looks like you are referring to https://gsds.gao-lab.org/

the example 'bed file' they give is quite unconventional

this script that I used gemini to create tries to convert gff3 into this 'bed file' type format. there are probably other considerations but ultimately you might consider using other software for plotting the gene structure, like R https://dzhang32.github.io/ggtranscript/

import sys

def convert_gff3_to_bed(input_file):
    with open(input_file, 'r') as f:
        for line in f:
            # Skip comments and empty lines
            if line.startswith('#') or not line.strip():
                continue

            parts = line.strip().split('\t')
            if len(parts) < 9:
                continue

            # Extract GFF3 columns
            seqid = parts[0]
            feature_type = parts[2]
            start = int(parts[3])
            end = int(parts[4])
            phase = parts[7]

            # Adjust to 0-based start for BED style
            # GFF [start, end] -> BED [start-1, end)
            bed_start = start - 1
            bed_end = end

            # Format the output (seqid, start, end, feature, phase)
            # We use '.' if the phase is undefined/empty
            out_phase = phase if phase != '.' else '.'

            print(f"{seqid}\t{bed_start}\t{bed_end}\t{feature_type}\t{out_phase}")

if __name__ == "__main__":
    # Usage: python script.py your_file.gff3
    if len(sys.argv) > 1:
        convert_gff3_to_bed(sys.argv[1])
    else:
        print("Please provide a GFF3 file path.")