jerryandClaude Fable 5
2f82c4a8dc
- 按生产 7900 容器黄金清单迁移(compile.manifest 449 条目,0 缺失) - 入口双态:api.app(生产同源 3 路由)/ api.main(裁剪 11 路由族 91 路径) - 修复:advanced/__init__ 空文件(包标记误覆盖,已从主项目恢复) - 修复:api/rag_routes.py 跨环境 site-packages 注入改 LEGACY_GF_SITE_PACKAGES 门控 - 修复:scripts/utils 缺失(动态加载 reasoning_engine) - 影子验证:kg/stats 数据连通(6.2s,与 7900 同源 normalized 后端) Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
97 lines
2.6 KiB
Python
Executable File
97 lines
2.6 KiB
Python
Executable File
#!/usr/bin/env python3
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"""
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应用 locus ID 到基因符号的映射
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"""
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import json
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def load_gene_list():
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"""加载基因列表"""
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with open('ftspl_gene_list.json') as f:
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return json.load(f)
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def create_mapping(gene_list):
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"""创建 locus ID -> gene symbol 映射"""
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mapping = {}
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for gene in gene_list:
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locus = gene['locus_id']
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symbol = gene['symbol']
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# 处理多种格式
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mapping[locus] = symbol
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mapping[locus.replace('.T01', '')] = symbol
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mapping[locus.replace('.01.T01', '')] = symbol
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return mapping
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def apply_mapping(data, mapping):
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"""应用映射到实体和关系"""
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# 映射实体 ID
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for e in data.get('entities', []):
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old_id = e['id']
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if old_id in mapping:
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e['id'] = mapping[old_id]
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e['name'] = mapping[old_id]
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# 映射关系中的 ID
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for r in data.get('relations', []):
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source = r.get('source', '')
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target = r.get('target', '')
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if source in mapping:
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r['source'] = mapping[source]
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if target in mapping:
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r['target'] = mapping[target]
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return data
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def main():
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print("=" * 70)
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print("Applying Locus ID to Gene Symbol Mapping")
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print("=" * 70)
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# 加载基因列表
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print("\n1. Loading gene list...")
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gene_list = load_gene_list()
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mapping = create_mapping(gene_list)
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print(f" Created mapping for {len(mapping)} genes")
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# 显示映射示例
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print("\n2. Mapping examples:")
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for i, (locus, symbol) in enumerate(list(mapping.items())[:5]):
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print(f" {locus} -> {symbol}")
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# 应用映射到各个结果文件
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files_to_process = [
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('evaluation/auto_results/pmid31286919_phylogeny.json',
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'evaluation/auto_results/pmid31286919_phylogeny_mapped.json'),
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]
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for input_path, output_path in files_to_process:
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print(f"\n3. Processing: {input_path}")
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with open(input_path) as f:
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data = json.load(f)
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# 应用映射
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data = apply_mapping(data, mapping)
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# 保存
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with open(output_path, 'w') as f:
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json.dump(data, f, indent=2)
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print(f" ✓ Saved to: {output_path}")
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# 显示结果
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print(f"\n Mapped relations:")
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for r in data.get('relations', []):
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rel_type = r.get('type') or r.get('relation', '')
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if 'classified' in rel_type.lower():
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print(f" {r['source']} --{rel_type}--> {r['target']}")
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if __name__ == "__main__":
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main()
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