gfapy-convert command not found

Introduction

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

gfapy-convert: command not found

or when using sudo you get the following error message

sudo: gfapy-convert: command not found

Solutions to gfapy-convert: command not found

How To Fix gfapy-convert: command not found in Ubuntu / Debian / Kali Linux / Raspbian

In Ubuntu gfapy-convert is provided by python3-gfapy package.

python3-gfapy is:

The Graphical Fragment Assembly (GFA) are formats for the representation of sequence graphs, including assembly, variation and splicing graphs. Two versions of GFA have been defined (GFA1 and GFA2) and several sequence analysis programs have been adopting the formats as an interchange format, which allow the user to easily combine different sequence analysis tools.

This library implements the GFA1 and GFA2 specification. It is possible to create a Gfa object from a file in the GFA format or from scratch, to enumerate the graph elements (segments, links, containments, paths and header lines), to traverse the graph (by traversing all links outgoing from or incoming to a segment), to search for elements (e.g. which links connect two segments) and to manipulate the graph (e.g. to eliminate a link or a segment or to duplicate a segment distributing the read counts evenly on the copies).

The GFA format can be easily extended by users by defining own custom tags and record types. In Gfapy, it is easy to write extensions modules, which allow one to define custom record types and datatypes for the parsing and validation of custom fields. The custom lines can be connected, using references, to each other and to lines of the standard record types.

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

sudo apt-get -y install python3-gfapy

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

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

sudo apt -y install python3-gfapy

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

sudo aptitude install python3-gfapy

Summary

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