3.2.6. Using installed packages

Where are the files installed?

You can use the pip3 show command with the name of the package to identify the path where it is installed:

pip3 show biopython

Output:

Name: biopython
Version: 1.78
Summary: Freely available tools for computational molecular biology.
Home-page: https://biopython.org/
Author: The Biopython Contributors
Author-email: biopython@biopython.org
License: UNKNOWN
Location: /home/user/.local/lib/python3.8/site-packages
Requires: numpy
Required-by:

The installation path will be listed next to the Location keyword.

Using Python packages and modules

Python packages and modules will be installed in $HOME/.local/lib/python3.8/site-packages.

Note

This is the path for Python 3.8.

If you have a different version of Python installed, this value will change.

This directory will be automatically included in $PYTHONPATH. So, you can import and use installed packages and modules in your scripts, without any extra effort.

For example, here is a simple Python script to test BioPython installed using pip:

from Bio.Seq import Seq

seq = Seq('ATGC')
comp = seq.complement()

print(f'The complement of {seq} is {comp}')

The Bio.Seq package is part of BioPython. Copy the code sample above and save it as biopy_test.py. Then run it from the terminal like so:

python3 biopy_test.py

Output:

The complement of ATGC is TACG

Using included commands

If the package includes commands, those will be installed in $HOME/.local/bin directory. For these commands to be easily accessible, you will need to add this directory to PATH, as mentioned under requirements.

As an example, when you install the Python package of cutadapt, the cutadapt command will be installed in $HOME/.local/bin, which you can then run from a terminal like this:

cutadapt --version

Output:

3.1