Add script for expanding the alignment dir with duplicates

This adds support for duplicate chain expansion for the alignment dir format. This script can be run on the flattened non-redundant RODA alignments to add explicit directories for all of the duplicate chains in the duplicate_chains file, symlinked to their representative chain alignment directory.

scripts/expand_roda_duplicates.py

+"""
+The RODA database is non-redundant, meaning that it only stores one explicit
+representative alignment directory for all PDB chains in a 100% sequence
+identity cluster. In order to add explicit alignments for all PDB chains, this
+script will add the missing chain directories and symlink them to their
+representative alignment directories.
+"""
+
+from argparse import ArgumentParser
+from pathlib import Path
+
+from tqdm import tqdm
+
+
+def create_duplicate_dirs(duplicate_chains: list[list[str]], alignment_dir: Path):
+    """
+    Create duplicate directory symlinks for all chains in the given duplicate lists.
+
+    Args:
+        duplicate_lists (list[list[str]]): A list of lists, where each inner list
+            contains chains that are 100% sequence identical.
+        alignment_dir (Path): Path to flattened alignment directory, with one
+            subdirectory per chain.
+    """
+    print("Creating duplicate directory symlinks...")
+    dirs_created = 0
+    for chains in tqdm(duplicate_chains):
+        # find the chain that has an alignment
+        for chain in chains:
+            if (alignment_dir / chain).exists():
+                representative_chain = chain
+                break
+        else:
+            print(f"No representative chain found for {chains}, skipping...")
+            continue
+
+        # create symlinks for all other chains
+        for chain in chains:
+            if chain != representative_chain:
+                target_path = alignment_dir / chain
+                if target_path.exists():
+                    print(f"Chain {chain} already exists, skipping...")
+                else:
+                    (target_path).symlink_to(alignment_dir / representative_chain)
+                    dirs_created += 1
+
+    print(f"Created directories for {dirs_created} duplicate chains.")
+
+
+def main(alignment_dir: Path, duplicate_chains_file: Path):
+    # read duplicate chains file
+    with open(duplicate_chains_file, "r") as fp:
+        duplicate_chains = [list(line.strip().split()) for line in fp]
+
+    create_duplicate_dirs(duplicate_chains, alignment_dir)
+
+
+if __name__ == "__main__":
+    parser = ArgumentParser(description=__doc__)
+    parser.add_argument(
+        "alignment_dir",
+        type=Path,
+        help="""Path to flattened alignment directory, with one subdirectory 
+                per chain.""",
+    )
+    parser.add_argument(
+        "duplicate_chains_file",
+        type=Path,
+        help="""Path to file containing duplicate chains, where each line
+                contains a space-separated list of chains that are 100%%
+                sequence identical.
+                """,
+    )
+    args = parser.parse_args()
+    main(args.alignment_dir, args.duplicate_chains_file)