228 lines
7.8 KiB
Python
228 lines
7.8 KiB
Python
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#!/home/xzq/miniconda3/envs/test4py311/bin/python
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"""
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PPI (Protein-Protein Interaction) Analysis v2
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支持非模式植物：通过同源基因映射查询模式植物STRING数据库
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方案2+3：输出TSV数据 + 生成STRING网页链接
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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 sys
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from pathlib import Path
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from typing import Any, Dict, List, Optional
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import hashlib
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import urllib.parse
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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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sys.path.insert(0, str(Path(__file__).parent))
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from string_api import StringAPI
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from gfa_core.mas.effective_members import (
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MemberResolutionError,
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candidate_member_prefixes,
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resolve_effective_members,
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)
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# 添加conda环境bin目录到PATHCONDA_BIN = "/home/xzq/miniconda3/envs/test4py311/bin"if CONDA_BIN not in os.environ.get("PATH", ""): os.environ["PATH"] = CONDA_BIN + ":" + os.environ.get("PATH", "")
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def parse_ortholog_mapping(mapping_file: Path) -> Dict[str, str]:
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"""解析同源基因映射文件"""
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mapping = {}
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with open(mapping_file, 'r') as f:
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for line in f:
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line = line.strip()
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if not line or line.startswith('#'):
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continue
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parts = line.split('\t')
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if len(parts) >= 2:
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source_id = parts[0].strip()
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target_id = parts[1].strip()
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target_id_base = target_id.split('.')[0]
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mapping[source_id] = target_id_base
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return mapping
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def generate_string_url(proteins: List[str], species: str = "3702") -> str:
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"""生成STRING网页链接"""
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base_url = "https://string-db.org/cgi/network"
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params = {
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"identifiers": "%0d".join(proteins),
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"species": species,
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"required_score": "400",
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"network_type": "functional"
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}
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return f"{base_url}?{urllib.parse.urlencode(params)}"
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def run_ppi_analysis_v2(
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gene_ids: List[str],
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ortholog_mapping: Optional[Dict[str, str]],
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species: str,
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output_dir: Path,
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prefix: str,
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required_score: int = 200
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) -> Dict[str, Any]:
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"""运行PPI分析"""
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result = {
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"success": False,
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"network_file": None,
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"string_url": None,
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"stats": {},
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"error": None
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}
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try:
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# 映射基因ID
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if ortholog_mapping:
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mapped_ids = []
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for gene_id in gene_ids:
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if gene_id in ortholog_mapping:
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mapped_ids.append(ortholog_mapping[gene_id])
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print(f"[INFO] Mapped {len(mapped_ids)}/{len(gene_ids)} genes")
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if not mapped_ids:
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result["error"] = "No genes could be mapped"
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return result
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query_ids = mapped_ids
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else:
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query_ids = [g.split('.')[0] for g in gene_ids]
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print(f"[INFO] Querying STRING for {len(query_ids)} genes...")
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api = StringAPI(species=species)
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network_data = api.get_network(
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proteins=query_ids,
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required_score=required_score
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)
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if isinstance(network_data, dict) and "error" in network_data:
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result["error"] = network_data["error"]
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return result
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if not network_data:
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result["error"] = f"No PPI interactions found"
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return result
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# 生成STRING网页链接
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string_url = generate_string_url(query_ids, api.species_id)
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result["string_url"] = string_url
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print(f"[INFO] STRING URL: {string_url}")
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# 保存TSV数据
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network_file = output_dir / f"{prefix}.ppi_network.tsv"
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with open(network_file, 'w') as f:
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f.write("protein1\tprotein2\tcombined_score\n")
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for interaction in network_data:
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node1 = interaction.get('preferredName_A', '')
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node2 = interaction.get('preferredName_B', '')
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score = int(interaction.get('score', 0) * 1000)
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f.write(f"{node1}\t{node2}\t{score}\n")
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result["network_file"] = network_file
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stats = {
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"total_nodes": len(set([n for i in network_data for n in [i.get('preferredName_A'), i.get('preferredName_B')]])),
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"total_edges": len(network_data)
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}
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result["stats"] = stats
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print(f"[INFO] Network: {stats['total_nodes']} nodes, {stats['total_edges']} edges")
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result["success"] = True
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except Exception as e:
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result["error"] = str(e)
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print(f"[ERROR] {e}", file=sys.stderr)
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return result
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def main():
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parser = argparse.ArgumentParser(description="PPI Network Analysis v2")
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parser.add_argument("-i", "--input", required=True)
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parser.add_argument("-s", "--species", default="ath")
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parser.add_argument("-o", "--output", required=True)
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parser.add_argument("-p", "--prefix", default="ppi")
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parser.add_argument("--score", type=int, default=200)
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parser.add_argument("--mapping", help="Ortholog mapping file")
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args = parser.parse_args()
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input_dir = Path(args.input)
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output_dir = Path(args.output)
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output_dir.mkdir(parents=True, exist_ok=True)
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final_dir = output_dir.parent / "final"
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final_dir.mkdir(exist_ok=True)
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# 读取基因ID
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gene_id_file = None
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last_resolution_error = ""
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for member_prefix in candidate_member_prefixes(final_dir, input_dir, args.prefix):
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try:
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resolved = resolve_effective_members(
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workspace=output_dir.parent,
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final_dir=final_dir,
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input_dir=input_dir,
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prefix=member_prefix,
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phase="auto",
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require="id",
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)
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if resolved.path_id:
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gene_id_file = resolved.path_id
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if resolved.warnings:
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print(f"[WARN] {'; '.join(resolved.warnings)}")
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print(f"[INFO] Member source: {resolved.source_kind} ({resolved.member_count} IDs)")
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break
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except MemberResolutionError as exc:
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last_resolution_error = str(exc)
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if not gene_id_file:
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print(f"Error: Gene ID file not found via effective member resolver. {last_resolution_error}", file=sys.stderr)
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sys.exit(1)
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with open(gene_id_file, 'r') as f:
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gene_ids = [line.strip() for line in f if line.strip()]
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print(f"[INFO] Loaded {len(gene_ids)} gene IDs")
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# 读取同源映射
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ortholog_mapping = None
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if args.mapping:
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mapping_file = Path(args.mapping)
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if mapping_file.exists():
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ortholog_mapping = parse_ortholog_mapping(mapping_file)
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print(f"[INFO] Loaded {len(ortholog_mapping)} mappings")
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# 运行分析
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result = run_ppi_analysis_v2(
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gene_ids=gene_ids,
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ortholog_mapping=ortholog_mapping,
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species=args.species,
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output_dir=final_dir,
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prefix=args.prefix,
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required_score=args.score
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)
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if result["success"]:
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# 保存 STRING 链接到文件
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if result["string_url"]:
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url_file = final_dir / f"{args.prefix}.ppi_url.txt"
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with open(url_file, 'w') as f:
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f.write(f"STRING Protein Interaction Network\n")
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f.write(f"{'='*50}\n\n")
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f.write(f"View online: {result['string_url']}\n\n")
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f.write(f"Network Statistics:\n")
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f.write(f" - Nodes: {result['stats']['total_nodes']}\n")
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f.write(f" - Edges: {result['stats']['total_edges']}\n")
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print(f"[INFO] URL saved: {url_file}")
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print(f"[INFO] View online: {result['string_url']}")
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print(f"[INFO] Results saved to {final_dir}")
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else:
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print(f"Error: {result.get('error', 'Unknown')}", file=sys.stderr)
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sys.exit(1)
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if __name__ == "__main__":
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main()
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