feat: add rewrite_fasta tool

Port rewrite_fasta.py from human-diversity-reference/scripts as a
defopt-compatible toolkit tool. Filters a FASTA file to keep only
canonical chromosomes (chr1-22, X, Y, MT). Fixes a potential
UnboundLocalError by initialising keep=False before the loop and
removes the unused header_line variable from the original.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

Author: ameynert

divref/divref/tools/rewrite_fasta.py

@@ -0,0 +1,30 @@
+"""Tool to filter a FASTA file to canonical chromosomes only."""
+
+from pathlib import Path
+
+import tqdm
+
+
+def rewrite_fasta(*, fasta_path: Path, output_path: Path) -> None:
+    """
+    Rewrite a FASTA file keeping only canonical chromosomes (chr1-22, X, Y, MT).
+
+    Filters out alt contigs, decoy sequences, and any other non-canonical sequences.
+    Reads the input file line by line so it can handle arbitrarily large FASTA files.
+
+    Args:
+        fasta_path: Path to the input FASTA file.
+        output_path: Path to write the filtered FASTA file.
+    """
+    contigs_to_keep = {f"chr{i}" for i in range(1, 23)} | {"chrX", "chrY", "chrMT"}
+
+    keep = False
+    with open(fasta_path) as f, open(output_path, "w") as out:
+        for line in tqdm.tqdm(f):
+            if line[0] == ">":
+                contig = line.split()[0][1:]
+                keep = contig in contigs_to_keep
+                if keep:
+                    out.write(line)
+            elif keep:
+                out.write(line)