Convert GFF3 file to GTF2.5

gff2gtf.sh

#!/bin/bash

########## Anuj Sharma      ##########
########## [email protected] ##########
########## github/rknx      ##########
########## 2022/01/04       ##########

[[ -z "$1" ]] && echo "Usage: gff2gtf.sh in.gff > out.gtf" >&2 && exit
[[ ! -s "$1" ]] && echo "Provide valid input file" >&2 && exit

# Remove everything (the sequences) starting with ##FASTA
# Remove contig names
# Simplify second column
# Change ID to gene_id, tRNA to transcript, and format 9th column
# only keep valid entries for 3rd column

sed -n '/##FASTA/q;p' $1 | \
    grep -v "^##" | \
    awk -vFS="\t" -vOFS="\t" '{split($2, a, ":"); $2=a[1]; print $0}' | \
    sed 's/ID=/gene_id=/g; s/=/ "/g; s/;/"; /g; s/$/"/g; s/tRNA/transcript/g' | \
    grep -E "gene|transcript|exon|CDS|UTR|start_codon|stop_codon|Selenocysteine"