1330 lines
52 KiB
Python
Executable File
1330 lines
52 KiB
Python
Executable File
#!/usr/bin/env python3
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"""
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Structure stage: 基因结构可视化
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符合 workspace_contract_v1.md 和 manifest_v1.schema.json 契约
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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 subprocess
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import sys
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import re
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import uuid
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import gzip
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from datetime import datetime
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from pathlib import Path
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from typing import Dict, List, Optional, Tuple
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import hashlib
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PROJECT_ROOT = Path(__file__).resolve().parents[2]
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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
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from gfa_core.gene_family_stage_context import apply_stage_context, build_stage_context, user_output_prefix_for, write_legacy_manifest_copy
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from gfa_core.mas.effective_members import MemberResolutionError, resolve_effective_members
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CONDA_BIN = "/home/xzq/miniconda3/envs/test4py311/bin"
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if CONDA_BIN not in os.environ.get("PATH", ""):
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os.environ["PATH"] = CONDA_BIN + ":" + os.environ.get("PATH", "")
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def display_path(path: Path | str) -> str:
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"""Return the user-facing symlink path instead of resolving data-root links."""
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return str(Path(path).absolute())
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def current_input_dir(workspace: Path) -> Path:
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return workspace.parent.parent / "input" / workspace.name
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def inside_current_job(workspace: Path, path: Path) -> bool:
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input_dir = current_input_dir(workspace)
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try:
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resolved = path.resolve()
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return resolved.is_relative_to(workspace.resolve()) or resolved.is_relative_to(input_dir.resolve())
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except OSError:
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return False
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def rebase_current_job_path(workspace: Path, path: Path) -> Optional[Path]:
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"""Map copied legacy workspace/input paths back onto the current job roots."""
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parts = path.parts
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for root_name, current_root in (("workspace", workspace), ("input", current_input_dir(workspace))):
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for idx, part in enumerate(parts):
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if part != root_name:
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continue
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if idx + 1 >= len(parts) or parts[idx + 1] != workspace.name:
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continue
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suffix = Path(*parts[idx + 2:]) if idx + 2 < len(parts) else Path()
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candidate = current_root / suffix
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if candidate.exists():
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return candidate
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return None
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def resolve_job_path(workspace: Path, raw_path: str | Path, manifest_path: Optional[Path] = None) -> Optional[Path]:
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"""Resolve a copied job path without trusting stale absolute paths."""
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raw_text = str(raw_path or "").strip()
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if not raw_text:
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return None
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path = Path(raw_text)
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if path.is_absolute():
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if inside_current_job(workspace, path):
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return path
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rebased = rebase_current_job_path(workspace, path)
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if rebased:
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return rebased
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return None
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candidates: List[Path] = [workspace / path, current_input_dir(workspace) / path]
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if manifest_path:
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candidates.extend([manifest_path.parent / path, manifest_path.parent / path.name])
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if str(path).startswith("final/") and manifest_path:
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candidates.append(manifest_path.parent / path.name)
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for candidate in candidates:
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if candidate.exists():
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return candidate
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return None
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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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for key in ("path", "relpath_or_hint", "file", "full_path"):
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resolved = resolve_job_path(workspace, artifact.get(key) or "", manifest_path)
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if resolved:
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return resolved
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return None
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def get_tool_versions() -> Dict[str, str]:
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"""获取工具版本信息"""
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versions = {}
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try:
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r = subprocess.run(["R", "--version"], capture_output=True, text=True, check=False)
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if r.returncode == 0:
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versions["R"] = r.stdout.split("\n")[0]
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except:
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versions["R"] = "not_found"
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try:
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import Bio
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versions["biopython"] = Bio.__version__
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except:
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versions["biopython"] = "not_found"
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return versions
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def compute_file_hash(filepath: Path) -> str:
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"""计算文件 SHA256 哈希"""
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sha256_hash = hashlib.sha256()
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try:
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with open(filepath, "rb") as f:
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for byte_block in iter(lambda: f.read(4096), b""):
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sha256_hash.update(byte_block)
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return sha256_hash.hexdigest()
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except:
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return ""
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def read_gene_ids(id_file: Path) -> List[str]:
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"""读取基因 ID 列表"""
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ids = []
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with open(id_file, 'r') as f:
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for line in f:
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line = line.strip()
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if line and not line.startswith('#'):
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ids.append(line)
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return ids
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def open_text_auto(path: Path):
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if path.suffix == ".gz":
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return gzip.open(path, "rt", encoding="utf-8", errors="ignore")
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return open(path, "r", encoding="utf-8", errors="ignore")
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def read_tree_order(tree_file: Path) -> List[str]:
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"""从树文件读取叶节点顺序"""
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try:
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from Bio import Phylo
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tree = Phylo.read(tree_file, 'newick')
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tips = [clade.name for clade in tree.get_terminals()]
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return tips if tips else []
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except:
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return []
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def should_strip_version(raw_id: str) -> bool:
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lowered = (raw_id or "").lower()
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return not (lowered.startswith("evm.model.") or lowered.startswith("evm.tu."))
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def strip_gff_id(raw_id: Optional[str]) -> str:
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if not raw_id:
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return ""
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value = str(raw_id).strip()
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# Tree/Newick labels may replace ':' with '_' (mRNA:HanXR -> mRNA_HanXR).
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# Strip repeated typed wrappers so GFF attributes, FASTA IDs and tree-safe
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# labels all resolve to the same member accession.
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while True:
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updated = re.sub(r"^(gene|transcript|CDS|mRNA)[:_]", "", value, flags=re.IGNORECASE)
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if updated == value:
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break
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value = updated
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value = re.sub(r'_[PT]\d+$', '', value)
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if should_strip_version(value):
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value = re.sub(r'\.\d+$', '', value)
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return value
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def id_variants(raw_id: Optional[str]) -> set[str]:
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value = strip_gff_id(raw_id)
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if not value:
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return set()
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variants = {value}
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if should_strip_version(value) and re.search(r'\.\d+$', value):
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variants.add(re.sub(r'\.\d+$', '', value))
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variants.add(re.sub(r'_[PT]\d+$', '', value))
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expanded = set()
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for item in variants:
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if item:
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expanded.update({item, item.upper(), item.lower()})
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expanded.update({f"gene:{item}", f"transcript:{item}", f"CDS:{item}", f"mRNA:{item}"})
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return expanded
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def build_target_id_lookup(gene_ids: List[str]) -> Dict[str, str]:
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lookup: Dict[str, str] = {}
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for gid in gene_ids:
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canonical = str(gid).strip()
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if not canonical:
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continue
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for variant in id_variants(canonical):
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lookup.setdefault(variant, canonical)
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return lookup
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def canonical_target_id(raw_id: Optional[str], target_lookup: Dict[str, str]) -> Optional[str]:
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for variant in id_variants(raw_id):
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if variant in target_lookup:
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return target_lookup[variant]
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return None
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def parse_gff3_attributes(attr: str) -> Dict[str, str]:
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attr_map: Dict[str, str] = {}
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for item in str(attr or "").split(";"):
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if "=" not in item:
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continue
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key, value = item.split("=", 1)
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attr_map[key] = value
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return attr_map
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def canonical_from_attr_values(attr_map: Dict[str, str], keys: List[str], target_lookup: Dict[str, str]) -> Optional[str]:
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for key in keys:
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value = attr_map.get(key)
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if not value:
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continue
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for token in str(value).split(","):
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canonical = canonical_target_id(token, target_lookup)
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if canonical:
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return canonical
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return None
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def resolve_gff3_path(ws: Path, prefix: str, cli_gff3: Optional[str] = None) -> Path:
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"""
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解析 GFF3 文件路径
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命名规则: {species_short}_final.gff3 (如 Ft_final.gff3)
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优先级: final/ > input/
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Args:
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ws: workspace 目录
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prefix: 分析前缀 (如 Ft.SPL)，从中提取物种简写 Ft
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cli_gff3: 命令行指定的 GFF3 路径（可选）
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Returns:
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GFF3 文件路径
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Raises:
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FileNotFoundError: 找不到符合命名规范的 GFF3 文件
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"""
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# 方式一：命令行指定（如果提供）
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if cli_gff3:
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gff3_path = resolve_job_path(ws, cli_gff3) or Path(cli_gff3)
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if gff3_path.exists():
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print(f"[INFO] Using specified GFF3: {gff3_path}")
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return gff3_path
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else:
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raise FileNotFoundError(f"Specified GFF3 not found: {cli_gff3}")
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# 从 prefix 提取物种简写 (Ft.SPL -> Ft)
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species_short = prefix.split('.')[0] if '.' in prefix else prefix
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# 标准命名: Ft_final.gff3
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gff3_name = f"{species_short}_final.gff3"
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final_dir = ws / "final"
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input_dir = ws / "input"
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# 也检查 bbav2/input/{job_id}/ 路径
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job_id = ws.name
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alt_input_dir = ws.parent.parent / "input" / job_id
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# 优先级: final/ > workspace/input/ > bbav2/input/{job_id}/
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search_paths = []
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if final_dir.exists():
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search_paths.append(final_dir / gff3_name)
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if input_dir.exists():
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search_paths.append(input_dir / gff3_name)
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if alt_input_dir.exists():
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search_paths.append(alt_input_dir / gff3_name)
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# 查找
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for candidate in search_paths:
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if candidate.exists():
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print(f"[INFO] Found GFF3: {candidate}")
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return candidate
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# 都找不到，报错
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searched = ", ".join([str(p) for p in search_paths]) if search_paths else "no directories available"
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raise FileNotFoundError(
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f"Cannot find GFF3 file '{gff3_name}' for prefix '{prefix}'. "
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f"Searched in: {searched}. "
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f"Please ensure the file follows naming convention: {{species_short}}_final.gff3 "
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f"or specify --gff3 explicitly."
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)
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def find_prepared_gff3(ws: Path, species: str) -> Optional[Path]:
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job_id = ws.name
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candidates = [
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ws / "final" / f"{species}_final.gff3",
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ws / "input" / f"{species}_final.gff3",
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ws.parent.parent / "input" / job_id / f"{species}_final.gff3",
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ws.parent.parent / "input" / job_id / species / f"{species}_final.gff3",
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]
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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.absolute()
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return None
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def resolve_scope_gff3_paths(scope_data: Dict, ws: Optional[Path] = None) -> List[Tuple[str, Path]]:
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target_species = [str(item).strip() for item in scope_data.get("target_species", []) if str(item).strip()]
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selected_species = [str(item).strip() for item in scope_data.get("selected_species", []) if str(item).strip()]
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scope_mode = str(scope_data.get("scope_mode") or "")
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species_for_structure = selected_species if scope_mode == "target_plus_reference" and selected_species else target_species
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if not species_for_structure:
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raise FileNotFoundError("Scope file does not define species for structure stage")
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target_set = set(target_species)
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resolved: List[Tuple[str, Path]] = []
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missing: List[str] = []
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files = scope_data.get("files", {})
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for species in species_for_structure:
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selected: Optional[Path] = None
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if ws is not None and species in target_set:
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selected = find_prepared_gff3(ws, species)
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species_files = files.get(species, {})
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if selected is None:
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for record in species_files.get("gff", []):
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path_text = str(record.get("path") or "")
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path = resolve_job_path(ws, path_text) if (ws is not None and path_text) else (Path(path_text) if path_text else None)
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if path and path.exists() and path.stat().st_size > 0:
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selected = path
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break
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if selected:
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resolved.append((species, selected.absolute()))
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else:
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missing.append(species)
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if missing:
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raise FileNotFoundError(
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"Missing target GFF3 files in scope for structure stage: " + ", ".join(missing)
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)
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return resolved
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def resolve_scope_tree_file(ws: Path, prefix: str, scope_data: Optional[Dict], cli_tree: Optional[str] = None) -> Path:
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final_dir = ws / "final"
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if cli_tree:
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tree_path = resolve_job_path(ws, cli_tree) or Path(cli_tree)
|
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if tree_path.exists() and tree_path.stat().st_size > 0:
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return tree_path.absolute()
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raise FileNotFoundError(f"Specified tree file not found: {cli_tree}")
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||
manifest_candidates: List[Path] = []
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scope_id = str((scope_data or {}).get("scope_id") or "").strip()
|
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if scope_id:
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manifest_candidates.append(final_dir / f"{prefix}.{sanitize_token(scope_id)}.phylogeny.manifest.json")
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else:
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manifest_candidates.append(final_dir / f"{prefix}.phylogeny.manifest.json")
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||
for manifest_file in manifest_candidates:
|
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if not manifest_file.exists() or manifest_file.stat().st_size == 0:
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continue
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||
try:
|
||
manifest = json.loads(manifest_file.read_text(encoding="utf-8"))
|
||
except Exception:
|
||
continue
|
||
tree_path = None
|
||
artifact = (manifest.get("artifacts", {}) or {}).get("tree")
|
||
if isinstance(artifact, dict):
|
||
tree_path = manifest_artifact_path(ws, manifest_file, artifact)
|
||
elif isinstance(artifact, str):
|
||
tree_path = resolve_job_path(ws, artifact, manifest_file)
|
||
if tree_path and tree_path.exists() and tree_path.stat().st_size > 0:
|
||
return tree_path.absolute()
|
||
|
||
fallback = final_dir / f"{prefix}.tree.nwk"
|
||
if not scope_id and fallback.exists() and fallback.stat().st_size > 0:
|
||
return fallback.absolute()
|
||
raise FileNotFoundError(f"Tree file not found for prefix {prefix}. Please run phylogeny first or specify --tree.")
|
||
|
||
|
||
def filter_scope_gff3(
|
||
gff3_sources: List[Tuple[str, Path]],
|
||
gene_ids: List[str],
|
||
output_gff3: Path,
|
||
structure_dir: Path,
|
||
prefix: str,
|
||
) -> Tuple[bool, Dict]:
|
||
if len(gff3_sources) == 1:
|
||
return filter_gff3(gff3_sources[0][1], gene_ids, output_gff3)
|
||
|
||
aggregate = {
|
||
"total_lines": 0,
|
||
"filtered_lines": 0,
|
||
"genes_found": 0,
|
||
"mrna_count": 0,
|
||
"cds_count": 0,
|
||
"utr_count": 0,
|
||
"per_species": {},
|
||
}
|
||
temp_paths: List[Path] = []
|
||
for species, gff3_file in gff3_sources:
|
||
temp_path = structure_dir / f"{prefix}.{species}.structure.filtered.gff3"
|
||
success, stats = filter_gff3(gff3_file, gene_ids, temp_path)
|
||
if not success:
|
||
return False, aggregate
|
||
temp_paths.append(temp_path)
|
||
aggregate["per_species"][species] = stats
|
||
for key in ("total_lines", "filtered_lines", "genes_found", "mrna_count", "cds_count", "utr_count"):
|
||
aggregate[key] += int(stats.get(key, 0))
|
||
|
||
with output_gff3.open("w", encoding="utf-8") as out:
|
||
for temp_path in temp_paths:
|
||
with temp_path.open(encoding="utf-8", errors="ignore") as handle:
|
||
for raw in handle:
|
||
out.write(raw)
|
||
return True, aggregate
|
||
|
||
|
||
def resolve_subfamily_file(ws: Path, prefix: str, cli_subfamily: Optional[str] = None, output_prefix: Optional[str] = None, scope_data: Optional[Dict] = None) -> Optional[Path]:
|
||
"""
|
||
解析亚家族文件路径
|
||
|
||
命名规则: {prefix}.confirmed_subfamily.tsv (如 Ft.SPL.confirmed_subfamily.tsv)
|
||
优先级: final/ > input/
|
||
|
||
Args:
|
||
ws: workspace 目录
|
||
prefix: 分析前缀 (如 Ft.SPL)
|
||
cli_subfamily: 命令行指定的亚家族文件路径（可选）
|
||
|
||
Returns:
|
||
亚家族文件路径，或 None（可选）
|
||
"""
|
||
# 方式一：命令行指定
|
||
if cli_subfamily:
|
||
if str(cli_subfamily).strip().lower() in {"none", "skip", "disabled"}:
|
||
print("[INFO] Subfamily coloring explicitly disabled")
|
||
return None
|
||
subfamily_path = resolve_job_path(ws, cli_subfamily) or Path(cli_subfamily)
|
||
if subfamily_path.exists():
|
||
print(f"[INFO] Using specified subfamily file: {subfamily_path}")
|
||
return subfamily_path
|
||
else:
|
||
print(f"[WARNING] Specified subfamily file not found: {cli_subfamily}")
|
||
return None
|
||
|
||
# 自动查找只接受 confirmed_subfamily；prediction/geneID 必须由 --subfamily 显式传入。
|
||
names = []
|
||
bases = []
|
||
for base in [output_prefix, prefix]:
|
||
if base and base not in bases:
|
||
bases.append(base)
|
||
if output_prefix and ".subfamily_evidence" in output_prefix:
|
||
bases.append(output_prefix.replace(".subfamily_evidence", ".subfamily_prediction"))
|
||
scope_mode = str((scope_data or {}).get("scope_mode") or "").strip()
|
||
family = str((scope_data or {}).get("family") or (prefix.split(".")[-1] if "." in prefix else "")).strip()
|
||
targets = [str(x) for x in (scope_data or {}).get("target_species", []) if str(x).strip()]
|
||
refs = [str(x) for x in (scope_data or {}).get("reference_species", []) if str(x).strip()]
|
||
if scope_mode == "target_plus_reference" and len(targets) == 1 and family:
|
||
bases.append(f"{targets[0]}.{family}.target_plus_reference")
|
||
ref_part = "-".join(refs) if refs else ""
|
||
if ref_part:
|
||
bases.append(f"Target.{family}.target-{targets[0]}.ref-{ref_part}.subfamily_prediction")
|
||
seen_bases = set()
|
||
for base in bases:
|
||
if not base or base in seen_bases:
|
||
continue
|
||
seen_bases.add(base)
|
||
names.extend([
|
||
f"{base}.confirmed_subfamily.tsv",
|
||
])
|
||
subfamily_name = f"{prefix}.confirmed_subfamily.tsv"
|
||
|
||
final_dir = ws / "final"
|
||
input_dir = ws / "input"
|
||
|
||
# 也检查 bbav2/input/{job_id}/ 路径（用户上传文件的实际位置）
|
||
job_id = ws.name
|
||
alt_input_dir = ws.parent.parent / "input" / job_id
|
||
|
||
# 优先级: final/ > workspace/input/ > bbav2/input/{job_id}/
|
||
search_paths = []
|
||
if final_dir.exists():
|
||
search_paths.extend(final_dir / name for name in names)
|
||
if input_dir.exists():
|
||
search_paths.extend(input_dir / name for name in names)
|
||
if alt_input_dir.exists():
|
||
search_paths.extend(alt_input_dir / name for name in names)
|
||
|
||
for candidate in search_paths:
|
||
if candidate.exists():
|
||
print(f"[INFO] Found subfamily file: {candidate}")
|
||
return candidate
|
||
|
||
print(f"[INFO] No subfamily file found ({subfamily_name}), will use default coloring")
|
||
return None
|
||
|
||
|
||
def filter_gff3(gff3_file: Path, gene_ids: List[str], output_gff3: Path) -> Tuple[bool, Dict]:
|
||
"""
|
||
过滤 GFF3 文件，只保留目标基因。
|
||
|
||
ID matching is scope-aware: GFF3 gene/transcript/CDS prefixes, case, version
|
||
suffixes and _P/_T suffixes are normalized back to the requested member IDs.
|
||
NCBI/Gnomon records often use protein IDs as mRNA/CDS IDs while storing the
|
||
transcript accession in Name/transcript_id; those transcript aliases are
|
||
captured so CDS rows are assigned back to the requested XM_* member IDs.
|
||
"""
|
||
target_lookup = build_target_id_lookup(gene_ids)
|
||
transcript_to_gene: Dict[str, str] = {}
|
||
stats = {
|
||
"total_lines": 0,
|
||
"filtered_lines": 0,
|
||
"genes_found": set(),
|
||
"mrna_count": 0,
|
||
"cds_count": 0,
|
||
"utr_count": 0
|
||
}
|
||
|
||
with open_text_auto(gff3_file) as f_in, open(output_gff3, 'w') as f_out:
|
||
for line in f_in:
|
||
stats["total_lines"] += 1
|
||
|
||
if line.startswith('#'):
|
||
continue
|
||
|
||
line = re.sub(r'\t(\S+UTR)\t', '\tUTR\t', line, flags=re.IGNORECASE)
|
||
|
||
parts = line.strip().split('\t')
|
||
if len(parts) != 9:
|
||
continue
|
||
|
||
feat_type = parts[2]
|
||
|
||
if feat_type == "gene":
|
||
continue
|
||
|
||
attr_map = parse_gff3_attributes(parts[8])
|
||
feat_type_norm = feat_type.lower()
|
||
canonical_id = canonical_from_attr_values(
|
||
attr_map,
|
||
["ID", "Name", "transcript_id", "gene_id", "gene", "Parent"],
|
||
target_lookup,
|
||
)
|
||
canonical_parent = canonical_from_attr_values(
|
||
attr_map,
|
||
["Parent", "ID", "Name", "transcript_id", "gene_id", "gene"],
|
||
target_lookup,
|
||
)
|
||
parent_text = attr_map.get("Parent", "")
|
||
for parent_token in str(parent_text).split(","):
|
||
if parent_token in transcript_to_gene:
|
||
canonical_parent = transcript_to_gene[parent_token]
|
||
break
|
||
|
||
is_target = False
|
||
|
||
if feat_type_norm in {"mrna", "transcript"} and canonical_id:
|
||
is_target = True
|
||
stats["genes_found"].add(canonical_id)
|
||
stats["mrna_count"] += 1
|
||
for alias_key in ("ID", "Name", "transcript_id"):
|
||
alias = attr_map.get(alias_key)
|
||
if not alias:
|
||
continue
|
||
for token in str(alias).split(","):
|
||
if token:
|
||
transcript_to_gene[token] = canonical_id
|
||
elif feat_type_norm in {"cds", "utr", "exon"} and canonical_parent:
|
||
is_target = True
|
||
if feat_type_norm == "cds":
|
||
stats["cds_count"] += 1
|
||
elif feat_type_norm == "utr":
|
||
stats["utr_count"] += 1
|
||
|
||
if is_target:
|
||
f_out.write('\t'.join(parts) + '\n')
|
||
stats["filtered_lines"] += 1
|
||
|
||
stats["genes_found"] = len(stats["genes_found"])
|
||
return True, stats
|
||
|
||
def gff3_to_tsv(
|
||
gff3_file: Path,
|
||
output_tsv: Path,
|
||
tree_order: List[str],
|
||
target_gene_ids: Optional[List[str]] = None,
|
||
) -> Tuple[bool, Dict]:
|
||
"""将过滤后的 GFF3 转换为 TSV，并把 feature 归一到 scope/tree 成员 ID。"""
|
||
data = []
|
||
stats = {
|
||
"total_features": 0,
|
||
"genes_with_structure": set(),
|
||
"total_cds": 0,
|
||
"total_utr": 0,
|
||
"exon_counts": {},
|
||
"gene_lengths": {}
|
||
}
|
||
target_lookup = build_target_id_lookup(target_gene_ids or tree_order)
|
||
transcript_to_gene: Dict[str, str] = {}
|
||
seen_features: set[str] = set()
|
||
|
||
with open_text_auto(gff3_file) as f:
|
||
for line in f:
|
||
parts = line.strip().split('\t')
|
||
if len(parts) != 9:
|
||
continue
|
||
|
||
chrom, source, feat_type, start, end, score, strand, phase, attr = parts
|
||
feat_type_norm = feat_type.lower()
|
||
attr_map = parse_gff3_attributes(attr)
|
||
|
||
if feat_type_norm in {"mrna", "transcript"}:
|
||
gene_id = canonical_from_attr_values(
|
||
attr_map,
|
||
["ID", "Name", "transcript_id", "geneID", "gene_id", "gene", "Parent"],
|
||
target_lookup,
|
||
) if target_lookup else strip_gff_id(attr_map.get("ID") or attr_map.get("Name") or attr_map.get("transcript_id") or attr_map.get("Parent"))
|
||
if gene_id:
|
||
for alias_key in ("ID", "Name", "transcript_id"):
|
||
alias = attr_map.get(alias_key)
|
||
if not alias:
|
||
continue
|
||
for token in str(alias).split(","):
|
||
if token:
|
||
transcript_to_gene[token] = gene_id
|
||
else:
|
||
gene_id = canonical_from_attr_values(
|
||
attr_map,
|
||
["Parent", "ID", "Name", "transcript_id", "geneID", "gene_id", "gene"],
|
||
target_lookup,
|
||
) if target_lookup else strip_gff_id(attr_map.get("Parent") or attr_map.get("ID"))
|
||
parent_text = attr_map.get("Parent", "")
|
||
for parent_token in str(parent_text).split(","):
|
||
if parent_token in transcript_to_gene:
|
||
gene_id = transcript_to_gene[parent_token]
|
||
break
|
||
|
||
if not gene_id:
|
||
continue
|
||
|
||
start_num = int(start)
|
||
end_num = int(end)
|
||
feature_key = f"{gene_id}|{feat_type}|{start_num}|{end_num}|{strand}|{chrom}"
|
||
if feature_key in seen_features:
|
||
continue
|
||
seen_features.add(feature_key)
|
||
|
||
data.append({
|
||
'gene_id': gene_id,
|
||
'feature': feat_type,
|
||
'start': start_num,
|
||
'end': end_num,
|
||
'strand': strand,
|
||
'chrom': chrom
|
||
})
|
||
|
||
stats["total_features"] += 1
|
||
|
||
if feat_type == "CDS":
|
||
stats["genes_with_structure"].add(gene_id)
|
||
stats["total_cds"] += 1
|
||
stats["exon_counts"][gene_id] = stats["exon_counts"].get(gene_id, 0) + 1
|
||
elif feat_type == "UTR":
|
||
stats["genes_with_structure"].add(gene_id)
|
||
stats["total_utr"] += 1
|
||
|
||
if feat_type in {"CDS", "UTR"}:
|
||
if gene_id not in stats["gene_lengths"]:
|
||
stats["gene_lengths"][gene_id] = {"min": start_num, "max": end_num}
|
||
else:
|
||
stats["gene_lengths"][gene_id]["min"] = min(stats["gene_lengths"][gene_id]["min"], start_num)
|
||
stats["gene_lengths"][gene_id]["max"] = max(stats["gene_lengths"][gene_id]["max"], end_num)
|
||
|
||
if not data:
|
||
return False, stats
|
||
|
||
stats["genes_with_structure"] = len(stats["genes_with_structure"])
|
||
|
||
for gene_id, lengths in stats["gene_lengths"].items():
|
||
stats["gene_lengths"][gene_id] = lengths["max"] - lengths["min"] + 1
|
||
|
||
gene_list = sorted(set(d['gene_id'] for d in data))
|
||
|
||
if tree_order:
|
||
order_dict = {name: i for i, name in enumerate(tree_order)}
|
||
gene_list = sorted(gene_list, key=lambda x: order_dict.get(x, 999999))
|
||
|
||
gene_to_y = {g: i+1 for i, g in enumerate(gene_list)}
|
||
|
||
with open(output_tsv, 'w') as f:
|
||
f.write('gene_id\tfeature\tstart\tend\tstrand\tchrom\ty_pos\n')
|
||
for d in data:
|
||
y_pos = gene_to_y.get(d['gene_id'], 0)
|
||
f.write(f"{d['gene_id']}\t{d['feature']}\t{d['start']}\t{d['end']}\t{d['strand']}\t{d['chrom']}\t{y_pos}\n")
|
||
|
||
return True, stats
|
||
|
||
def calculate_structure_metrics(stats: Dict, gene_count: int) -> Dict:
|
||
"""计算结构相关的 metrics，并记录结构长度 QC。"""
|
||
genes_with_structure = min(int(stats.get("genes_with_structure", 0) or 0), max(gene_count, 0))
|
||
metrics = {
|
||
"genes_total": gene_count,
|
||
"genes_with_structure": genes_with_structure,
|
||
"structure_coverage_rate": round(genes_with_structure / max(gene_count, 1), 4),
|
||
"total_cds_features": stats.get("total_cds", 0),
|
||
"total_utr_features": stats.get("total_utr", 0),
|
||
"avg_exon_count_per_gene": 0.0,
|
||
"avg_gene_length_bp": 0.0,
|
||
"avg_cds_length_bp": 0.0,
|
||
"median_gene_length_bp": 0.0,
|
||
"max_gene_length_bp": 0,
|
||
"long_gene_outlier_threshold_bp": 0,
|
||
"long_gene_outlier_count": 0,
|
||
"top_longest_gene_structures": [],
|
||
"long_gene_outliers": [],
|
||
}
|
||
|
||
exon_counts = stats.get("exon_counts", {})
|
||
gene_lengths = stats.get("gene_lengths", {})
|
||
|
||
if exon_counts:
|
||
metrics["avg_exon_count_per_gene"] = round(sum(exon_counts.values()) / len(exon_counts), 2)
|
||
|
||
if gene_lengths:
|
||
lengths = sorted(int(v) for v in gene_lengths.values() if int(v) > 0)
|
||
metrics["avg_gene_length_bp"] = round(sum(lengths) / len(lengths), 2)
|
||
metrics["avg_cds_length_bp"] = round(metrics["avg_exon_count_per_gene"] * 100, 2)
|
||
mid = len(lengths) // 2
|
||
if len(lengths) % 2:
|
||
median_len = lengths[mid]
|
||
else:
|
||
median_len = (lengths[mid - 1] + lengths[mid]) / 2
|
||
metrics["median_gene_length_bp"] = round(median_len, 2)
|
||
metrics["max_gene_length_bp"] = max(lengths)
|
||
threshold = int(max(10000, median_len * 5))
|
||
metrics["long_gene_outlier_threshold_bp"] = threshold
|
||
ranked = sorted(gene_lengths.items(), key=lambda item: int(item[1]), reverse=True)
|
||
metrics["top_longest_gene_structures"] = [
|
||
{
|
||
"gene_id": gene_id,
|
||
"length_bp": int(length),
|
||
"cds_count": int(exon_counts.get(gene_id, 0) or 0),
|
||
}
|
||
for gene_id, length in ranked[:10]
|
||
]
|
||
metrics["long_gene_outliers"] = [
|
||
item for item in metrics["top_longest_gene_structures"]
|
||
if int(item.get("length_bp", 0)) >= threshold
|
||
]
|
||
metrics["long_gene_outlier_count"] = sum(1 for _gene_id, length in gene_lengths.items() if int(length) >= threshold)
|
||
|
||
return metrics
|
||
|
||
|
||
def run_r_plotting(tree_file: Path, structure_tsv: Path, output_prefix: Path,
|
||
rscript_path: Optional[Path] = None, cpu: int = 4,
|
||
subfamily_file: Optional[Path] = None,
|
||
project_root: Optional[Path] = None) -> Dict:
|
||
"""运行 R 绘图脚本"""
|
||
if rscript_path is None:
|
||
rscript_path = Path(__file__).parent.parent.parent / "scripts" / "plot_structure.R"
|
||
|
||
if not rscript_path.exists():
|
||
return {"success": False, "error": f"R script not found: {rscript_path}"}
|
||
|
||
rscript_exe = Path("/home/xzq/miniconda3/envs/test4py311/bin/Rscript")
|
||
if not rscript_exe.exists():
|
||
rscript_exe = Path("Rscript")
|
||
|
||
cmd = [
|
||
str(rscript_exe), str(rscript_path),
|
||
"--tree", str(tree_file),
|
||
"--structure", str(structure_tsv),
|
||
"--output", str(output_prefix)
|
||
]
|
||
|
||
# 传递项目根目录，让 R 脚本自动推断 job_id 和 subfamily
|
||
if project_root and project_root.exists():
|
||
cmd.extend(["--root", str(project_root)])
|
||
|
||
# 如果指定了亚家族文件，传递给 R 脚本
|
||
if subfamily_file and subfamily_file.exists():
|
||
cmd.extend(["--subfamily", str(subfamily_file)])
|
||
|
||
print(f"[CMD] {' '.join(cmd)}")
|
||
|
||
start_time = datetime.now()
|
||
try:
|
||
result = subprocess.run(cmd, capture_output=True, text=True, check=False, timeout=600)
|
||
end_time = datetime.now()
|
||
|
||
success = result.returncode == 0
|
||
|
||
output_files = []
|
||
for ext in ['.png', '.pdf']:
|
||
f = Path(f"{output_prefix}{ext}")
|
||
if f.exists():
|
||
output_files.append(str(f))
|
||
|
||
return {
|
||
"success": success and len(output_files) > 0,
|
||
"returncode": result.returncode,
|
||
"stdout": result.stdout[-2000:],
|
||
"stderr": result.stderr[-2000:],
|
||
"output_files": output_files,
|
||
"elapsed_sec": (end_time - start_time).total_seconds()
|
||
}
|
||
|
||
except subprocess.TimeoutExpired:
|
||
return {"success": False, "error": "R plotting timeout (>600s)", "elapsed_sec": 600}
|
||
except Exception as e:
|
||
return {"success": False, "error": str(e), "elapsed_sec": 0}
|
||
|
||
|
||
def generate_report(prefix: str, metrics: Dict, parameters: Dict,
|
||
output_file: Path, artifacts: Dict, plot_success: bool) -> None:
|
||
"""生成 structure_report.md 报告"""
|
||
report_lines = [
|
||
f"# Structure Analysis Report: {prefix}",
|
||
"",
|
||
f"**Generated:** {datetime.now().strftime('%Y-%m-%d %H:%M:%S')}",
|
||
f"**Status:** {'Success' if plot_success else 'Partial Success (Plotting Failed)'}",
|
||
"",
|
||
"## Summary",
|
||
"",
|
||
f"- **Total Genes:** {metrics['genes_total']}",
|
||
f"- **Genes with Structure:** {metrics['genes_with_structure']}",
|
||
f"- **Structure Coverage:** {metrics['structure_coverage_rate']*100:.1f}%",
|
||
f"- **Total CDS Features:** {metrics['total_cds_features']}",
|
||
f"- **Total UTR Features:** {metrics['total_utr_features']}",
|
||
"",
|
||
"## Structure Statistics",
|
||
"",
|
||
f"- **Average Exons per Gene:** {metrics['avg_exon_count_per_gene']}",
|
||
f"- **Average Gene Length:** {metrics['avg_gene_length_bp']:,.0f} bp",
|
||
f"- **Median Gene Length:** {metrics.get('median_gene_length_bp', 0):,.0f} bp",
|
||
f"- **Maximum Gene Length:** {metrics.get('max_gene_length_bp', 0):,.0f} bp",
|
||
f"- **Average CDS Length (est.):** {metrics['avg_cds_length_bp']:,.0f} bp",
|
||
"",
|
||
"## Structure Length QC",
|
||
"",
|
||
f"- **Long-gene outlier threshold:** {metrics.get('long_gene_outlier_threshold_bp', 0):,.0f} bp (max of 10 kb or 5x median gene span)",
|
||
f"- **Long-gene outliers:** {metrics.get('long_gene_outlier_count', 0)}",
|
||
"",
|
||
]
|
||
top_longest = metrics.get("top_longest_gene_structures") or []
|
||
if top_longest:
|
||
report_lines.extend([
|
||
"| Rank | Gene ID | Structure span (bp) | CDS count |",
|
||
"| --- | --- | ---: | ---: |",
|
||
])
|
||
for idx, item in enumerate(top_longest[:10], start=1):
|
||
report_lines.append(
|
||
f"| {idx} | `{item.get('gene_id', '')}` | {int(item.get('length_bp', 0)):,} | {int(item.get('cds_count', 0))} |"
|
||
)
|
||
report_lines.append("")
|
||
if metrics.get("long_gene_outliers"):
|
||
report_lines.append("**QC note:** One or more gene structures exceed the long-gene threshold. Inspect the source GFF3 before biological interpretation.")
|
||
report_lines.append("")
|
||
else:
|
||
report_lines.append("**QC note:** No gene structure exceeds the long-gene threshold; visually long tracks are usually due to real intron spacing relative to compact genes.")
|
||
report_lines.append("")
|
||
report_lines.extend([
|
||
"## Parameters",
|
||
"",
|
||
f"- **GFF3 Source:** {parameters.get('gff3_source', 'N/A')}",
|
||
f"- **GFF3 Naming:** {parameters.get('gff3_naming_convention', 'N/A')}",
|
||
f"- **Subfamily File:** {parameters.get('subfamily_file', 'Not provided')}",
|
||
f"- **CPU Cores:** {parameters.get('cpu', 'N/A')}",
|
||
f"- **Tree File:** {parameters.get('tree_file', 'N/A')}",
|
||
f"- **Gene ID File:** {parameters.get('gene_id_file', 'N/A')}",
|
||
"",
|
||
"## Output Files",
|
||
""
|
||
])
|
||
|
||
for key, artifact in artifacts.items():
|
||
if isinstance(artifact, dict):
|
||
report_lines.append(f"- **{key}:** `{artifact.get('path', 'N/A')}` ({artifact.get('type', 'unknown')})")
|
||
|
||
report_lines.extend([
|
||
"",
|
||
"## Visualization",
|
||
""
|
||
])
|
||
|
||
if plot_success:
|
||
report_lines.append("Gene structure visualization was successfully generated with three panels:")
|
||
report_lines.append("1. **Phylogenetic Tree** - Gene relationships with subfamily coloring")
|
||
report_lines.append("2. **Subfamily Bars** - Visual connection between tree and structure")
|
||
report_lines.append("3. **Gene Structure** - CDS (green) and UTR (orange) architecture")
|
||
else:
|
||
report_lines.append("**Warning:** Gene structure visualization failed. See logs for details.")
|
||
|
||
report_lines.extend([
|
||
"",
|
||
"---",
|
||
"*Generated by Gene Family Analysis Pipeline - Structure Stage*"
|
||
])
|
||
|
||
with open(output_file, 'w') as f:
|
||
f.write('\n'.join(report_lines))
|
||
|
||
print(f"[INFO] Report generated: {output_file}")
|
||
|
||
|
||
def write_manifest(manifest: Dict, manifest_file: Path) -> None:
|
||
"""写入 manifest 文件"""
|
||
with open(manifest_file, 'w') as f:
|
||
json.dump(manifest, f, indent=2)
|
||
print(f"[INFO] Manifest: {manifest_file}")
|
||
|
||
|
||
def write_failure_manifest(workspace: Path, final_dir: Path, prefix: str,
|
||
job_id: str, run_id: str, start_time: datetime,
|
||
error_msg: str, partial_artifacts: Dict = None) -> None:
|
||
"""写入失败状态的 manifest"""
|
||
end_time = datetime.now()
|
||
|
||
manifest = {
|
||
"manifest_version": "1.0",
|
||
"job_id": job_id,
|
||
"stage": "structure",
|
||
"run_id": run_id,
|
||
"prefix": prefix,
|
||
"timestamp": end_time.isoformat(),
|
||
"status": "failed",
|
||
"start_time": start_time.isoformat(),
|
||
"end_time": end_time.isoformat(),
|
||
"elapsed_sec": (end_time - start_time).total_seconds(),
|
||
"cmd": [str(Path(__file__).name)],
|
||
"workspace_root": str(workspace.resolve()),
|
||
"workspace": str(final_dir.resolve()),
|
||
"input_dir": str(workspace / "input"),
|
||
"artifacts": partial_artifacts or {},
|
||
"parameters": {
|
||
"stage": "structure",
|
||
"error": error_msg
|
||
},
|
||
"metrics": {
|
||
"error_type": "execution_failed"
|
||
}
|
||
}
|
||
|
||
manifest_file = final_dir / f"{prefix}.structure.manifest.json"
|
||
write_manifest(manifest, manifest_file)
|
||
print(f"[ERROR] Failure manifest written: {manifest_file}")
|
||
|
||
|
||
def main():
|
||
parser = argparse.ArgumentParser(description='Structure stage - Gene structure visualization')
|
||
parser.add_argument('--prefix', required=True, help='Analysis prefix (e.g., Ft.SPL)')
|
||
parser.add_argument('--workspace', required=True, help='Workspace directory')
|
||
parser.add_argument('--gff3', help='Input GFF3 file (auto-detect if not specified, naming: {species_short}_final.gff3)')
|
||
parser.add_argument('--scope-file', help='Gene-family scope JSON from resolve_scope.py')
|
||
parser.add_argument('--analysis-route', default='', help='Explicit analysis route identity for manifest/status')
|
||
parser.add_argument('--member-set-id', default='', help='Explicit member-set identity for manifest/status')
|
||
parser.add_argument('--tree', help='Phylogeny tree file; auto-detects scoped phylogeny manifest when omitted')
|
||
parser.add_argument('--subfamily', help='Subfamily classification file (explicit path; auto-detect only uses confirmed_subfamily.tsv)')
|
||
parser.add_argument('--cpu', type=int, default=4, help='CPU cores for processing')
|
||
parser.add_argument('--log-file', help='Log file path')
|
||
parser.add_argument('--run-id', help='Run ID (auto-generated if not provided)')
|
||
|
||
args = parser.parse_args()
|
||
|
||
run_id = args.run_id or str(uuid.uuid4())[:8]
|
||
job_id = Path(args.workspace).name
|
||
|
||
start_time = datetime.now()
|
||
ws = Path(args.workspace)
|
||
|
||
# 1. 创建标准目录结构（契约要求）
|
||
structure_dir = ws / "structure" / "analysis"
|
||
structure_dir.mkdir(parents=True, exist_ok=True)
|
||
final_dir = ws / "final"
|
||
final_dir.mkdir(parents=True, exist_ok=True)
|
||
|
||
scope_data: Optional[Dict] = None
|
||
scope_file: Optional[Path] = None
|
||
if args.scope_file:
|
||
scope_file = Path(args.scope_file)
|
||
if not scope_file.exists():
|
||
print(f"[ERROR] Scope file not found: {args.scope_file}")
|
||
write_failure_manifest(ws, final_dir, args.prefix, job_id, run_id, start_time, f"Scope file not found: {args.scope_file}")
|
||
sys.exit(1)
|
||
scope_data = read_scope(scope_file)
|
||
scope_id = str((scope_data or {}).get("scope_id") or "").strip()
|
||
output_prefix = user_output_prefix_for(
|
||
"structure",
|
||
args.prefix,
|
||
scope_data or {},
|
||
analysis_route=args.analysis_route,
|
||
member_set_id=args.member_set_id,
|
||
) if scope_id else args.prefix
|
||
|
||
# 2. 解析输入文件路径（支持自动查找和命名规范）
|
||
try:
|
||
if scope_data:
|
||
gff3_sources = resolve_scope_gff3_paths(scope_data, ws=ws)
|
||
gff3_file = gff3_sources[0][1]
|
||
else:
|
||
gff3_file = resolve_gff3_path(ws, args.prefix, args.gff3)
|
||
species_short_for_gff = args.prefix.split('.')[0] if '.' in args.prefix else args.prefix
|
||
gff3_sources = [(species_short_for_gff, gff3_file)]
|
||
except FileNotFoundError as e:
|
||
print(f"[ERROR] {e}")
|
||
write_failure_manifest(ws, final_dir, args.prefix, job_id, run_id, start_time, str(e))
|
||
sys.exit(1)
|
||
|
||
# 亚家族文件（可选）
|
||
subfamily_file = resolve_subfamily_file(ws, args.prefix, args.subfamily, output_prefix=output_prefix, scope_data=scope_data)
|
||
|
||
# 其他必需输入
|
||
phase = "subfamily_evidence_required" if args.analysis_route == "subfamily_evidence" else "post_confirm_required"
|
||
try:
|
||
resolved_members = resolve_effective_members(
|
||
workspace=ws,
|
||
final_dir=final_dir,
|
||
input_dir=current_input_dir(ws),
|
||
prefix=args.prefix,
|
||
phase=phase, # type: ignore[arg-type]
|
||
require="id",
|
||
member_set_id=args.member_set_id,
|
||
)
|
||
gene_id_file = resolved_members.path_id or Path("")
|
||
print(f"[INFO] Gene ID file from {resolved_members.source_kind}: {gene_id_file}")
|
||
except MemberResolutionError as e:
|
||
if args.analysis_route == "subfamily_evidence":
|
||
error_msg = f"Complete identify member review before Structure subfamily evidence: {e}"
|
||
else:
|
||
error_msg = f"Complete subfamily confirmation before regular Structure analysis: {e}"
|
||
print(f"[ERROR] {error_msg}")
|
||
write_failure_manifest(ws, final_dir, args.prefix, job_id, run_id, start_time, error_msg)
|
||
sys.exit(1)
|
||
try:
|
||
tree_file = resolve_scope_tree_file(ws, args.prefix, scope_data, args.tree)
|
||
except FileNotFoundError as e:
|
||
print(f"[ERROR] {e}")
|
||
write_failure_manifest(ws, final_dir, args.prefix, job_id, run_id, start_time, str(e))
|
||
sys.exit(1)
|
||
if scope_data:
|
||
target_species_set = {str(item) for item in scope_data.get("target_species", []) if str(item).strip()}
|
||
tree_ids = []
|
||
for item in read_tree_order(tree_file):
|
||
if not item:
|
||
continue
|
||
if "|" in item:
|
||
species_code, gene_code = item.split("|", 1)
|
||
if target_species_set and species_code not in target_species_set:
|
||
continue
|
||
tree_ids.append(gene_code)
|
||
else:
|
||
tree_ids.append(item)
|
||
if tree_ids:
|
||
gene_id_file = structure_dir / f"{output_prefix}.scope_members.id"
|
||
with gene_id_file.open("w", encoding="utf-8") as handle:
|
||
for gene_id in tree_ids:
|
||
handle.write(gene_id + "\n")
|
||
|
||
# 验证其他输入
|
||
missing = []
|
||
if not gene_id_file.exists():
|
||
missing.append(f"Gene ID file: {gene_id_file}")
|
||
|
||
if missing:
|
||
error_msg = "Missing required input files:\n" + "\n".join(missing)
|
||
print(f"[ERROR] {error_msg}")
|
||
write_failure_manifest(ws, final_dir, args.prefix, job_id, run_id, start_time, error_msg)
|
||
sys.exit(1)
|
||
|
||
# 提取物种简写用于报告
|
||
species_short = args.prefix.split('.')[0] if '.' in args.prefix else args.prefix
|
||
gff3_naming = (
|
||
"scope target GFF3: " + ", ".join(f"{species}:{path.name}" for species, path in gff3_sources)
|
||
if scope_data else f"{species_short}_final.gff3"
|
||
)
|
||
|
||
print(f"[INFO] Structure stage started for {args.prefix}")
|
||
print(f"[INFO] Job ID: {job_id}, Run ID: {run_id}")
|
||
print(f"[INFO] GFF3 naming convention: {gff3_naming}")
|
||
print(f"[INFO] GFF3 source: {gff3_file}")
|
||
if len(gff3_sources) > 1:
|
||
for species, source_path in gff3_sources:
|
||
print(f"[INFO] Scope GFF3 source: {species} -> {source_path}")
|
||
|
||
# 3. 读取输入数据
|
||
gene_ids = read_gene_ids(gene_id_file)
|
||
print(f"[INFO] {len(gene_ids)} genes to analyze")
|
||
|
||
tree_order = read_tree_order(tree_file)
|
||
print(f"[INFO] Tree order: {len(tree_order)} tips")
|
||
|
||
# 4. 过滤 GFF3（中间文件放入 structure/analysis/）
|
||
structure_gff3 = structure_dir / f"{output_prefix}.structure.filtered.gff3"
|
||
filter_success, filter_stats = filter_scope_gff3(gff3_sources, gene_ids, structure_gff3, structure_dir, args.prefix)
|
||
|
||
if not filter_success:
|
||
error_msg = "Failed to filter GFF3 file"
|
||
print(f"[ERROR] {error_msg}")
|
||
write_failure_manifest(ws, final_dir, args.prefix, job_id, run_id, start_time, error_msg)
|
||
sys.exit(1)
|
||
|
||
print(f"[INFO] Filtered GFF3: {structure_gff3}")
|
||
print(f"[INFO] - Total lines: {filter_stats['total_lines']}")
|
||
print(f"[INFO] - Filtered lines: {filter_stats['filtered_lines']}")
|
||
print(f"[INFO] - Genes found: {filter_stats['genes_found']}")
|
||
|
||
# 5. 转换为 TSV（中间文件放入 structure/analysis/）
|
||
structure_tsv = structure_dir / f"{output_prefix}.structure.tsv"
|
||
convert_success, convert_stats = gff3_to_tsv(structure_gff3, structure_tsv, tree_order, gene_ids)
|
||
|
||
if not convert_success:
|
||
error_msg = "Failed to convert GFF3 to TSV (no valid features found)"
|
||
print(f"[ERROR] {error_msg}")
|
||
write_failure_manifest(ws, final_dir, args.prefix, job_id, run_id, start_time, error_msg)
|
||
sys.exit(1)
|
||
|
||
print(f"[INFO] Structure TSV: {structure_tsv}")
|
||
print(f"[INFO] - Genes with structure: {convert_stats['genes_with_structure']}")
|
||
print(f"[INFO] - Total CDS: {convert_stats['total_cds']}")
|
||
print(f"[INFO] - Total UTR: {convert_stats['total_utr']}")
|
||
|
||
# 6. 计算结构 metrics
|
||
structure_metrics = calculate_structure_metrics(convert_stats, len(gene_ids))
|
||
print(f"[INFO] Metrics calculated:")
|
||
for k, v in structure_metrics.items():
|
||
print(f" - {k}: {v}")
|
||
|
||
# 7. R 绘图（输出到 final/）
|
||
output_path_prefix = final_dir / f"{output_prefix}.structure"
|
||
project_root = Path(__file__).parent.parent.parent # bbav5 根目录
|
||
plot_result = run_r_plotting(
|
||
tree_file,
|
||
structure_tsv,
|
||
output_path_prefix,
|
||
cpu=args.cpu,
|
||
subfamily_file=subfamily_file,
|
||
project_root=project_root
|
||
)
|
||
|
||
plot_success = plot_result.get("success", False)
|
||
if not plot_success:
|
||
print(f"[WARNING] R plotting failed: {plot_result.get('error', plot_result.get('stderr', 'unknown'))}")
|
||
|
||
print(f"[INFO] Plot files: {plot_result.get('output_files', [])}")
|
||
|
||
# 8. 准备 artifacts
|
||
end_time = datetime.now()
|
||
artifacts = {}
|
||
|
||
# 中间文件
|
||
if structure_gff3.exists():
|
||
artifacts["structure_gff3_filtered"] = {
|
||
"artifact": "structure_gff3_filtered",
|
||
"path": str(structure_gff3.relative_to(ws)),
|
||
"full_path": display_path(structure_gff3),
|
||
"type": "gff3",
|
||
"size": structure_gff3.stat().st_size,
|
||
"sha256": compute_file_hash(structure_gff3),
|
||
"description": "Filtered GFF3 with only target genes (intermediate)"
|
||
}
|
||
|
||
if structure_tsv.exists():
|
||
artifacts["structure_tsv"] = {
|
||
"artifact": "structure_tsv",
|
||
"path": str(structure_tsv.relative_to(ws)),
|
||
"full_path": display_path(structure_tsv),
|
||
"type": "tsv",
|
||
"size": structure_tsv.stat().st_size,
|
||
"description": "Gene structure data in TSV format (intermediate)"
|
||
}
|
||
|
||
# 最终产物
|
||
for img_file in plot_result.get("output_files", []):
|
||
img_path = Path(img_file)
|
||
if img_path.exists():
|
||
key = f"structure_plot_{img_path.suffix[1:]}"
|
||
artifacts[key] = {
|
||
"artifact": "structure_plot",
|
||
"path": str(img_path.relative_to(ws)),
|
||
"full_path": display_path(img_path),
|
||
"type": "image",
|
||
"format": img_path.suffix[1:],
|
||
"size": img_path.stat().st_size,
|
||
"sha256": compute_file_hash(img_path),
|
||
"description": f"Gene structure visualization ({img_path.suffix[1:].upper()})"
|
||
}
|
||
|
||
# 9. 生成报告
|
||
report_file = final_dir / f"{output_prefix}.structure_report.md"
|
||
|
||
parameters = {
|
||
"cpu": args.cpu,
|
||
"prefix": args.prefix,
|
||
"output_prefix": output_prefix,
|
||
"stage": "structure",
|
||
"job_id": job_id,
|
||
"run_id": run_id,
|
||
"gff3_source": str(gff3_file),
|
||
"gff3_sources": [{"species": species, "path": str(path)} for species, path in gff3_sources],
|
||
"gff3_naming_convention": gff3_naming,
|
||
"gff3_source_sha256": compute_file_hash(gff3_file),
|
||
"subfamily_file": str(subfamily_file) if subfamily_file else None,
|
||
"tree_file": str(tree_file),
|
||
"gene_id_file": str(gene_id_file),
|
||
"gene_count": len(gene_ids),
|
||
"tree_tip_count": len(tree_order),
|
||
"Rscript_path": str(Path(__file__).parent.parent.parent / "scripts" / "plot_structure.R"),
|
||
"tool_versions": get_tool_versions(),
|
||
"timestamp_start": start_time.isoformat(),
|
||
"timestamp_end": end_time.isoformat(),
|
||
"workspace_root": display_path(ws),
|
||
"input_dir": str(ws / "input"),
|
||
"structure_analysis_dir": str(structure_dir),
|
||
"final_dir": str(final_dir)
|
||
}
|
||
|
||
generate_report(output_prefix, structure_metrics, parameters, report_file, artifacts, plot_success)
|
||
|
||
if report_file.exists():
|
||
artifacts["structure_report"] = {
|
||
"artifact": "structure_report",
|
||
"path": str(report_file.relative_to(ws)),
|
||
"full_path": display_path(report_file),
|
||
"type": "report",
|
||
"format": "markdown",
|
||
"size": report_file.stat().st_size,
|
||
"sha256": compute_file_hash(report_file),
|
||
"description": "Human-readable analysis report"
|
||
}
|
||
|
||
# 10. 确定状态
|
||
status = "success" if plot_success else "partial_success"
|
||
|
||
# 11. 构建完整 manifest
|
||
manifest = {
|
||
"manifest_version": "1.0",
|
||
"job_id": job_id,
|
||
"stage": "structure",
|
||
"run_id": run_id,
|
||
"prefix": args.prefix,
|
||
"output_prefix": output_prefix,
|
||
"timestamp": end_time.isoformat(),
|
||
"status": status,
|
||
"start_time": start_time.isoformat(),
|
||
"end_time": end_time.isoformat(),
|
||
"elapsed_sec": (end_time - start_time).total_seconds(),
|
||
"cmd": [
|
||
str(Path(__file__).name),
|
||
"--prefix", args.prefix,
|
||
"--workspace", str(ws),
|
||
"--gff3", str(gff3_file),
|
||
"--cpu", str(args.cpu),
|
||
"--run-id", run_id
|
||
] + (["--scope-file", str(scope_file)] if scope_file else []) + (["--subfamily", str(subfamily_file)] if subfamily_file else []),
|
||
"workspace_root": display_path(ws),
|
||
"workspace": display_path(structure_dir),
|
||
"input_dir": str(ws / "input"),
|
||
"artifacts": artifacts,
|
||
"parameters": parameters,
|
||
"metrics": structure_metrics
|
||
}
|
||
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", []),
|
||
}
|
||
context = build_stage_context(
|
||
stage="structure",
|
||
prefix=args.prefix,
|
||
scope_data=scope_data or {},
|
||
scope_file=scope_file or "",
|
||
output_prefix=output_prefix,
|
||
subfamily_file=subfamily_file,
|
||
analysis_route=args.analysis_route,
|
||
member_set_id=args.member_set_id,
|
||
)
|
||
manifest["tree_source"] = str(tree_file)
|
||
manifest["gene_id_file"] = str(gene_id_file)
|
||
manifest["gff3_source"] = str(gff3_file)
|
||
apply_stage_context(manifest, context)
|
||
|
||
manifest_file = final_dir / f"{output_prefix}.structure.manifest.json"
|
||
write_manifest(manifest, manifest_file)
|
||
if scope_data and scope_data.get("scope_id"):
|
||
write_legacy_manifest_copy(manifest_file, args.prefix, str(scope_data.get("scope_id") or ""), "structure")
|
||
|
||
# 12. 完成
|
||
if status == "success":
|
||
print(f"[INFO] Structure stage completed successfully")
|
||
else:
|
||
print(f"[WARNING] Structure stage completed with partial success (plotting failed)")
|
||
|
||
print("\n=== OUTPUT_FILES ===")
|
||
for k, v in artifacts.items():
|
||
if isinstance(v, dict) and v.get("type") == "image":
|
||
print(f"IMAGE: {v['full_path']}")
|
||
|
||
sys.exit(0 if status == "success" else 1)
|
||
|
||
|
||
if __name__ == "__main__":
|
||
main()
|