How To Install seqmagick on Ubuntu

Posted on April 1, 2023  (Last modified on May 20, 2023 )

2 minutes  • 397 words

Introduction

In this tutorial we learn how to install seqmagick on Ubuntu.

What is seqmagick

seqmagick is:

Seqmagick is a little utility to expose the file format conversion in BioPython in a convenient way.

Features include:

• Modifying sequences:
  • Remove gaps
  • Reverse & reverse complement
  • Trim to a range of residues
  • Change case
  • Sort by length or ID
• Displaying information about sequence files
• Subsetting sequence files by:
  • Position
  • ID
  • Deduplication
• Filtering sequences by quality score
• Trimming alignments to a region of interest defined by the forward and reverse primers

There are three methods to install seqmagick 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 seqmagick Using apt-get

Update apt database with apt-get using the following command.

sudo apt-get update

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

sudo apt-get -y install seqmagick

Install seqmagick Using apt

Update apt database with apt using the following command.

sudo apt update

After updating apt database, We can install seqmagick using apt by running the following command:

sudo apt -y install seqmagick

Install seqmagick 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 seqmagick using aptitude by running the following command:

sudo aptitude -y install seqmagick

How To Uninstall seqmagick on Ubuntu

To uninstall only the seqmagick package we can use the following command:

sudo apt-get remove seqmagick

Uninstall seqmagick And Its Dependencies

To uninstall seqmagick and its dependencies that are no longer needed by Ubuntu, we can use the command below:

sudo apt-get -y autoremove seqmagick

Remove seqmagick Configurations and Data

To remove seqmagick configuration and data from Ubuntu we can use the following command:

sudo apt-get -y purge seqmagick

Remove seqmagick configuration, data, and all of its dependencies

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

sudo apt-get -y autoremove --purge seqmagick

Dependencies

seqmagick have the following dependencies:

• python3-biopython
• python3-pygtrie
• python3

References

• seqmagick website

Summary

In this tutorial we learn how to install seqmagick package on Ubuntu using different package management tools: apt, apt-get and aptitude.