How To Install python-pyvcf on Ubuntu 18.04
Introduction
In this tutorial we learn how to install python-pyvcf on Ubuntu 18.04.
What is python-pyvcf
python-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 2 modules.
There are three methods to install python-pyvcf on Ubuntu 18.04. We can use apt-get, apt and aptitude. In the following sections we will describe each method. You can choose one of them.
Install python-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 python-pyvcf using apt-get by running the following command:
sudo apt-get -y install python-pyvcf
Install python-pyvcf Using apt
Update apt database with apt using the following command.
sudo apt update
After updating apt database, We can install python-pyvcf using apt by running the following command:
sudo apt -y install python-pyvcf
Install python-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 Ubuntu. Update apt database with aptitude using the following command.
sudo aptitude update
After updating apt database, We can install python-pyvcf using aptitude by running the following command:
sudo aptitude -y install python-pyvcf
How To Uninstall python-pyvcf on Ubuntu 18.04
To uninstall only the python-pyvcf package we can use the following command:
sudo apt-get remove python-pyvcf
Uninstall python-pyvcf And Its Dependencies
To uninstall python-pyvcf and its dependencies that are no longer needed by Ubuntu 18.04, we can use the command below:
sudo apt-get -y autoremove python-pyvcf
Remove python-pyvcf Configurations and Data
To remove python-pyvcf configuration and data from Ubuntu 18.04 we can use the following command:
sudo apt-get -y purge python-pyvcf
Remove python-pyvcf configuration, data, and all of its dependencies
We can use the following command to remove python-pyvcf configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge python-pyvcf
References
Summary
In this tutorial we learn how to install python-pyvcf package on Ubuntu 18.04 using different package management tools: apt, apt-get and aptitude.
