How To Install python3-pyvcf on Debian 9
Introduction
In this tutorial we learn how to install python3-pyvcf on Debian 9.
What is python3-pyvcf
python3-pyvcf is:
The Variant Call Format (VCF) specifies the format of a text file used in bioinformatics for storing gene sequence variations. The format has been developed with the advent of large-scale genotyping and DNA sequencing projects, such as the 1000 Genomes Project.
The intent of this module is to mimic the csv module in the Python
stdlib, as opposed to more flexible serialization formats like JSON or
YAML. vcf will attempt to parse the content of each record based on
the data types specified in the meta-information lines – specifically
the ##INFO and
##FORMAT lines. If these lines are missing or incomplete, it will check
against the reserved types mentioned in the spec. Failing that, it will
just return strings.
This package provides the Python 3 modules.
There are three methods to install python3-pyvcf on Debian 9. 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-pyvcf 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-pyvcf using apt-get by running the following command:
sudo apt-get -y install python3-pyvcf
Install python3-pyvcf Using apt
Update apt database with apt using the following command.
sudo apt update
After updating apt database, We can install python3-pyvcf using apt by running the following command:
sudo apt -y install python3-pyvcf
Install python3-pyvcf 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-pyvcf using aptitude by running the following command:
sudo aptitude -y install python3-pyvcf
How To Uninstall python3-pyvcf on Debian 9
To uninstall only the python3-pyvcf package we can use the following command:
sudo apt-get remove python3-pyvcf
Uninstall python3-pyvcf And Its Dependencies
To uninstall python3-pyvcf and its dependencies that are no longer needed by Debian 9, we can use the command below:
sudo apt-get -y autoremove python3-pyvcf
Remove python3-pyvcf Configurations and Data
To remove python3-pyvcf configuration and data from Debian 9 we can use the following command:
sudo apt-get -y purge python3-pyvcf
Remove python3-pyvcf configuration, data, and all of its dependencies
We can use the following command to remove python3-pyvcf configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge python3-pyvcf
Dependencies
python3-pyvcf have the following dependencies:
References
Summary
In this tutorial we learn how to install python3-pyvcf package on Debian 9 using different package management tools: apt, apt-get and aptitude.