import pandas as pd from Bio import SeqIO def run_full_split_workflow(tsv_path, fasta_path, train_pct=0.6, val_pct=0.2, test_pct=0.2): df = pd.read_csv(tsv_path, sep='\t', names=['rep', 'member']) cluster_groups = df.groupby('rep')['member'].apply(list).to_dict() sorted_reps = sorted(cluster_groups.keys(), key=lambda x: len(cluster_groups[x]), reverse=True) total_seqs = len(df) targets = {'train': total_seqs * train_pct, 'val': total_seqs * val_pct, 'test': total_seqs * test_pct} split_ids = {'train': set(), 'val': set(), 'test': set()} counts = {'train': 0, 'val': 0, 'test': 0} for rep in sorted_reps: members = cluster_groups[rep] deficit = {k: targets[k] - counts[k] for k in split_ids.keys()} best_fit = max(deficit, key=deficit.get) split_ids[best_fit].update(members) counts[best_fit] += len(members) files = {k: open(f"{k}.fasta", "w") for k in split_ids.keys()} written_counts = {k: 0 for k in split_ids.keys()} for record in SeqIO.parse(fasta_path, "fasta"): for split_name, id_set in split_ids.items(): if record.id in id_set: SeqIO.write(record, files[split_name], "fasta") written_counts[split_name] += 1 break for f in files.values(): f.close() mmseqs_tsv = "iiab_db_cluster.tsv" fasta = "iiab_db.fasta" run_full_split_workflow(mmseqs_tsv, fasta)