blat2gff command not found

In this troubleshooting guide we learn how to fix blat2gff command not found error message

Introduction

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

blat2gff: command not found

or when using sudo you get the following error message

sudo: blat2gff: command not found

Solutions to blat2gff: command not found

How To Fix blat2gff: command not found in Ubuntu / Debian / Kali Linux / Raspbian

In Ubuntu blat2gff is provided by gff2aplot package.

gff2aplot is:

A program to visualize the alignment of two genomic sequences together with their annotations. From GFF-format input files it produces PostScript figures for that alignment. The following menu lists many features of gff2aplot:

  • Comprehensive alignment plots for any GFF-feature. Attributes are defined separately so you can modify only whatsoever attributes for a given file or share same customization across different data-sets.
  • All parameters are set by default within the program, but it can be also fully configured via gff2ps-like flexible customization files. Program can handle several of such files, summarizing all the settings before producing the corresponding figure. Moreover, all customization parameters can be set via command-line switches, which allows users to play with those parameters before adding any to a customization file.
  • Source order is taken from input files, if you swap file order you can visualize alignment and its annotation with the new input arrangement.
  • All alignment scores can be visualized in a PiP box below gff2aplot area, using grey-color scale, user-defined color scale or score-dependent gradients.
  • Scalable fonts, which can also be chosen among the basic PostScript default fonts. Feature and group labels can be rotated to improve readability in both annotation axes.
  • The program is still defined as a Unix filter so it can handle data from files, redirections and pipes, writing output to standard-output and warnings to standard error.
  • gff2aplot is able to manage many physical page formats (from A0 to A10, and more -see available page sizes in its manual-), including user-defined ones. This allows, for instance, the generation of poster size genomic maps, or the use of a continuous-paper supporting plotting device, either in portrait or landscape.
  • You can draw different alignments on same alignment plot and distinguish them by using different colors for each.
  • Shape dictionary has been expanded, so that further feature shapes are now available (see manual).
  • Annotation projections through alignment plots (so called ribbons) emulate transparencies via complementary color fill patterns. This feature allows one to show color pseudo-blending when horizontal and vertical ribbons overlap.

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

sudo apt-get -y install gff2aplot

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

You can also use apt command to install gff2aplot.

sudo apt -y install gff2aplot

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

sudo aptitude install gff2aplot

Summary

In this tutorial we learn how to fix blat2gff command not found error in Ubuntu / Debian / Kali Linux or Raspbian distribution.