?

ImportError: cannot import name 'permanova' from 'skbio.stats.ordination' (/Users/user/miniconda3/envs/qiime2-2021.11/lib/python3.8/site-packages/skbio/stats/ordination/__init__.py)

Thanks in advance,
Malena

[crusher083 (Valentyn Bezshapkin)]

Please, check the version of software and docs you are using.
Version 0.5.2 permanova is located in skbio.stats.distance module.
http://scikit-bio.org/docs/0.5.2/generated/generated/skbio.stats.distance.permanova.html

Cheers,
V

[malenaamer (Malena)]

Thank you for your quick response!
I'm using version 5.6, and this is what prints when I ask for the directory:

0.5.6 ['DNA', 'DistanceMatrix', 'GeneticCode', 'OrdinationResults', 'Protein', 'RNA', 'Sequence', 'TabularMSA', 'TreeNode', '__all__', '__builtins__', '__cached__', '__credits__', '__doc__', '__file__', '__loader__', '__name__', '__package__', '__path__', '__spec__', '__version__', '_base', 'alignment', 'art', 'diversity', 'io', 'local_pairwise_align_ssw', 'metadata', 'motto', 'mottos', 'nj', 'read', 'sequence', 'skbio', 'stats', 'title', 'tree', 'util', 'write']

In [ ]:

Do I need to install the older version?
​

[crusher083 (Valentyn Bezshapkin)]

Please, check the documentation for the respective version:
http://scikit-bio.org/docs/0.5.6/generated/skbio.stats.distance.permanova.html?highlight=permanova#skbio.stats.distance.permanova

Cheers