eggnog-mapper_COGextraction

Introduction

• Extraction of COG functional classes and save the data in csv format for downstream analysis
• This works on the annotated file ends with ".emapper.annotations" generated by eggnog-mapper (https://github.com/jhcepas/eggnog-mapper).
• This is a simple shell script written for the convenience of extracting COG classes and save it in csv format for downstream analysis and visualisation.
• script extract_COG_local.sh can be used for annotation files generated using local machine while extract_COG_web.sh can be used for web version annotations.

Usage

% ./extract_COG_local.sh FILENAME

• This will generate the final extracted file FILENAME-COG-final.csv with column 1 the COG classes and column 2 is the hit counts (separated by commas).