147 lines
4.6 KiB
Python
147 lines
4.6 KiB
Python
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#!/usr/bin/env python3
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"""SQLite版知识图谱（临时替代Neo4j）"""
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import json
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import sqlite3
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from pathlib import Path
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class GeneFamilyKG_SQLite:
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def __init__(self, db_path="/home/xzq/gene-family-mas-v2/kg.db"):
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self.db_path = db_path
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self.conn = sqlite3.connect(db_path)
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self.init_schema()
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def init_schema(self):
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"""初始化Schema"""
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cursor = self.conn.cursor()
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# 基因家族表
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cursor.execute('''
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CREATE TABLE IF NOT EXISTS gene_families (
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name TEXT PRIMARY KEY,
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full_name TEXT,
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description TEXT
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)
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''')
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# 物种表
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cursor.execute('''
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CREATE TABLE IF NOT EXISTS species (
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name TEXT PRIMARY KEY,
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common_name TEXT
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)
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''')
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# 基因表
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cursor.execute('''
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CREATE TABLE IF NOT EXISTS genes (
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id TEXT PRIMARY KEY,
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name TEXT,
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species TEXT,
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family TEXT,
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FOREIGN KEY (species) REFERENCES species(name),
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FOREIGN KEY (family) REFERENCES gene_families(name)
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)
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''')
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# 系统发育分组表
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cursor.execute('''
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CREATE TABLE IF NOT EXISTS phylogeny_groups (
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id INTEGER PRIMARY KEY AUTOINCREMENT,
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name TEXT,
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gene_family TEXT,
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UNIQUE(name, gene_family)
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)
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''')
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# 基因-分组关系表
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cursor.execute('''
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CREATE TABLE IF NOT EXISTS gene_groups (
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gene_id TEXT,
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group_id INTEGER,
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FOREIGN KEY (gene_id) REFERENCES genes(id),
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FOREIGN KEY (group_id) REFERENCES phylogeny_groups(id),
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PRIMARY KEY (gene_id, group_id)
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)
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''')
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self.conn.commit()
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print("SQLite Schema初始化完成")
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def import_phylogeny_data(self, json_path: Path):
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"""导入v5提取数据"""
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with open(json_path) as f:
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data = json.load(f)
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gene_family = data.get("gene_family", "Unknown")
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species = data.get("species", "Unknown")
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groups = data.get("groups", {})
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cursor = self.conn.cursor()
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# 插入基因家族
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cursor.execute(
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"INSERT OR REPLACE INTO gene_families (name) VALUES (?)",
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(gene_family,)
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)
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# 插入物种
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cursor.execute(
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"INSERT OR REPLACE INTO species (name) VALUES (?)",
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(species,)
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)
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# 插入分组和基因
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for group_name, genes in groups.items():
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# 插入分组
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cursor.execute(
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"INSERT OR REPLACE INTO phylogeny_groups (name, gene_family) VALUES (?, ?)",
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(group_name, gene_family)
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)
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cursor.execute(
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"SELECT id FROM phylogeny_groups WHERE name=? AND gene_family=?",
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(group_name, gene_family)
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)
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group_id = cursor.fetchone()[0]
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# 插入基因并建立关系
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for gene_id in genes:
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cursor.execute(
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"INSERT OR REPLACE INTO genes (id, name, species, family) VALUES (?, ?, ?, ?)",
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(gene_id, gene_id, species, gene_family)
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)
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cursor.execute(
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"INSERT OR REPLACE INTO gene_groups (gene_id, group_id) VALUES (?, ?)",
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(gene_id, group_id)
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)
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self.conn.commit()
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print(f"导入完成: {gene_family}")
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print(f" - 分组数: {len(groups)}")
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print(f" - 基因数: {sum(len(g) for g in groups.values())}")
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def get_stats(self):
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"""获取统计信息"""
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cursor = self.conn.cursor()
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stats = {}
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for table in ['gene_families', 'species', 'genes', 'phylogeny_groups']:
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cursor.execute(f"SELECT COUNT(*) FROM {table}")
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stats[table] = cursor.fetchone()[0]
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return stats
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def close(self):
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self.conn.close()
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if __name__ == "__main__":
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kg = GeneFamilyKG_SQLite()
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# 导入番茄P450数据
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data_path = Path("/home/xzq/gene-family-mas-v2/evaluation/auto_results/番茄p450基因家族BMCgenomics2020_v5.json")
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if data_path.exists():
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kg.import_phylogeny_data(data_path)
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print("\n统计信息:", kg.get_stats())
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else:
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print(f"数据文件不存在: {data_path}")
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kg.close()
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