#!/usr/bin/env python3"""draw_sequence_logo.py - Generate sequence logos from multiple sequence alignments. Renders information-content or probability logos from aligned FASTA or Clustalfiles using logomaker and BioPython. Usage:    python draw_sequence_logo.py --input alignment.fasta --output logo.png    python draw_sequence_logo.py --input alignment.fasta --output logo.svg --type probability    python draw_sequence_logo.py --input alignment.fasta --output logo.png --start 10 --end 30""" import argparseimport sys try:    from Bio import AlignIOexcept ImportError:    print("Error: BioPython is required. Install with: pip install biopython", file=sys.stderr)    sys.exit(1) try:    import logomakerexcept ImportError:    print("Error: logomaker is required. Install with: pip install logomaker", file=sys.stderr)    sys.exit(1) import matplotlibmatplotlib.use("Agg")import matplotlib.pyplot as pltimport pandas as pdimport numpy as np  def alignment_to_matrix(alignment, logo_type="information"):    seqs = [str(rec.seq) for rec in alignment]    length = len(seqs[0])    n_seqs = len(seqs)     # Detect alphabet    all_chars = set("".join(seqs)) - {"-", "."}    is_protein = len(all_chars) > 4     if is_protein:        alphabet = sorted(all_chars)    else:        alphabet = ["A", "C", "G", "T"]     # Build counts matrix    counts = pd.DataFrame(0, index=range(length), columns=alphabet, dtype=float)    for seq in seqs:        for i, char in enumerate(seq):            if char in alphabet:                counts.at[i, char] += 1     if logo_type == "probability":        matrix = counts.div(counts.sum(axis=1), axis=0).fillna(0)    else:        # Information content        matrix = logomaker.transform_matrix(            counts,            from_type="counts",            to_type="information",        )     return matrix  def detect_format(path):    with open(path) as f:        first_line = f.readline().strip()    if first_line.startswith(">"):        return "fasta"    if first_line.startswith("CLUSTAL") or first_line.startswith("MUSCLE"):        return "clustal"    return "fasta"  def main():    parser = argparse.ArgumentParser(description="Generate sequence logos from alignments")    parser.add_argument("--input", required=True, help="Aligned FASTA or Clustal file")    parser.add_argument("--output", required=True, help="Output image path (PNG/SVG/PDF)")    parser.add_argument("--type", choices=["information", "probability"], default="information",                        help="Logo type (default: information)")    parser.add_argument("--start", type=int, default=None, help="Start position (0-indexed)")    parser.add_argument("--end", type=int, default=None, help="End position (exclusive)")    parser.add_argument("--title", default=None, help="Figure title")    parser.add_argument("--figsize", default="10x3", help="Figure size as WxH (default: 10x3)")    parser.add_argument("--dpi", type=int, default=300, help="Resolution in DPI (default: 300)")    args = parser.parse_args()     fmt = detect_format(args.input)    alignment = AlignIO.read(args.input, fmt)     matrix = alignment_to_matrix(alignment, args.type)     # Slice if requested    if args.start is not None or args.end is not None:        start = args.start or 0        end = args.end or len(matrix)        matrix = matrix.iloc[start:end].reset_index(drop=True)     # Parse figsize    try:        parts = args.figsize.lower().split("x")        figw, figh = float(parts[0]), float(parts[1])    except (ValueError, IndexError):        figw, figh = 10, 3     fig, ax = plt.subplots(figsize=(figw, figh))    logo = logomaker.Logo(matrix, ax=ax, shade_below=0.5, fade_below=0.5)     if args.type == "information":        # Determine max info content        all_chars = set()        for col in matrix.columns:            all_chars.add(col)        max_bits = np.log2(len(matrix.columns))        ax.set_ylabel("Information (bits)", fontsize=12)        ax.set_ylim(0, max_bits * 1.1)    else:        ax.set_ylabel("Probability", fontsize=12)        ax.set_ylim(0, 1.05)     ax.set_xlabel("Position", fontsize=12)    if args.title:        ax.set_title(args.title, fontsize=14, fontweight="bold")     logo.style_spines(visible=False)    logo.style_spines(spines=["left", "bottom"], visible=True)     plt.tight_layout()    plt.savefig(args.output, dpi=args.dpi, bbox_inches="tight")    plt.close()     n_seqs = len(alignment)    n_pos = len(matrix)    print(f"Sequence logo saved to {args.output} ({n_seqs} sequences, {n_pos} positions, type={args.type})")  if __name__ == "__main__":    main()