How To Install python3-cyvcf2 on Debian 10

Learn how to install python3-cyvcf2 on Debian 10 with this tutorial. python3-cyvcf2 is VCF parser based on htslib (Python 3)

Introduction

In this tutorial we learn how to install python3-cyvcf2 on Debian 10.

What is `python3-cyvcf2`

python3-cyvcf2 is:

This modules allows fast parsing of VCF and BCF including region-queries with Python. This is essential for efficient analyses of nucleotide variation with Python on high-throughput sequencing data.

cyvcf2 is a cython wrapper around htslib. Attributes like variant.gt_ref_depths return a numpy array directly so they are immediately ready for downstream use.

This package installs the library for Python 3.

There are three methods to install python3-cyvcf2 on Debian 10. 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-cyvcf2 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-cyvcf2 using apt-get by running the following command:

sudo apt-get -y install python3-cyvcf2

Install python3-cyvcf2 Using apt

Update apt database with apt using the following command.

sudo apt update

After updating apt database, We can install python3-cyvcf2 using apt by running the following command:

sudo apt -y install python3-cyvcf2

Install python3-cyvcf2 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-cyvcf2 using aptitude by running the following command:

sudo aptitude -y install python3-cyvcf2

How To Uninstall python3-cyvcf2 on Debian 10

To uninstall only the python3-cyvcf2 package we can use the following command:

sudo apt-get remove python3-cyvcf2

Uninstall python3-cyvcf2 And Its Dependencies

To uninstall python3-cyvcf2 and its dependencies that are no longer needed by Debian 10, we can use the command below:

sudo apt-get -y autoremove python3-cyvcf2

Remove python3-cyvcf2 Configurations and Data

To remove python3-cyvcf2 configuration and data from Debian 10 we can use the following command:

sudo apt-get -y purge python3-cyvcf2

Remove python3-cyvcf2 configuration, data, and all of its dependencies

We can use the following command to remove python3-cyvcf2 configurations, data and all of its dependencies, we can use the following command:

sudo apt-get -y autoremove --purge python3-cyvcf2

Dependencies

python3-cyvcf2 have the following dependencies:

References

Summary

In this tutorial we learn how to install python3-cyvcf2 package on Debian 10 using different package management tools: apt, apt-get and aptitude.