How To Install python3-pybigwig on Debian 12
Introduction
In this tutorial we learn how to install python3-pybigwig on Debian 12.
What is python3-pybigwig
python3-pybigwig is:
This is a Python extension, written in C, for quick access to bigBed files, and access to and creation of bigWig files.
The bigWig format was originally created in the context of genome
browsers. There, computing exact summary statistics for a given interval
is less important than quickly being able to compute an approximate
statistic. Because of this, bigWig files contain not only interval-value
associations, but also sum of values/sum of squared values/minimum value/maximum value/number of bases covered for equally sized
bins of various sizes. These different sizes are referred to as “zoom
levels”. The smallest zoom level has bins that are 16 times the mean
interval size in the file and each subsequent zoom level has bins 4 times
larger than the previous. This methodology is used in Kent’s tools and,
therefore, likely used in almost every currently existing bigWig file.
When a bigWig file is queried for a summary statistic, the size of the interval is used to determine whether to use a zoom level and, if so, which one. The optimal zoom level is that which has the largest bins no more than half the width of the desired interval. If no such zoom level exists, the original intervals are instead used for the calculation.
There are three methods to install python3-pybigwig on Debian 12. We can use apt-get, apt and aptitude. In the following sections we will describe each method. You can choose one of them.
Install python3-pybigwig Using apt-get
Update apt database with apt-get using the following command.
sudo apt-get update
After updating apt database, We can install python3-pybigwig using apt-get by running the following command:
sudo apt-get -y install python3-pybigwig
Install python3-pybigwig Using apt
Update apt database with apt using the following command.
sudo apt update
After updating apt database, We can install python3-pybigwig using apt by running the following command:
sudo apt -y install python3-pybigwig
Install python3-pybigwig Using aptitude
If you want to follow this method, you might need to install aptitude first since aptitude is usually not installed by default on Debian. Update apt database with aptitude using the following command.
sudo aptitude update
After updating apt database, We can install python3-pybigwig using aptitude by running the following command:
sudo aptitude -y install python3-pybigwig
How To Uninstall python3-pybigwig on Debian 12
To uninstall only the python3-pybigwig package we can use the following command:
sudo apt-get remove python3-pybigwig
Uninstall python3-pybigwig And Its Dependencies
To uninstall python3-pybigwig and its dependencies that are no longer needed by Debian 12, we can use the command below:
sudo apt-get -y autoremove python3-pybigwig
Remove python3-pybigwig Configurations and Data
To remove python3-pybigwig configuration and data from Debian 12 we can use the following command:
sudo apt-get -y purge python3-pybigwig
Remove python3-pybigwig configuration, data, and all of its dependencies
We can use the following command to remove python3-pybigwig configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge python3-pybigwig
Dependencies
python3-pybigwig have the following dependencies:
References
Summary
In this tutorial we learn how to install python3-pybigwig package on Debian 12 using different package management tools: apt, apt-get and aptitude.
