longest_transcript.pl

Selects the transcript with the longest total CDS length for each gene from a GFF3 annotation file.

The script:

1. Reads mRNA and CDS features from a GFF3 file.
2. Groups transcripts according to the Parent attribute.
3. Calculates the total CDS length of each transcript.
4. Retains the transcript with the longest CDS for each gene.
5. Outputs the selected mRNA and CDS annotation lines as a new GFF3 file.

Requirements

• Perl
• GFF3 annotation file
• gffread for extracting peptide sequences

The GFF3 file should contain:

• mRNA features with ID and Parent
• CDS features with Parent
• mRNA features should appear before their corresponding CDS features

Usage

perl longest_transcript.pl input.gff3 > longest_transcript.gff3

gffread longest_isoform.gff3 \
    -g input.fa \
    -y longest_isoform.pep.fa

## Notes
This script selects transcripts according to total CDS length rather than total transcript length. It is intended for extracting one representative protein-coding transcript per gene.
The script does not retain the original `gene`, `exon`, `UTR`, or other annotation features unless they are explicitly printed by the script.