axt_to_maf.py command not found

In this troubleshooting guide we learn how to fix axt_to_maf.py command not found error message

Introduction

When you run more command in linux terminal / console, you get the following error message

axt_to_maf.py: command not found

or when using sudo you get the following error message

sudo: axt_to_maf.py: command not found

Solutions to axt_to_maf.py: command not found

How To Fix axt_to_maf.py: command not found in Ubuntu / Debian / Kali Linux / Raspbian

In Ubuntu axt_to_maf.py is provided by python3-bx package.

python3-bx is:

The bx-python project is a Python3 library and associated set of scripts to allow for rapid implementation of genome scale analyses. The library contains a variety of useful modules, but the particular strengths are:

Classes for reading and working with genome-scale multiple local alignments (in MAF, AXT, and LAV formats)
Generic data structure for indexing on disk files that contain blocks of data associated with intervals on various sequences (used, for example, to provide random access to individual alignments in huge files; optimized for use over network filesystems)
Data structures for working with intervals on sequences
“Binned bitsets” which act just like chromosome sized bit arrays, but lazily allocate regions and allow large blocks of all set or all unset bits to be stored compactly
“Intersecter” for performing fast intersection tests that preserve both query and target intervals and associated annotation

To fix this problem, we can install more using the command below.

sudo apt-get -y install python3-bx

This command might take some time to finish depending on your machine internet connection.

You can also use apt command to install python3-bx.

sudo apt -y install python3-bx

Or if you have aptitude installed you can use the following command.

sudo aptitude install python3-bx

Summary

In this tutorial we learn how to fix axt_to_maf.py command not found error in Ubuntu / Debian / Kali Linux or Raspbian distribution.