reroot-trees 0.1.0__py3-none-any.whl

reroot_trees/_init_.py

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+# src/reroot_trees/__init__.py
+__version__ = "1.0.0"

reroot_trees/cli.py

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+def main():
+    EXAMPLES = r"""
+示例：
+  1) 默认外类群（脚本内置），处理当前目录所有 .tre
+     python reroot_trees.py "*.tre"
+
+  2) 替换“默认外类群”（仅当不提供 --outgroups/--outgroup_file 时生效）
+     python reroot_trees.py "*.tre" --default_outgroups AJ01,AJ02,AJ03
+
+  3) 指定外类群（逗号分隔），至少命中1个即尝试定根
+     python reroot_trees.py "*.tre" --outgroups AJBB1124,AJBB1128,AJKa01
+
+  4) 用外类群文件（每行一个标签），至少命中2个才定根
+     python reroot_trees.py "*.tre" --outgroup_file outgroups.txt --min_match 2
+
+  5) 总是使用 -l（以内群为根）
+     python reroot_trees.py "*.tre" --outgroups AJBB1124,AJBB1128 --always_lax
+
+  6) 指定输出目录与后缀
+     python reroot_trees.py "*.tre" --outdir rooted --suffix _rerooted
+
+  7) 原地覆盖（谨慎）
+     python reroot_trees.py "*.tre" --in_place
+
+  8) 指定输入文件编码（例如 Windows 生成文件）
+     python reroot_trees.py "*.tre" --encoding cp936
+
+  9) 关闭自动安装 newick_utils（服务器不允许装软件时用）
+     python reroot_trees.py "*.tre" --no_auto_install
+"""
+    parser = argparse.ArgumentParser(
+        description="Batch reroot Newick trees via nw_reroot（每行一棵树）",
+        formatter_class=argparse.RawDescriptionHelpFormatter,
+        epilog=EXAMPLES
+    )
+
+    # 让 pattern 变为可选，以便 --print-examples 独立使用
+    parser.add_argument("pattern", nargs="?", help="输入通配符，如 '*.tre'（请用引号避免被 shell 预展开）")
+    parser.add_argument("--print-examples", action="store_true", help="只打印用法示例后退出")
+
+    parser.add_argument("--outgroups", help="逗号分隔的外类群标签，例如 A,B,C")
+    parser.add_argument("--outgroup_file", help="外类群文件（每行一个标签）")
+
+    # ✅ 你要的：替换默认外类群（作为新的默认）
+    parser.add_argument("--default_outgroups",
+                        help="替换脚本内置默认外类群（逗号分隔）。仅当不提供 --outgroups/--outgroup_file 时生效")
+
+    parser.add_argument("--min_match", type=int, default=1,
+                        help="至少出现多少个外类群标签才尝试定根（默认1）")
+    parser.add_argument("--always_lax", action="store_true",
+                        help="总是使用 -l（以内群为根）")
+    parser.add_argument("--suffix", default="_rooted", help="输出文件后缀（默认 _rooted）")
+    parser.add_argument("--outdir", default="", help="输出目录（默认与输入同目录）")
+    parser.add_argument("--in_place", action="store_true", help="覆盖原文件（忽略 --suffix/--outdir）")
+    parser.add_argument("--encoding", default="utf-8", help="输入文件编码（默认 utf-8）")
+
+    # ✅ 自动检测/安装 newick_utils
+    parser.add_argument("--no_auto_install", action="store_true",
+                        help="关闭自动安装 newick_utils（默认会自动安装）")
+
+    args = parser.parse_args()
+
+    if args.print_examples:
+        print(EXAMPLES.strip("\n"))
+        return
+
+    if not args.pattern:
+        sys.exit("⚠️ 需要提供输入通配符（例如 \"*.tre\"）。或使用 --print-examples 查看示例。")
+
+    if args.min_match < 1:
+        sys.exit("❌ --min_match 必须 >= 1")
+
+    # 先确保 nw_reroot 可用
+    ensure_nw_reroot(auto_install=(not args.no_auto_install))
+
+    # 读外类群（带替换默认逻辑）
+    OUTGROUPS = read_outgroups(args.outgroup_file, args.outgroups, args.default_outgroups)
+
+    files = sorted(glob.glob(args.pattern))
+    if not files:
+        sys.exit(f"⚠️ 未找到匹配文件：{args.pattern}")
+    print(f"\n🔍 待处理文件数：{len(files)}")
+
+    changed, skipped = 0, 0
+    for infile in files:
+        outdir = Path(os.path.dirname(infile)) if not args.outdir else Path(args.outdir)
+        outdir.mkdir(parents=True, exist_ok=True)
+
+        if args.in_place:
+            outfile = Path(infile)
+            tmpfile = outfile.with_suffix(outfile.suffix + ".tmp")
+        else:
+            stem, ext = os.path.splitext(os.path.basename(infile))
+            outfile = outdir / f"{stem}{args.suffix}{ext}"
+            tmpfile = outfile
+
+        print(f"\n🌳 {infile} -> {outfile}")
+        n_total, n_rooted = 0, 0
+
+        with open(infile, encoding=args.encoding) as fin, open(tmpfile, "w", encoding="utf-8") as fout:
+            for line in fin:
+                tree = line.strip()
+                if not tree:
+                    continue
+                n_total += 1
+
+                labels = extract_labels(tree)
+                present = [og for og in OUTGROUPS if og in labels]
+
+                if len(present) >= args.min_match:
+                    newick = run_reroot(tree, present, args.always_lax)
+                    if newick:
+                        fout.write(newick + "\n")
+                        n_rooted += 1
+                        continue
+
+                # 未定根或不满足门槛：原样写回
+                fout.write(tree + "\n")
+
+        if args.in_place:
+            # 用 tmp 覆盖原文件
+            with open(tmpfile, "r", encoding="utf-8") as fr, open(outfile, "w", encoding="utf-8") as fw:
+                fw.write(fr.read())
+            try:
+                os.remove(tmpfile)
+            except OSError:
+                pass
+
+        print(f"   ✅ 定根 {n_rooted}/{n_total}")
+        changed += n_rooted
+        skipped += (n_total - n_rooted)
+
+    print(f"\n✅ 完成。共定根 {changed} 棵；保留原状 {skipped} 棵。")
+
+if __name__ == "__main__":
+    main()

reroot_trees-0.1.0.dist-info/METADATA

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+Metadata-Version: 2.4
+Name: reroot-trees
+Version: 0.1.0
+Summary: Batch reroot Newick trees using nw_reroot (newick_utils).
+Author: Your Name
+License: MIT
+Keywords: phylogeny,newick,raxml,tree
+Classifier: Programming Language :: Python :: 3
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: OS Independent
+Requires-Python: >=3.8
+Description-Content-Type: text/markdown
+
+# reroot-trees
+
+Install:
+
+pip install reroot-trees

reroot_trees-0.1.0.dist-info/RECORD

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+reroot_trees/_init_.py,sha256=oAnPCEq9o7aNog3kkxQ_2dIkeCjJPt9PGd9Hi8JH-V0,53
+reroot_trees/cli.py,sha256=LJxDImY-NEjpaEkl3FulLXVGGPiZm601a0UEi-7PTHc,5801
+reroot_trees-0.1.0.dist-info/METADATA,sha256=HmnZABlGnpzbUQm-IZ9qQHHyPd2mx-xC4i6xZaNW1sU,453
+reroot_trees-0.1.0.dist-info/WHEEL,sha256=wUyA8OaulRlbfwMtmQsvNngGrxQHAvkKcvRmdizlJi0,92
+reroot_trees-0.1.0.dist-info/entry_points.txt,sha256=2nLcsOjZ0dtY48EFWi8glKcNMimnq2Hw55XFWEbGj9A,55
+reroot_trees-0.1.0.dist-info/top_level.txt,sha256=C7-PfETor7DJnJ4g4w9SwW0LJFSIDfVtUOMN2_lcYVc,13
+reroot_trees-0.1.0.dist-info/RECORD,,

reroot_trees-0.1.0.dist-info/WHEEL

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+Wheel-Version: 1.0
+Generator: setuptools (80.10.2)
+Root-Is-Purelib: true
+Tag: py3-none-any
+

reroot_trees-0.1.0.dist-info/entry_points.txt

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+[console_scripts]
+reroot-trees = reroot_trees.cli:main

reroot_trees-0.1.0.dist-info/top_level.txt

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+reroot_trees