How To Install python-pyfaidx on Ubuntu 18.04
Introduction
In this tutorial we learn how to install python-pyfaidx on Ubuntu 18.04.
What is python-pyfaidx
python-pyfaidx is:
Samtools provides a function “faidx” (FAsta InDeX), which creates a small flat index file “.fai” allowing for fast random access to any subsequence in the indexed FASTA file, while loading a minimal amount of the file in to memory. This Python module implements pure Python classes for indexing, retrieval, and in-place modification of FASTA files using a samtools compatible index. The pyfaidx module is API compatible with the pygr seqdb module. A command-line script “faidx” is installed alongside the pyfaidx module, and facilitates complex manipulation of FASTA files without any programming knowledge.
This package provides the Python 2 modules to access fasta files.
There are three methods to install python-pyfaidx 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-pyfaidx 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-pyfaidx using apt-get by running the following command:
sudo apt-get -y install python-pyfaidx
Install python-pyfaidx Using apt
Update apt database with apt using the following command.
sudo apt update
After updating apt database, We can install python-pyfaidx using apt by running the following command:
sudo apt -y install python-pyfaidx
Install python-pyfaidx 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-pyfaidx using aptitude by running the following command:
sudo aptitude -y install python-pyfaidx
How To Uninstall python-pyfaidx on Ubuntu 18.04
To uninstall only the python-pyfaidx package we can use the following command:
sudo apt-get remove python-pyfaidx
Uninstall python-pyfaidx And Its Dependencies
To uninstall python-pyfaidx and its dependencies that are no longer needed by Ubuntu 18.04, we can use the command below:
sudo apt-get -y autoremove python-pyfaidx
Remove python-pyfaidx Configurations and Data
To remove python-pyfaidx configuration and data from Ubuntu 18.04 we can use the following command:
sudo apt-get -y purge python-pyfaidx
Remove python-pyfaidx configuration, data, and all of its dependencies
We can use the following command to remove python-pyfaidx configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge python-pyfaidx
References
Summary
In this tutorial we learn how to install python-pyfaidx package on Ubuntu 18.04 using different package management tools: apt, apt-get and aptitude.
