2026-08-02

99.scripts/miscs/make_bpp_seq.py

@@ -0,0 +1,84 @@
+#!/usr/bin/env python
+"""
+Prepare input sequence file from fasta file in a directory for BPP.
+"""
+
+import argparse
+import sys
+from pathlib import Path
+from Bio import SeqIO
+
+
+def get_fasta_files(input_dir: Path, ext=".fasta") -> list[Path]:
+    """
+    Get a list of fasta files in the specified directory with the given extension.
+    Args:
+        input_dir (Path): Path to the directory containing fasta files.
+        ext (str): Extension of the fasta files.
+    Returns:
+        list[Path]: List of Paths to the fasta files.
+    """
+    files = list(input_dir.glob(f"*{ext}"))
+    if not files:
+        print(f"No fasta files with extension '{ext}' found in directory '{input_dir}'")
+        sys.exit(1)
+    return files
+
+
+def transform_fasta_to_bpp(fasta_file: Path):
+    """
+    Transform a fasta file into BPP sequence format.
+    Args:
+        fasta_file (Path): Path to the input fasta file.
+    Returns:
+        list[str]: Lines formatted for BPP input.
+    """
+    num_ind = 0
+    output_lines = []
+    seq_len = []
+    for record in SeqIO.parse(fasta_file, "fasta"):
+        ind_id = record.id
+        num_ind += 1
+        output_lines.append(f"^{ind_id}    {str(record.seq)}\n")
+        seq_len.append(len(record.seq))
+    if len(set(seq_len)) != 1:
+        print(f"Error: Sequences in file '{fasta_file}' have different lengths.")
+        sys.exit(1)
+    header = f"{num_ind} {seq_len[0]}\n"
+    return [header, "\n", *output_lines, "\n"]
+
+
+def make_bpp_seq(input_dir: Path, output_file: Path, ext=".fasta"):
+    """
+    Create a BPP formatted sequence file from fasta files in a directory.
+    Args:
+        input_dir (Path): Path to the directory containing fasta files.
+        output_file (Path): Path to the output BPP formatted file.
+        ext (str): Extension of the fasta files.
+    """
+    fasta_files = get_fasta_files(input_dir, ext)
+    with open(output_file, "w") as out_f:
+        for fasta_file in fasta_files:
+            bpp_lines = transform_fasta_to_bpp(fasta_file)
+            out_f.writelines(bpp_lines)
+    print(f"BPP formatted sequence file written to '{output_file}'")
+
+
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser(
+        description="Create a BPP formatted sequence file from fasta files in a directory."
+    )
+    parser.add_argument(
+        "input_dir", type=Path, help="Directory containing fasta files."
+    )
+    parser.add_argument(
+        "output_file", type=Path, help="Output BPP formatted sequence file."
+    )
+    parser.add_argument(
+        "--ext",
+        type=str,
+        default=".fasta",
+        help="Extension of the fasta files (default: .fasta).",
+    )
+    args = parser.parse_args()
+    make_bpp_seq(args.input_dir, args.output_file, args.ext)