tbtools-cli 1.2.0__py3-none-any.whl

tbtools_cli/cli.py

@@ -0,0 +1,528 @@
+"""tbtools-cli 主入口 — Python click 重构版"""
+import os
+import sys
+
+import click
+
+# ---- 配置 ----
+# 仅源码直跑时(父目录有 pyproject.toml)才插入搜索路径;pip 安装后不需要(评审: 避免污染搜索路径)
+if os.path.isfile(os.path.join(os.path.dirname(os.path.dirname(os.path.abspath(__file__))), "pyproject.toml")):
+    sys.path.insert(0, os.path.dirname(os.path.dirname(os.path.abspath(__file__))))
+import tbtools_cli.auto_commands as _ac
+from tbtools_cli.cli_tools_registry import CLI_TOOLS
+from tbtools_cli.core import (
+    _,
+    JAR,
+    ROOT,
+    cp,
+    ensure_bridge,
+    get_pitfall_hint,
+    pre_flight,
+    safe_temp,
+    resolve_output,
+    run_java,
+    run_plot,
+    stdout_path,
+)
+from tbtools_cli.presets import apply_preset
+from tbtools_cli.cli_rpc import build_rpc_group
+import tbtools_cli.cli_load as cli_load
+from tbtools_cli.cli_top import register_top  # 批次 B: 顶层命令拆分
+from tbtools_cli import __version__ as _CLI_VERSION  # 单一源: pyproject
+
+from tbtools_cli.cli_load import (  # 批次 B: 动态注册拆分
+    CATEGORY_MAP,
+    _groups,
+    _load_auto_commands,
+    _load_dynamic_commands,
+    build_and_load,
+)
+
+
+
+# ---- 通用选项 ----
+def common_options(f):
+    """通用选项装饰器：--verbose, --quiet, --format, --preset, --width, --height, --threads"""
+    f = click.option("--verbose", "-V", is_flag=True, default=False, help="显示完整堆栈（debug 模式）")(f)
+    f = click.option("--quiet", "-q", is_flag=True, default=False, help="静默模式（只显示错误）")(f)
+    f = click.option("--format", "-f", "fmt", default=None, help="输出格式: svg|png|pdf")(f)
+    f = click.option("--preset", default=None, help="出版预设: nature|cell|plant_journal|wide|poster")(f)
+    f = click.option("--height", "-H", type=int, default=None, help="画布高度")(f)
+    f = click.option("--width", "-W", type=int, default=None, help="画布宽度")(f)
+    f = click.option("--threads", "-t", type=int, default=None, help="线程数")(f)
+    return f
+
+
+
+def _plot_prelude(cmd, in_file, out_file, preset, width, height, fmt, bridge):
+    """绘图命令公共前奏: pre_flight → preset → resolve_output → ensure_bridge。
+    （第三轮审查:消除 volcano/heatmap 等命令前缀的逐字复制）返回 (out_file, width, height)。"""
+    pre_flight(cmd, in_file)
+    if preset:
+        p = apply_preset(preset, width=width, height=height)
+        if not p:
+            print(f"❌ 未知预设: {preset}", file=sys.stderr)
+            sys.exit(1)
+        if 'width' in p and not width:
+            width = p['width']
+        if 'height' in p and not height:
+            height = p['height']
+    out_file = resolve_output(out_file, fmt)
+    if bridge:
+        ensure_bridge(bridge)
+    return out_file, width, height
+
+
+def _append_size(args, width, height):
+    """公共尾部: width/height 拼装(--width/--height 风格)"""
+    if width:
+        args += ["--width", str(width)]
+    if height:
+        args += ["--height", str(height)]
+    return args
+# ---- 主命令组 ----
+class RootGroup(click.Group):
+    """顶层：未知命令时给分组建议 + 拼写纠错"""
+    def resolve_command(self, ctx, args):
+        try:
+            return super().resolve_command(ctx, args)
+        except click.UsageError:
+            if not args:
+                raise
+            name = args[0]
+            # 兼容旧写法/README：顶层裸命令自动转发到分组（如 tbtools seqlogo → tbtools seq logo）
+            for gname, g in _groups.items():
+                if name in g.commands:
+                    return gname, g.commands[name], args[1:]  # F841 修复: 删未用 sub 变量
+            # 拼写纠错（对分组名+顶层命令；前缀匹配优先——venn2 案例：n=3 截断挤掉正确建议）
+            import difflib
+            candidates = sorted(set(list(_groups.keys()) + [c for c in cli.commands.keys()]))
+            prefix_hits = [c for c in candidates if c.startswith(name)]
+            close = prefix_hits[:5] or difflib.get_close_matches(name, candidates, n=3, cutoff=0.6)
+            if close:
+                click.echo(_("❌ 未知命令: {n}", "❌ Unknown command: {n}").format(n=name), err=True)
+                click.echo(f"   你是不是想用: {' / '.join(close)}?", err=True)
+            else:
+                click.echo(_("❌ 未知命令: {n}", "❌ Unknown command: {n}").format(n=name), err=True)
+                click.echo("   查看: tbtools list", err=True)
+            ctx.exit(2)
+
+
+@click.group(cls=RootGroup, invoke_without_command=True)
+@click.version_option(_CLI_VERSION, prog_name="tbtools-cli")
+@click.pass_context
+def cli(ctx):
+    """TBtools-II 全功能 CLI（命令/工具/RPC 数字见 tbtools list）"""
+    if ctx.invoked_subcommand is None:
+        click.echo(ctx.get_help())
+
+# ---- 命令组：序列/结构 ----
+@cli.group("seq")
+def seq_group():
+    """序列/结构域命令"""
+
+@seq_group.command("logo")
+@click.argument("input_file")
+@click.argument("output_file")
+@click.option("--scale-ic/--no-scale-ic", default=True, help="按信息含量缩放")
+@click.option("--show-pos/--no-show-pos", default=False, help="显示位置编号")
+@common_options
+def seqlogo(input_file, output_file, scale_ic, show_pos, verbose, quiet, fmt, preset, height, width, threads):
+    """序列 LOGO 图"""
+    output_file, width, height = _plot_prelude("logo", input_file, output_file, preset, width, height, fmt, None)
+    args = ["java", "-Xmx2g", "-cp", JAR,
+            "biocjava.bioDoer.seqLogo.makeSeqLogo",
+            "--inFile", input_file, "--OutGraph", output_file]
+    if not scale_ic:
+        args += ["--scaleIC=false"]
+    if show_pos:
+        args += ["--showPos=true"]
+    ec = run_plot(args, verbose=verbose, quiet=quiet, command_name="seqlogo")
+    sys.exit(ec)
+
+@seq_group.command("msa")
+@click.argument("aligned_fasta")
+@click.argument("output_file")
+@click.option("--padding", type=int, default=0, help="序列间填充")
+@common_options
+def seq_msa(aligned_fasta, output_file, padding, verbose, quiet, fmt, preset, height, width, threads):
+    """多序列比对可视化"""
+    output_file, width, height = _plot_prelude("msa", aligned_fasta, output_file, preset, width, height, fmt, "MSACli")
+    args = ["java", "-Xmx3g", "-cp", cp(os.path.join(ROOT, "build"), JAR),
+            "MSACli", aligned_fasta, output_file]
+    if padding:
+        args += ["--padding", str(padding)]
+    ec = run_plot(args, verbose=verbose, quiet=quiet, command_name="msa")
+    sys.exit(ec)
+
+@seq_group.command("structure")
+@click.argument("gff_file")
+@click.argument("id_list")
+@click.argument("output_file")
+@click.option("--genome", "-g", default=None, help="基因组 FASTA（可选）")
+@common_options
+def seq_structure(gff_file, id_list, output_file, genome, verbose, quiet, fmt, preset, height, width, threads):
+    """基因结构图（外显子/UTR 从 GFF）"""
+    output_file, width, height = _plot_prelude("structure", gff_file, output_file, preset, width, height, fmt, "GeneStructureCli")
+    args = ["java", "-Xmx3g", "-cp", cp(os.path.join(ROOT, "build"), JAR),
+            "GeneStructureCli", gff_file, id_list, output_file]
+    if genome:
+        args += [genome]
+    if width: args += [str(width)]
+    if height: args += [str(height)]
+    ec = run_plot(args, verbose=verbose, quiet=quiet, command_name="structure")
+    sys.exit(ec)
+
+
+# 旧名别名（README/老用户兼容）：genestructure == structure
+seq_group.add_command(seq_structure, name="genestructure")
+
+@seq_group.command("motif")
+@click.argument("meme_xml")
+@click.argument("id_list")
+@click.argument("output_file")
+@common_options
+def seq_motif(meme_xml, id_list, output_file, verbose, quiet, fmt, preset, height, width, threads):
+    """Motif 分布图（MEME XML）"""
+    output_file, width, height = _plot_prelude("motif", meme_xml, output_file, preset, width, height, fmt, "MotifCli")
+    args = ["java", "-Xmx3g", "-cp", cp(os.path.join(ROOT, "build"), JAR),
+            "MotifCli", meme_xml, id_list, output_file]
+    if width: args += [str(width)]
+    if height: args += [str(height)]
+    ec = run_plot(args, verbose=verbose, quiet=quiet, command_name="motif")
+    sys.exit(ec)
+
+# ---- 命令组：表达/统计 ----
+@cli.group("expr")
+def expr_group():
+    """表达/统计命令"""
+
+@expr_group.command("volcano")
+@click.argument("deg_file")
+@click.argument("output_file")
+@click.option("--pval-cutoff", "-p", type=float, default=0.05, help="P值阈值")
+@click.option("--fc-cutoff", "-c", type=float, default=1.0, help="Log2FC 阈值")
+@common_options
+def volcano(deg_file, output_file, pval_cutoff, fc_cutoff, verbose, quiet, fmt, preset, height, width, threads):
+    """火山图（DEG: GeneID Log2FC pvalue）"""
+    output_file, width, height = _plot_prelude("volcano", deg_file, output_file, preset, width, height, fmt, "GenericCli")
+    args = ["java", "-Xmx2g", "-cp", cp(os.path.join(ROOT, "build"), JAR),
+            "GenericCli", "biocjava.bioDoer.JIGplotToolkit.VocanoPlot.vocanoPlot", "show",
+            output_file, "--set", "inData", deg_file]
+    args += ["--set", "log2FoldChange", "true", "--set", "negLogPvalue", "true"]
+    args += ["--set", "pvalueCutOff", str(pval_cutoff), "--set", "foldChangeCutOff", str(fc_cutoff)]
+    args += ["--set", "normPointSize", "5.0", "--set", "showTopChangeNum", "5"]
+    if width:
+        args += ["--width", str(width)]
+    if height:
+        args += ["--height", str(height)]
+    ec = run_plot(args, verbose=verbose, quiet=quiet, command_name="volcano")
+    sys.exit(ec)
+
+@expr_group.command("heatmap")
+@click.argument("matrix_file")
+@click.argument("output_file")
+@click.option("--log2/--no-log2", default=False, help="log2 转换")
+@click.option("--row-scale/--no-row-scale", default=False, help="行标准化")
+@click.option("--cluster-row/--no-cluster-row", default=False, help="行聚类")
+@click.option("--cluster-col/--no-cluster-col", default=False, help="列聚类")
+@common_options
+def heatmap(matrix_file, output_file, log2, row_scale, cluster_row, cluster_col, verbose, quiet, fmt, preset, height, width, threads):
+    """热图（表达矩阵）"""
+    output_file, width, height = _plot_prelude("heatmap", matrix_file, output_file, preset, width, height, fmt, "HeatmapCli")
+    args = ["java", "-Xmx3g", "-cp", cp(os.path.join(ROOT, "build"), JAR),
+            "HeatmapCli", matrix_file, output_file]
+    if log2:
+        args += ["--log2"]
+    if row_scale:
+        args += ["--rowScale"]
+    if cluster_row:
+        args += ["--clusterRow"]
+    if cluster_col:
+        args += ["--clusterCol"]
+    if width:
+        args += ["--width", str(width)]
+    if height:
+        args += ["--height", str(height)]
+    ec = run_plot(args, verbose=verbose, quiet=quiet, command_name="heatmap")
+    sys.exit(ec)
+
+@expr_group.command("pca")
+@click.argument("matrix_file")
+@click.argument("output_file")
+@click.argument("direction", type=click.Choice(["row", "col"]), default="row")
+@click.option("--scale/--no-scale", default=False, help="标准化")
+@common_options
+def expr_pca(matrix_file, output_file, direction, scale, verbose, quiet, fmt, preset, height, width, threads):
+    """PCA 图"""
+    output_file, width, height = _plot_prelude("pca", matrix_file, output_file, preset, width, height, fmt, "GenericCli")
+    args = ["java", "-Xmx3g", "-cp", cp(os.path.join(ROOT, "build"), JAR),
+            "GenericCli", "biocjava.bioDoer.JIGplotToolkit.PCAanalysis.PCAanalysis",
+            "doPCA+postGraph", output_file,
+            "--set", "inTabFile", matrix_file,
+            "--set", "rowName", "true", "--set", "colName", "true",
+            "--set", "processDirect", "Rows" if direction == "row" else "Columns"]
+    if scale: args += ["--set", "scale", "true"]
+    args += ["--set", "pointSize", "8.0", "--set", "showLabel", "true"]
+    if width: args += ["--width", str(width)]
+    if height: args += ["--height", str(height)]
+    ec = run_plot(args, verbose=verbose, quiet=quiet, command_name="pca")
+    sys.exit(ec)
+
+@expr_group.command("hclust")
+@click.argument("distance_file")
+@click.argument("output_file")
+@common_options
+def expr_hclust(distance_file, output_file, verbose, quiet, fmt, preset, height, width, threads):
+    """层次聚类树（三列距离文件 GeneA\tGeneB\tdist）"""
+    output_file, width, height = _plot_prelude("hclust", distance_file, output_file, preset, width, height, fmt, "HclustCli")
+    args = ["java", "-Xmx3g", "-cp", cp(os.path.join(ROOT, "build"), JAR),
+            "HclustCli", distance_file, output_file]
+    ec = run_plot(args, verbose=verbose, quiet=quiet, command_name="hclust")
+    sys.exit(ec)
+
+@expr_group.command("dehist")
+@click.argument("deg_file")
+@click.argument("output_file")
+@common_options
+def expr_dehist(deg_file, output_file, verbose, quiet, fmt, preset, height, width, threads):
+    """差异表达双直方图"""
+    pre_flight("dehist", deg_file)
+    output_file = resolve_output(output_file, fmt)
+    # FIX(G5): 原注册类 DiffExp.DualHistPlot.DiffExpDualHistPlot 在 2.535 jar 不存在，
+    # 真实类 RNAseqViz.DiffExpDualHistPlot main 硬编码 → DeHistCli 桥（doctor 死命令探测发现）
+    ensure_bridge("DeHistCli")
+    args = ["java", "-Xmx2g", "-cp", cp(os.path.join(ROOT, "build"), JAR),
+            "DeHistCli", deg_file, output_file]
+    if width: args += [str(width)]
+    if height: args += [str(height)]
+    ec = run_plot(args, verbose=verbose, quiet=quiet, command_name="dehist")
+    sys.exit(ec)
+
+# ---- 命令组：树/进化 ----
+@cli.group("tree")
+def tree_group():
+    """树/进化命令"""
+
+@tree_group.command("draw")
+@click.argument("config_file")
+@click.argument("output_file")
+@common_options
+def tree_draw(config_file, output_file, verbose, quiet, fmt, preset, height, width, threads):
+    """树+注释图（TreeTreeTree 多轨道）"""
+    output_file, width, height = _plot_prelude("draw", config_file, output_file, preset, width, height, fmt, "TreeCli")
+    args = ["java", "-Xmx3g", "-cp", cp(os.path.join(ROOT, "build"), JAR),
+            "TreeCli", config_file, output_file]
+    ec = run_plot(args, verbose=verbose, quiet=quiet, command_name="draw")
+    sys.exit(ec)
+
+@tree_group.command("unrooted")
+@click.argument("newick_file")
+@click.argument("output_file")
+@common_options
+def tree_unrooted(newick_file, output_file, verbose, quiet, fmt, preset, height, width, threads):
+    """无根树可视化"""
+    output_file, width, height = _plot_prelude("unrooted", newick_file, output_file, preset, width, height, fmt, "UnrootedTreeCli")
+    args = ["java", "-Xmx3g", "-cp", cp(os.path.join(ROOT, "build"), JAR),
+            "UnrootedTreeCli", newick_file, output_file]
+    if width: args += ["--width", str(width)]
+    if height: args += ["--height", str(height)]
+    ec = run_plot(args, verbose=verbose, quiet=quiet, command_name="unrooted")
+    sys.exit(ec)
+
+@tree_group.command("rooting")
+@click.argument("input_nwk")
+@click.argument("output_nwk")
+@common_options
+def tree_rooting(input_nwk, output_nwk, verbose, quiet, fmt, preset, height, width, threads):
+    """MAD 系统发育定根"""
+    # FIX(G5): 原注册类 newickParser.TreeTreeTree.TreeRootingByMAD 在 2.535 jar 不存在，
+    # 改走既有 TreeRootingCli 桥（quickMadRoot，08/29 已验证）
+    ensure_bridge("TreeRootingCli")
+    args = ["java", "-Xmx2g", "-cp", cp(os.path.join(ROOT, "build"), JAR),
+            "TreeRootingCli", input_nwk, output_nwk]
+    ec = run_java(args, verbose=verbose, quiet=quiet, command_name="rooting")
+    sys.exit(ec)
+
+
+# 旧名别名（README/老用户兼容）：treeRooting == rooting
+tree_group.add_command(tree_rooting, name="treeRooting")
+
+@tree_group.command("one-step")
+@click.argument("pep_fasta")
+@click.argument("output_prefix")
+@click.option("--bb-time", "-b", type=int, default=1000, help="IQ-TREE bootstrap iterations")
+@common_options
+def tree_onesteptree(pep_fasta, output_prefix, bb_time, verbose, quiet, fmt, preset, height, width, threads):
+    """一步法 ML 树（muscle → trimal → IQ-TREE）"""
+    # FIX(G5): 原注册类 Phylogenetics.OneStepTree 在 2.475/2.535 jar 均不存在（外部测试 P1-1
+    # + 本地 doctor 探测复核）；真实引擎为 BioSoftPipeServer.OneStepMLTree。
+    # ⚠️ 该引擎 ArgsParser 只认 --inPepFie/--outFilePrefix/--clean/--bbTime，没有 --threads！
+    args = ["java", "-Xmx4g", "-cp", JAR,
+            "biocjava.bioIO.BioSoftPipeServer.OneStepMLTree",
+            "--inPepFie", pep_fasta, "--outFilePrefix", output_prefix,
+            "--bbTime", str(bb_time)]
+    ec = run_java(args, verbose=verbose, quiet=quiet, command_name="onesteptree")
+    sys.exit(ec)
+
+# ---- 命令组：工具 ----
+# N2: GUI 面板类工具黑名单（headless 无参直通会弹 Swing 窗口悬挂）
+_GUI_TOOLS = {"RNAplotAdvance", "PlotRNAfold", "AmazingGeneView", "BlastZone", "SequenceZone"}
+
+class ToolGroup(click.Group):
+    """tool 分组：未知子命令自动转发 auto_commands + --help 列出全部"""
+    def resolve_command(self, ctx, args):
+        try:
+            return super().resolve_command(ctx, args)
+        except click.UsageError:
+            if args:
+                name = args[0]
+                impl = getattr(_ac, f'_{name}_impl', None)
+                if impl:
+                    doc = (impl.__doc__ or '').split(':',1)[1].strip() if ':' in (impl.__doc__ or '') else f'{name} [参数...]'
+                    pitfall = get_pitfall_hint(name)
+                    help_text = doc + (f'\n\n⚠️ {pitfall}' if pitfall else '')
+                    # FIX(P0-1): 旧写法闭包捕获 tool 分组自身 Context（ctx.args 恒空），
+                    # 所有参数被丢弃。改用 pass_context 拿子命令自己的 Context。
+                    # （外部测试 2026-09-19 实测,Windows 已验证）
+                    @click.pass_context
+                    def _fwd(sctx, _impl=impl):
+                        sys.exit(_impl(list(sctx.args)))
+                    cmd = click.Command(name=name,
+                        callback=_fwd,
+                        context_settings={"ignore_unknown_options": True, "allow_extra_args": True},
+                        help=help_text)
+                    return name, cmd, args[1:]
+                # FIX(P0-3): 回退到共享注册表（82 个 CLI 工具，原仅旧入口 tbcli.py 可达，
+                # 外部测试 §3.3：rpkmCal/statFasta/tpmCalc 等在新入口全部未找到）
+                cls = CLI_TOOLS.get(name)
+                if cls:
+                    @click.pass_context
+                    def _fwd_reg(sctx, _cls=cls, _name=name):
+                        # N2: GUI 类工具无参直通会弹 Swing 窗口悬挂——黑名单无参时打印用法即退出
+                        if _name in _GUI_TOOLS and not sctx.args:
+                            click.echo(f"❌ {_name} 是 GUI 面板类工具，headless 下不可用；请提供参数直接调用引擎[Usage]查看签名", file=sys.stderr)
+                            click.echo(f"   💡 查看引擎真实参数: java -cp $TBTOOLS_JAR {_cls} --bogus x（逼出 Usage）", file=sys.stderr)
+                            sys.exit(1)
+                        java_args = ["java", "-Xmx4g", "-cp", JAR, _cls] + list(sctx.args)
+                        sys.exit(run_java(java_args, command_name=_name))
+                    cmd = click.Command(name=name,
+                        callback=_fwd_reg,
+                        context_settings={"ignore_unknown_options": True, "allow_extra_args": True},
+                        help=f"{name} [引擎命名参数...]\n\n⚠️ ArgsParser 系引擎一律 --key value 空格分隔，--key=value 会被拒绝")
+                    return name, cmd, args[1:]
+                click.echo(f"❌ 未知工具: {name}", file=sys.stderr)
+                count = 0
+                for n in sorted(dir(_ac)):
+                    if n.startswith('_') and n.endswith('_impl') and not n.startswith('__'):
+                        cmd = n[1:-5]
+                        doc = getattr(_ac, n).__doc__ or ''
+                        short = doc.split(':',1)[1].strip()[:50] if ':' in doc else ''
+                        click.echo(f"  {cmd:20s} {short}", file=sys.stderr)
+                        count += 1
+                for tname in sorted(CLI_TOOLS):
+                    if getattr(_ac, f'_{tname}_impl', None):
+                        continue
+                    click.echo(f"  {tname:20s} {CLI_TOOLS[tname].split('.')[-1]}", file=sys.stderr)
+                    count += 1
+                click.echo(f"\n共 {count} 个工具，查看: tbtools list tools", file=sys.stderr)
+                ctx.exit(2)
+            raise
+    
+    def format_options(self, ctx, formatter):
+        """重写 --help：手动命令 + auto_command 工具全列出"""
+        super().format_options(ctx, formatter)
+        plot_groups = {'seq', 'expr', 'tree', 'syn', 'sets', 'chipseq'}
+        entries = []
+        for n in sorted(dir(_ac)):
+            if n.startswith('_') and n.endswith('_impl') and not n.startswith('__'):
+                cmd = n[1:-5]
+                cat = CATEGORY_MAP.get(cmd, 'engine')
+                if cat in plot_groups:
+                    continue
+                doc = getattr(_ac, n).__doc__ or ''
+                short = doc.split(':',1)[1].strip()[:50] if ':' in doc else ''
+                entries.append(f"{cmd:20s} {short}")
+        if entries:
+            with formatter.section(f'可用工具（共 {len(entries)} 个，完整列表: tbtools list tools）'):
+                for e in entries[:20]:
+                    formatter.write_text(e)
+                if len(entries) > 20:
+                    formatter.write_text(f"... 及其他 {len(entries)-20} 个")
+
+@cli.group("tool", cls=ToolGroup)
+def tool_group():
+    """命令行工具（82 个）"""
+
+@tool_group.command("stat-fasta")
+@click.argument("input_file")
+@click.argument("output_file")
+@common_options
+def tool_stat_fasta(input_file, output_file, verbose, quiet, fmt, preset, height, width, threads):
+    """FASTA 序列统计"""
+    # stdin 管道支持
+    if input_file == "-":
+        tmp = safe_temp(suffix=".fa")
+        with open(tmp, "wb") as f:
+            f.write(sys.stdin.buffer.read())
+        input_file = tmp
+    if output_file == "-":
+        output_file = stdout_path()
+    args = ["java", "-Xmx2g", "-cp", JAR,
+            "biocjava.bioIO.FastX.FastaIndex.QuickStatFasta",
+            "--inFasta", input_file, "--outPutFile", output_file]
+    ec = run_java(args, verbose=verbose, quiet=quiet, command_name="stat_fasta")
+    sys.exit(ec)
+
+@tool_group.command("cds2protein")
+@click.argument("cds_fasta")
+@click.argument("output_file")
+@common_options
+def tool_cds2protein(cds_fasta, output_file, verbose, quiet, fmt, preset, height, width, threads):
+    """CDS → 蛋白质翻译"""
+    if output_file == "-": output_file = stdout_path()
+    # FIX(G5): 原注册类 JIGplotToolkit.Protein.CdsToProtein 在 2.535 jar 不存在，
+    # 真实引擎 bioIO.ORF.Translater（ArgsParser: --inFa/--outFa）
+    args = ["java", "-Xmx2g", "-cp", JAR,
+            "biocjava.bioIO.ORF.Translater",
+            "--inFa", cds_fasta, "--outFa", output_file]
+    ec = run_java(args, verbose=verbose, quiet=quiet, command_name="cds2protein")
+    sys.exit(ec)
+
+@tool_group.command("fasta-extract")
+@click.argument("input_fasta")
+@click.argument("id_list")
+@click.argument("output_file")
+@common_options
+def tool_fasta_extract(input_fasta, id_list, output_file, verbose, quiet, fmt, preset, height, width, threads):
+    """按 ID 列表提取 FASTA 序列（idList: 一行一个 ID,不带 > 号;与原始 header 精确匹配）"""
+    if input_fasta == "-":
+        tmp = safe_temp(suffix=".fa")
+        with open(tmp, "wb") as f: f.write(sys.stdin.buffer.read())
+        input_fasta = tmp
+    if output_file == "-": output_file = stdout_path()
+    # FIX(G5): 原注册类 bioIO.FastX.FastaIndex.ExtractFasta 路径错误，
+    # 真实类 bioDoer.Fasta.ExtractFasta（ArgsParser: --inFa/--inIDList/--outFa）
+    args = ["java", "-Xmx2g", "-cp", JAR,
+            "biocjava.bioDoer.Fasta.ExtractFasta",
+            "--inFa", input_fasta, "--inIDList", id_list, "--outFa", output_file]
+    ec = run_java(args, verbose=verbose, quiet=quiet, command_name="fasta_extract")
+    sys.exit(ec)
+
+# ---- 动态装配(批次 B: cli_load)----
+build_and_load(cli)
+register_top(cli, cli_load)
+
+_load_dynamic_commands()
+_load_auto_commands()
+
+
+# 旧名别名（README/老用户兼容，顶层/分组均可用）——须在 cli() 前注册
+seq_group.add_command(seqlogo, name="seqlogo")
+expr_group.add_command(heatmap, name="heatmap2")
+# ---- RPC 分组注册（批次 B: 从 cli_rpc 模块组装）----
+cli.add_command(build_rpc_group())
+
+
+if __name__ == "__main__":
+    cli()