How To Install pyvcf on Ubuntu
Posted on April 1, 2023 (Last modified on May 20, 2023 )
3 minutes • 450 words
Introduction
In this tutorial we learn how to install pyvcf on Ubuntu.
What is pyvcf
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 helper scripts using python3-pyvcf.
There are three methods to install pyvcf on Ubuntu. We can use apt-get, apt and aptitude. In the following sections we will describe each method. You can choose one of them.
Install 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 pyvcf using apt-get by running the following command:
sudo apt-get -y install pyvcf
Install pyvcf Using apt
Update apt database with apt using the following command.
sudo apt update
After updating apt database, We can install pyvcf using apt by running the following command:
sudo apt -y install pyvcf
Install 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 pyvcf using aptitude by running the following command:
sudo aptitude -y install pyvcf
How To Uninstall pyvcf on Ubuntu
To uninstall only the pyvcf package we can use the following command:
sudo apt-get remove pyvcf
Uninstall pyvcf And Its Dependencies
To uninstall pyvcf and its dependencies that are no longer needed by Ubuntu, we can use the command below:
sudo apt-get -y autoremove pyvcf
Remove pyvcf Configurations and Data
To remove pyvcf configuration and data from Ubuntu we can use the following command:
sudo apt-get -y purge pyvcf
Remove pyvcf configuration, data, and all of its dependencies
We can use the following command to remove pyvcf configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge pyvcf
Dependencies
pyvcf have the following dependencies:
References
Summary
In this tutorial we learn how to install pyvcf package on Ubuntu using different package management tools: apt, apt-get and aptitude.