607 lines
24 KiB
Python
Executable File
607 lines
24 KiB
Python
Executable File
#!/home/xzq/miniconda3/envs/test4py311/bin/python
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"""
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Combo Plot Stage - Tree + Motif + Structure + Domain 组合图
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将多个分析阶段的结果整合到一张图中：
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- Panel A: Phylogenetic tree
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- Panel B: Subfamily
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- Panel C: Motif
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- Panel D: Gene structure
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- Panel E: Domain
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"""
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import os
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import argparse
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import json
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import shutil
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import subprocess
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import sys
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from pathlib import Path
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from typing import Dict, List, Optional, Tuple
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# 项目根目录
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PROJECT_ROOT = Path(__file__).parent.parent.parent.resolve()
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SCRIPTS_DIR = PROJECT_ROOT / "scripts"
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if str(PROJECT_ROOT) not in sys.path:
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sys.path.insert(0, str(PROJECT_ROOT))
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from gfa_core.gene_family_scope import read_scope, sanitize_token, scope_hash
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from gfa_core.gene_family_stage_context import build_stage_context, user_output_prefix_for, write_legacy_manifest_copy
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# R 脚本路径由统一路径配置解析；gfpy312 环境没有 Rscript。
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from gfa_core.project_paths import get_conda_env_bin, get_conda_env_rscript
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RSCRIPT_PATH = get_conda_env_rscript("test4py311")
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# 添加 conda 环境 bin 目录到 PATH。
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CONDA_BIN = str(get_conda_env_bin("test4py311"))
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if CONDA_BIN not in os.environ.get("PATH", ""):
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os.environ["PATH"] = CONDA_BIN + os.pathsep + os.environ.get("PATH", "")
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def find_file_by_glob(pattern: Path, name: str) -> Optional[Path]:
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"""递归查找文件"""
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matches = list(pattern.rglob(name))
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return matches[0] if matches else None
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def find_meme_xml(workspace: Path, prefix: str) -> Optional[Path]:
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"""查找 MEME XML 文件"""
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# 优先在 motif/analysis/meme_out/ 中查找
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meme_dir = workspace / "motif" / "analysis" / "meme_out"
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if meme_dir.exists():
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xml_file = meme_dir / "meme.xml"
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if xml_file.exists():
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return xml_file
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# 备选：递归搜索
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return find_file_by_glob(workspace, "meme.xml")
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def resolve_meme_xml_from_manifest(workspace: Path, motif_data: Dict, prefix: str) -> Optional[Path]:
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artifacts = motif_data.get("artifacts", {}) or {}
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meme_xml = artifacts.get("meme_xml") if isinstance(artifacts, dict) else None
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candidates = []
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if isinstance(meme_xml, dict):
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for key in ("full_path", "path"):
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text = str(meme_xml.get(key) or "").strip()
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if text:
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path = Path(text)
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candidates.append(path if path.is_absolute() else workspace / path)
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meme_results = artifacts.get("meme_results") if isinstance(artifacts, dict) else None
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if isinstance(meme_results, dict):
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for key in ("full_path", "path"):
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text = str(meme_results.get(key) or "").strip()
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if text:
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path = Path(text)
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path = path if path.is_absolute() else workspace / path
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candidates.append(path / "meme.xml")
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motif_txt = artifacts.get("motif_prot_txt") if isinstance(artifacts, dict) else None
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if isinstance(motif_txt, dict):
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text = str(motif_txt.get("full_path") or motif_txt.get("path") or "").strip()
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if text:
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path = Path(text)
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path = path if path.is_absolute() else workspace / path
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candidates.append(path.parent / "meme_out" / "meme.xml")
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for candidate in candidates:
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if candidate.exists() and candidate.stat().st_size > 0:
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return candidate.resolve()
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return find_meme_xml(workspace, prefix)
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def load_manifest(manifest_path: Path) -> Dict:
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"""加载 manifest 文件"""
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if not manifest_path.exists():
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raise FileNotFoundError(f"Manifest not found: {manifest_path}")
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return json.loads(manifest_path.read_text(encoding="utf-8"))
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def manifest_artifact_path(workspace: Path, manifest_path: Path, artifact: Dict) -> Optional[Path]:
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if not isinstance(artifact, dict):
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return None
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raw = str(artifact.get("full_path") or artifact.get("path") or "").strip()
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if not raw:
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return None
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path = Path(raw)
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if path.is_absolute():
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return path
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candidate = workspace / path
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if candidate.exists():
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return candidate
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return manifest_path.parent / path.name
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def materialize_aggregate_subfamily_file(workspace: Path, prefix: str, scope_data: Optional[Dict]) -> Optional[Path]:
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"""Build a combined subfamily table from per-target reference-classification manifests."""
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scope_id = str((scope_data or {}).get("scope_id") or "").strip()
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if not scope_id:
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return None
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final_dir = workspace / "final"
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aggregate_manifest = final_dir / f"{prefix}.{sanitize_token(scope_id)}.reference_classification.manifest.json"
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if not aggregate_manifest.exists():
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return None
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try:
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aggregate = load_manifest(aggregate_manifest)
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except Exception:
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return None
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rows = []
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for artifact in (aggregate.get("artifacts") or {}).values():
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child_manifest = manifest_artifact_path(workspace, aggregate_manifest, artifact)
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if not child_manifest or not child_manifest.exists() or not child_manifest.name.endswith(".manifest.json"):
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continue
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try:
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child = load_manifest(child_manifest)
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except Exception:
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continue
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child_artifacts = child.get("artifacts") or {}
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sub_artifact = child_artifacts.get("subfamily_file") or child_artifacts.get("geneID_subfamily_compat")
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sub_path = manifest_artifact_path(workspace, child_manifest, sub_artifact)
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if not sub_path or not sub_path.exists():
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continue
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for raw in sub_path.read_text(encoding="utf-8", errors="ignore").splitlines():
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line = raw.strip()
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if not line or line.lower().startswith("gene"):
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continue
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rows.append(line)
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if not rows:
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return None
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out = final_dir / f"{prefix}.{sanitize_token(scope_id)}.reference_classification.subfamily.tsv"
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seen = set()
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with out.open("w", encoding="utf-8") as handle:
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for line in rows:
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key = line.split("\t", 1)[0] if "\t" in line else line.split(None, 1)[0]
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if key in seen:
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continue
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seen.add(key)
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handle.write(line + "\n")
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print(f"[INFO] Materialized aggregate subfamily file: {out}")
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return out
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def find_latest_manifest(workspace: Path, stage: str, prefix: str, scope_data: Optional[Dict] = None) -> Optional[Path]:
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"""查找最新的 manifest 文件"""
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final_dir = workspace / "final"
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if not final_dir.exists():
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return None
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scope_id = str((scope_data or {}).get("scope_id") or "").strip()
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if scope_data and scope_data.get("scope_id"):
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scoped = final_dir / f"{prefix}.{sanitize_token(scope_id)}.{stage}.manifest.json"
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if scoped.exists():
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return scoped
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compact = final_dir / f"{compact_output_prefix(prefix, scope_data)}.{stage}.manifest.json"
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if compact.exists():
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return compact
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pattern = f"*{stage}*.manifest.json"
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candidates = list(final_dir.glob(pattern))
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if scope_id:
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for path in sorted(candidates, key=lambda p: p.stat().st_mtime, reverse=True):
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if scope_id in path.name:
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return path
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for path in sorted(candidates, key=lambda p: p.stat().st_mtime, reverse=True):
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try:
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data = json.loads(path.read_text(encoding="utf-8"))
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except Exception:
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continue
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if data.get("stage") == stage and data.get("scope_id") == scope_id:
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return path
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# 按修改时间排序，返回最新的
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if candidates:
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return max(candidates, key=lambda p: p.stat().st_mtime)
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return None
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def compact_output_prefix(prefix: str, scope_data: Optional[Dict]) -> str:
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"""Return a bounded user-facing output prefix.
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Full scope details stay in scope JSON and manifest. Result filenames should
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not enumerate every target/reference/comparative species.
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"""
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if not scope_data:
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return prefix
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family = str(scope_data.get("family") or (prefix.split(".")[-1] if "." in prefix else "")).strip()
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mode = str(scope_data.get("scope_mode") or "").strip()
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targets = [str(x) for x in scope_data.get("target_species") or [] if str(x).strip()]
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scope_id = str(scope_data.get("scope_id") or "").strip()
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if len(targets) == 1 and family:
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return ".".join(x for x in [targets[0], family, mode] if x)
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if mode:
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base = prefix if prefix else f"Target.{family}".strip(".")
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if scope_id:
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return f"{base}.{mode}.h{scope_hash(scope_id, 6)}"
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return f"{base}.{mode}"
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return prefix
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def normalize_panels(raw_panels: str) -> List[str]:
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"""Normalize the panel selector used by the isolated combo replot test."""
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allowed = ["motif", "structure", "domain"]
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aliases = {
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"gene_structure": "structure",
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"gene-structure": "structure",
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"genestructure": "structure",
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"domains": "domain",
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"motifs": "motif",
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"all": "all",
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}
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selected: List[str] = []
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for token in str(raw_panels or "").replace(";", ",").split(","):
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key = token.strip().lower().replace(" ", "_")
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if not key:
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continue
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key = aliases.get(key, key)
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if key == "all":
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return allowed
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if key not in allowed:
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raise ValueError(f"Unsupported combo panel: {token}. Allowed: {', '.join(allowed)}")
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if key not in selected:
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selected.append(key)
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selected = selected or allowed
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if len(selected) < 2:
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raise ValueError("Combo panel test requires at least two data panels; single-panel views already exist in motif/structure/domain stages.")
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return selected
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def run_combo_plot(
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workspace: Path,
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prefix: str,
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output_prefix: str,
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tree_file: Path,
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subfamily_file: Optional[Path],
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meme_xml: Optional[Path],
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gff3_file: Optional[Path],
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domtblout_file: Optional[Path],
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panels: List[str],
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evalue_cutoff: float = 1e-5,
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coverage_percent: Optional[float] = None,
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rscript: Optional[Path] = None,
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) -> Dict:
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"""
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运行 R 脚本绘制组合图
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"""
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if rscript is None:
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rscript = SCRIPTS_DIR / "combo_tree_motif_structure_domain_panel_test.R"
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if not rscript.exists():
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return {
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"success": False,
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"error": f"R script not found: {rscript}"
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}
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# 输出文件
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output_pdf = workspace / "final" / f"{output_prefix}.combo_panel_test.pdf"
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# 构建命令
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cmd = [
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str(RSCRIPT_PATH), str(rscript),
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str(tree_file),
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str(subfamily_file) if subfamily_file else "NONE", # 传递 NONE 表示无亚家族
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str(meme_xml) if meme_xml else "NONE",
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str(gff3_file) if gff3_file else "NONE",
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str(domtblout_file) if domtblout_file else "NONE",
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str(evalue_cutoff), # E-value cutoff
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]
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# 添加 coverage（可选）
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if coverage_percent is not None:
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cmd.append(str(coverage_percent))
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else:
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cmd.append("0") # 不启用 coverage 过滤
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# 添加输出文件和 panel 选择
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cmd.append(str(output_pdf))
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cmd.append(",".join(panels))
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print(f"[CMD] {' '.join(cmd)}")
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try:
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result = subprocess.run(
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cmd,
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capture_output=True,
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text=True,
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check=False,
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timeout=300
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)
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success = output_pdf.exists()
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return {
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"success": success,
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"output_pdf": str(output_pdf) if success else None,
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"output_png": str(output_pdf.with_suffix(".png")) if success else None,
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"returncode": result.returncode,
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"stdout": result.stdout[-2000:] if result.stdout else "",
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"stderr": result.stderr[-2000:] if result.stderr else "",
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}
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except Exception as e:
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return {"success": False, "error": str(e)}
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def promote_scoped_combo_outputs(workspace: Path, prefix: str, scope_id: str, result: Dict) -> Dict:
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"""Materialize scoped combo outputs and make them the manifest artifacts.
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The R plotting command writes the short user-facing filename first for
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backwards compatibility. When a scope is active, the manifest should point
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at the scoped copies so strict artifact validation follows the same identity
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as the stage manifest.
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"""
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if not scope_id or not result.get("success"):
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return result
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scoped_prefix = f"{prefix}.{sanitize_token(scope_id)}"
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final_dir = workspace / "final"
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promoted = dict(result)
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for key, suffix in (("output_pdf", ".combo_panel_test.pdf"), ("output_png", ".combo_panel_test.png")):
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source_text = promoted.get(key)
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if not source_text:
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continue
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source = Path(source_text)
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if not source.exists():
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continue
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target = final_dir / f"{scoped_prefix}{suffix}"
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if source.resolve() != target.resolve():
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shutil.copy2(source, target)
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promoted[f"short_{key}"] = str(source)
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promoted[key] = str(target)
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return promoted
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def main():
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parser = argparse.ArgumentParser(
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description="Combo Plot: Tree + Motif + Structure + Domain"
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)
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parser.add_argument("--prefix", required=True, help="Analysis prefix (e.g., Ft.SPL)")
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parser.add_argument("--workspace", required=True, help="Workspace directory")
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parser.add_argument("--evalue", type=float, default=1e-5, help="E-value cutoff")
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parser.add_argument("--coverage", type=float, default=None, help="Coverage percent (0-100)")
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parser.add_argument("--subfamily", type=str, default=None, help="Subfamily file path")
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parser.add_argument("--scope-file", type=str, default=None, help="Gene-family scope JSON from resolve_scope.py")
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parser.add_argument("--analysis-route", type=str, default="", help="Analysis route identity, e.g. single_species/subfamily_prediction")
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parser.add_argument("--member-set-id", type=str, default="", help="Member set identity for scoped outputs")
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parser.add_argument("--cpu", type=int, default=8, help="CPU cores (unused, for compatibility)")
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parser.add_argument("--run-id", type=str, default=None, help="Run ID")
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parser.add_argument("--replot", action="store_true", help="Replot even if exists")
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parser.add_argument("--panels", type=str, default="motif,structure,domain", help="Comma-separated panels to show; choose at least two from motif,structure,domain")
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args = parser.parse_args()
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workspace = Path(args.workspace)
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prefix = args.prefix
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try:
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panels = normalize_panels(args.panels)
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except ValueError as exc:
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print(f"[ERROR] {exc}")
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sys.exit(1)
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scope_data: Optional[Dict] = None
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scope_file: Optional[Path] = None
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if args.scope_file:
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scope_file = Path(args.scope_file)
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if not scope_file.exists():
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print(f"[ERROR] Scope file not found: {args.scope_file}")
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sys.exit(1)
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scope_data = read_scope(scope_file)
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print(f"[INFO] Combo panel test stage for {prefix}")
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print(f"[INFO] Workspace: {workspace}")
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print(f"[INFO] Panels: {', '.join(panels)}")
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scope_id = str((scope_data or {}).get("scope_id") or "").strip()
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output_prefix = user_output_prefix_for(
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"combo",
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prefix,
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scope_data or {},
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analysis_route=args.analysis_route,
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member_set_id=args.member_set_id,
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) if scope_id else prefix
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if output_prefix != prefix:
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print(f"[INFO] Output prefix: {output_prefix}")
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# 1. 查找 tree 文件
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phylo_manifest = find_latest_manifest(workspace, "phylogeny", prefix, scope_data)
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if not phylo_manifest:
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print("[ERROR] Phylogeny manifest not found")
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sys.exit(1)
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phylo_data = load_manifest(phylo_manifest)
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tree_file = Path(phylo_data["artifacts"]["tree"]["full_path"])
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print(f"[INFO] Tree file: {tree_file}")
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# 2. 查找 subfamily 文件
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if args.subfamily:
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subfamily_file = Path(args.subfamily)
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else:
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# 自动查找只接受 confirmed_subfamily；prediction/geneID 必须由 --subfamily 显式传入。
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confirmed_name = f"{prefix}.confirmed_subfamily.tsv"
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scoped_confirmed_name = f"{output_prefix}.confirmed_subfamily.tsv"
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search_paths = [
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workspace / "final" / scoped_confirmed_name,
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workspace / "final" / confirmed_name,
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workspace / "input" / confirmed_name,
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workspace.parent.parent / "input" / workspace.name / confirmed_name,
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]
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if scope_data and scope_data.get("scope_mode") in {"target_only", "target_plus_reference"}:
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family = str(scope_data.get("family") or (prefix.split(".")[-1] if "." in prefix else "")).strip()
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targets = [str(x) for x in scope_data.get("target_species") or [] if str(x).strip()]
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refs = [str(x) for x in scope_data.get("reference_species") or [] if str(x).strip()]
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if len(targets) == 1 and family:
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cross_prefix = f"{targets[0]}.{family}.target_plus_reference"
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scoped_prediction = None
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if refs:
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scoped_prediction = f"Target.{family}.target-{targets[0]}.ref-{'-'.join(refs)}.subfamily_prediction"
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extra_paths = [
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workspace / "final" / f"{cross_prefix}.confirmed_subfamily.tsv",
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]
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if scoped_prediction:
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extra_paths.extend([
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workspace / "final" / f"{scoped_prediction}.confirmed_subfamily.tsv",
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])
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search_paths[0:0] = extra_paths
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subfamily_file = None
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for p in search_paths:
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if p.exists():
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subfamily_file = p
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break
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# Do not materialize aggregate prediction labels during automatic lookup.
|
||
# Unconfirmed prediction tables require an explicit --subfamily path.
|
||
|
||
if not subfamily_file or not subfamily_file.exists():
|
||
print("[INFO] Subfamily file not found, will run without subfamily coloring")
|
||
subfamily_file = None
|
||
else:
|
||
print(f"[INFO] Subfamily file: {subfamily_file}")
|
||
|
||
# 3. 查找 panel 需要的输入文件
|
||
meme_xml: Optional[Path] = None
|
||
if "motif" in panels:
|
||
motif_manifest = find_latest_manifest(workspace, "motif", prefix, scope_data)
|
||
if not motif_manifest:
|
||
print("[ERROR] Motif manifest not found")
|
||
sys.exit(1)
|
||
motif_data = load_manifest(motif_manifest)
|
||
meme_xml = resolve_meme_xml_from_manifest(workspace, motif_data, prefix)
|
||
if not meme_xml or not meme_xml.exists():
|
||
print("[ERROR] MEME XML not found")
|
||
sys.exit(1)
|
||
print(f"[INFO] MEME XML: {meme_xml}")
|
||
|
||
gff3_file: Optional[Path] = None
|
||
if "structure" in panels:
|
||
struct_manifest = find_latest_manifest(workspace, "structure", prefix, scope_data)
|
||
if not struct_manifest:
|
||
print("[ERROR] Structure manifest not found")
|
||
sys.exit(1)
|
||
struct_data = load_manifest(struct_manifest)
|
||
gff3_file = Path(struct_data["artifacts"]["structure_gff3_filtered"]["full_path"])
|
||
print(f"[INFO] GFF3 file: {gff3_file}")
|
||
|
||
domtblout_file: Optional[Path] = None
|
||
if "domain" in panels:
|
||
domain_manifest = find_latest_manifest(workspace, "domain", prefix, scope_data)
|
||
if not domain_manifest:
|
||
print("[ERROR] Domain manifest not found")
|
||
sys.exit(1)
|
||
domain_data = load_manifest(domain_manifest)
|
||
domtblout_file = Path(domain_data["artifacts"]["domtblout"]["full_path"])
|
||
print(f"[INFO] domtblout file: {domtblout_file}")
|
||
|
||
# 6. 运行组合图
|
||
result = run_combo_plot(
|
||
workspace=workspace,
|
||
prefix=prefix,
|
||
output_prefix=output_prefix,
|
||
tree_file=tree_file,
|
||
subfamily_file=subfamily_file,
|
||
meme_xml=meme_xml,
|
||
gff3_file=gff3_file,
|
||
domtblout_file=domtblout_file,
|
||
panels=panels,
|
||
evalue_cutoff=args.evalue,
|
||
coverage_percent=args.coverage,
|
||
)
|
||
result = promote_scoped_combo_outputs(workspace, prefix, scope_id, result)
|
||
|
||
if result.get("success"):
|
||
print(f"[OK] Combo plot generated: {result['output_pdf']}")
|
||
|
||
# 检查 PNG 是否存在
|
||
png_path = result.get("output_png")
|
||
png_exists = png_path and Path(png_path).exists() if png_path else False
|
||
|
||
# 生成 manifest
|
||
artifacts = {
|
||
"combo_plot_pdf": {
|
||
"artifact": "combo_plot",
|
||
"path": str(Path(result["output_pdf"]).relative_to(workspace)),
|
||
"full_path": result["output_pdf"],
|
||
"type": "image",
|
||
"format": "pdf",
|
||
"description": f"Tree + {' + '.join(p.title() for p in panels)} combo panel test visualization"
|
||
}
|
||
}
|
||
|
||
if png_exists:
|
||
artifacts["combo_plot_png"] = {
|
||
"artifact": "combo_plot",
|
||
"path": str(Path(png_path).relative_to(workspace)),
|
||
"full_path": png_path,
|
||
"type": "image",
|
||
"format": "png",
|
||
"description": f"Tree + {' + '.join(p.title() for p in panels)} combo panel test visualization (PNG)"
|
||
}
|
||
|
||
stage_context = build_stage_context(
|
||
stage="combo",
|
||
prefix=prefix,
|
||
scope_data=scope_data or {},
|
||
scope_file=str(scope_file or ""),
|
||
output_prefix=output_prefix,
|
||
subfamily_file=str(subfamily_file or ""),
|
||
analysis_route=args.analysis_route or "",
|
||
member_set_id=args.member_set_id or "",
|
||
).to_dict()
|
||
manifest = {
|
||
"manifest_version": "1.0",
|
||
"job_id": workspace.name,
|
||
"stage": "combo",
|
||
"run_id": args.run_id or "unknown",
|
||
"prefix": prefix,
|
||
"output_prefix": output_prefix,
|
||
"status": "success",
|
||
"analysis_route": stage_context.get("analysis_route", ""),
|
||
"result_group": stage_context.get("result_group", ""),
|
||
"member_set_id": stage_context.get("member_set_id", ""),
|
||
"stage_context": stage_context,
|
||
"artifacts": artifacts,
|
||
"parameters": {
|
||
"evalue": args.evalue,
|
||
"coverage": args.coverage,
|
||
"output_prefix": output_prefix,
|
||
"subfamily_file": str(subfamily_file),
|
||
"tree_file": str(tree_file),
|
||
"meme_xml": str(meme_xml or ""),
|
||
"gff3_file": str(gff3_file or ""),
|
||
"domtblout_file": str(domtblout_file or ""),
|
||
"panels": panels,
|
||
"analysis_route": stage_context.get("analysis_route", ""),
|
||
"member_set_id": stage_context.get("member_set_id", ""),
|
||
}
|
||
}
|
||
if scope_data:
|
||
manifest["scope_id"] = scope_data.get("scope_id", "")
|
||
manifest["scope_mode"] = scope_data.get("scope_mode", "")
|
||
manifest["scope_file"] = str(scope_file)
|
||
manifest["target_species"] = scope_data.get("target_species", [])
|
||
manifest["reference_species"] = scope_data.get("reference_species", [])
|
||
manifest["comparative_species"] = scope_data.get("comparative_species", [])
|
||
manifest["selected_species"] = scope_data.get("selected_species", [])
|
||
manifest["scope"] = {
|
||
"family": scope_data.get("family", ""),
|
||
"prefix": scope_data.get("prefix", ""),
|
||
"scope_id": scope_data.get("scope_id", ""),
|
||
"scope_mode": scope_data.get("scope_mode", ""),
|
||
"target_species": scope_data.get("target_species", []),
|
||
"reference_species": scope_data.get("reference_species", []),
|
||
"comparative_species": scope_data.get("comparative_species", []),
|
||
"selected_species": scope_data.get("selected_species", []),
|
||
}
|
||
|
||
manifest_path = workspace / "final" / f"{output_prefix}.combo_panel_test.manifest.json"
|
||
manifest_path.write_text(json.dumps(manifest, indent=2, ensure_ascii=False))
|
||
print(f"[INFO] Manifest: {manifest_path}")
|
||
if scope_data and scope_data.get("scope_id"):
|
||
scoped_manifest = write_legacy_manifest_copy(manifest_path, prefix, str(scope_data.get("scope_id") or ""), "combo_panel_test")
|
||
if scoped_manifest:
|
||
print(f"[INFO] Legacy scoped manifest: {scoped_manifest}")
|
||
|
||
else:
|
||
print(f"[ERROR] Combo plot failed: {result.get('error', result.get('stderr', 'unknown'))}")
|
||
if result.get("stdout"):
|
||
print(result["stdout"])
|
||
sys.exit(1)
|
||
|
||
|
||
if __name__ == "__main__":
|
||
main()
|