ImportError for skbio module

Question

I am running Python 3 and have skbio v0.5.5 installed. Following the examples in this tutorial, I am trying to run the import statements for some skbio classes, but am getting errors. For example,

from skbio.alignment import Alignment

results in

ImportError: cannot import name 'Alignment' from 'skbio.alignment'

Also,

from skbio import BiologicalSequence

results in

ImportError: cannot import name 'Alignment' from 'BiologicalSequence'

How do I resolve this?

What version of skbio are you using? These don't seem to exist in the latest version. — Clarence Leung, May 11 '19 at 23:21
I am using the skbio version of 0.5.5. But in this tutorial http://readiab.org/book/0.1.1/1/1, you will see they are seeming to running these modules. — Asad Tan, May 12 '19 at 19:13
Please remember to accept an answer if it helped to solve your problem. Thanks! — Clarence Leung, May 16 '19 at 16:33

score 1 · Accepted Answer · answered May 13 '19 at 14:05

The Alignment class is from an older version of the skbio library, specifically from before version 0.3.

If you would like to use those classes, you would need to install scikit-bio from before that version, by doing something like:

pip install scikit-bio==0.2

If you're just going through the Introduction to Applied Bioinformatics book, like you mentioned in your comment, it's better to use the latest version of the book instead, which will use the latest version of the scikit-bio library.

Thank you very much @Clarence Leung – Asad Tan May 17 '19 at 14:03 — Asad Tan, May 17 '19 at 14:03

ImportError for skbio module

1 Answers1