feat(bioflow): P0 内核移植与 8 环境镜像——副本 100 处适配零硬编码/8 镜像验证清单全过/金标 24 ID diff 空/TL 复查 4 项修正(gfpy 储备裁决+镜像备份排除+冒烟零硬编码+金标固化)

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
2026-09-06 02:59:26 +08:00
parent 486670b75d
commit 99e774a2a0
589 changed files with 5300776 additions and 116 deletions
@@ -0,0 +1,60 @@
+#!/usr/bin/env python3
+"""
+使用 matplotlib + Bio.Phylo 绘制进化树 (无头模式)
+"""
+import sys
+import os
+os.environ['QT_QPA_PLATFORM'] = 'offscreen'  # 无头模式
+os.environ['MPLBACKEND'] = 'Agg'  # 使用Agg后端
+
+from pathlib import Path
+import matplotlib
+matplotlib.use('Agg')  # 无头后端
+import matplotlib.pyplot as plt
+from Bio import Phylo
+
+def plot_tree(treefile, output_dir):
+    """绘制进化树并输出PDF和PNG"""
+    treefile = Path(treefile)
+    output_dir = Path(output_dir)
+    output_dir.mkdir(parents=True, exist_ok=True)
+    
+    # 读取树 (Newick格式)
+    tree = Phylo.read(str(treefile), "newick")
+    
+    # 输出文件名
+    base_name = treefile.stem.replace('.iqtree', '').replace('.treefile', '')
+    pdf_file = output_dir / f"{base_name}.pdf"
+    png_file = output_dir / f"{base_name}.png"
+    
+    # 创建图形
+    fig, ax = plt.subplots(figsize=(14, 10))
+    
+    # 绘制进化树
+    Phylo.draw(tree, axes=ax, do_show=False, 
+               branch_labels=lambda c: c.confidence if c.confidence else None)
+    
+    # 设置标题
+    ax.set_title("Interspecies Phylogenetic Tree", fontsize=14, fontweight='bold')
+    
+    # 保存PDF
+    plt.savefig(str(pdf_file), format='pdf', bbox_inches='tight', dpi=300)
+    print(f"PDF: {pdf_file}")
+    
+    # 保存PNG
+    plt.savefig(str(png_file), format='png', bbox_inches='tight', dpi=300)
+    print(f"PNG: {png_file}")
+    
+    plt.close()
+    print("完成")
+    return True
+
+if __name__ == "__main__":
+    if len(sys.argv) < 2:
+        print("用法: python plot_tree.py <treefile> [output_dir]")
+        sys.exit(1)
+    
+    treefile = sys.argv[1]
+    output_dir = sys.argv[2] if len(sys.argv) >= 3 else Path(treefile).parent
+    
+    plot_tree(treefile, output_dir)