adding source files

src/seq_cluster.sh

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+#!/bin/bash
+
+mkdir tmp
+
+mmseqs easy-linclust iiab_db.fasta iiab_db tmp

src/set_splits.sh

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+#!/bin/bash
+
+grep ">" test.fasta | sed 's/>//;s/[[:space:]].*//' > test_keys.txt
+grep ">" train.fasta | sed 's/>//;s/[[:space:]].*//' > train_keys.txt
+grep ">" val.fasta | sed 's/>//;s/[[:space:]].*//' > validate_keys.txt
+
+awk -F',' '
+	FILENAME == "test_keys.txt" { test[$1]; next }
+	FILENAME == "train_keys.txt" { train[$1]; next }
+	FILENAME == "validate_keys.txt" { validate[$1]; next }
+
+	FILENAME == "iiab_db.csv" {
+		if (FNR == 1) {
+			print $0 > "test_data.csv"
+			print $0 > "train_data.csv"
+			print $0 > "validate_data.csv"
+			next
+		}
+
+		if ($1 in test) {
+			print $0 >> "test_data.csv"
+		} else if ($1 in train) {
+			print $0 >> "train_data.csv"
+		} else if ($1 in validate) {
+			print $0 >> "validate_data.csv"
+		}
+	}
+' test_keys.txt train_keys.txt validate_keys.txt iiab_db.csv
+
+head -n 5 test_keys.txt
+
+rm test_keys.txt train_keys.txt validate_keys.txt
+

src/splitter.py

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+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)