How To Install python3-pairix on Kali Linux
Introduction
In this tutorial we learn how to install python3-pairix on Kali Linux.
What is python3-pairix
python3-pairix is:
Pairix is a tool for indexing and querying on a block-compressed text file containing pairs of genomic coordinates.
Pairix is a stand-alone C program that was written on top of tabix as a tool for the 4DN-standard pairs file format describing Hi-C data: pairs_format_specification.md
However, Pairix can be used as a generic tool for indexing and querying any bgzipped text file containing genomic coordinates, for either 2D- or 1D- indexing and querying.
For example: given the custom text file below, you want to extract specific lines from the Pairs file further below. An awk command would read the Pairs file from beginning to end. Pairix creates an index and uses it to access the file from a relevant position by taking advantage of bgzf compression, allowing for a fast query on large files.
There are three methods to install python3-pairix on Kali Linux. 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-pairix Using apt-get
Update apt database with apt-get using the following command.
sudo apt-get updateAfter updating apt database, We can install python3-pairix using apt-get by running the following command:
sudo apt-get -y install python3-pairixInstall python3-pairix Using apt
Update apt database with apt using the following command.
sudo apt updateAfter updating apt database, We can install python3-pairix using apt by running the following command:
sudo apt -y install python3-pairixInstall python3-pairix Using aptitude
If you want to follow this method, you might need to install aptitude on Kali Linux first since aptitude is usually not installed by default on Kali Linux. Update apt database with aptitude using the following command.
sudo aptitude updateAfter updating apt database, We can install python3-pairix using aptitude by running the following command:
sudo aptitude -y install python3-pairixHow To Uninstall python3-pairix on Kali Linux
To uninstall only the python3-pairix package we can use the following command:
sudo apt-get remove python3-pairixUninstall python3-pairix And Its Dependencies
To uninstall python3-pairix and its dependencies that are no longer needed by Kali Linux, we can use the command below:
sudo apt-get -y autoremove python3-pairixRemove python3-pairix Configurations and Data
To remove python3-pairix configuration and data from Kali Linux we can use the following command:
sudo apt-get -y purge python3-pairixRemove python3-pairix configuration, data, and all of its dependencies
We can use the following command to remove python3-pairix configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge python3-pairixDependencies
python3-pairix have the following dependencies:
References
Summary
In this tutorial we learn how to install python3-pairix package on Kali Linux using different package management tools: apt, apt-get and aptitude.