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import json
import sys
import os
sys.path.append(os.path.dirname(os.path.dirname(os.path.abspath(__file__))))
from collections import defaultdict
# 全局变量声明
_go_data = None
_protein_go_dict = None
def _load_go_data(go_info_path):
"""懒加载GO数据"""
global _go_data
if _go_data is None:
try:
with open(go_info_path, 'r') as f:
_go_data = json.load(f)
except Exception as e:
print(f"加载GO数据文件时发生错误: {str(e)}")
_go_data = None
def _load_protein_go_dict(protein2gopath):
"""懒加载蛋白质-GO映射数据"""
global _protein_go_dict
if _protein_go_dict is None:
try:
_protein_go_dict = {}
with open(protein2gopath, 'r') as f:
for line in f:
data = json.loads(line)
_protein_go_dict[data['protein_id']] = data['GO_id']
except Exception as e:
print(f"加载蛋白质-GO映射数据时发生错误: {str(e)}")
_protein_go_dict = None
def get_go_definition(go_id, go_info_path):
"""获取GO term的定义"""
_load_go_data(go_info_path)
if _go_data is None:
return None
if not go_id.startswith('GO_'):
go_id = f"GO_{go_id}"
full_id = f"http://purl.obolibrary.org/obo/{go_id}"
for node in _go_data['graphs'][0]['nodes']:
if node['id'] == full_id:
if 'meta' in node and 'definition' in node['meta']:
return node['meta']['definition']['val']
return None
def analyze_protein_go(protein_id, protein2gopath, go_info_path):
"""
分析蛋白质的GO注释信息，包括GO ID和定义
参数：
protein_id: str - 蛋白质ID
protein2gopath: str - 蛋白质-GO映射文件路径
返回：
dict - 包含GO信息的字典
"""
_load_protein_go_dict(protein2gopath)
if _protein_go_dict is None:
return {
"status": "error",
"message": "GO数据加载失败"
}
if protein_id not in _protein_go_dict:
return {
"status": "error",
"message": f"未找到蛋白质 {protein_id} 的GO注释"
}
go_ids = _protein_go_dict[protein_id]
go_info = []
all_definitions = {}
for go_id in go_ids:
# 获取GO定义
definition = get_go_definition(go_id, go_info_path)
if definition:
all_definitions[go_id] = definition
go_info.append({
"go_id": go_id
})
return {
"status": "success",
"protein_id": protein_id,
"go_annotations": go_info,
"all_related_definitions": all_definitions
}
# 使用示例
if __name__ == "__main__":
import argparse
parser = argparse.ArgumentParser(description='Analyze protein GO annotations')
parser.add_argument('--protein_id', type=str, default='A8CF74')
parser.add_argument('--protein2gopath', type=str, default='data/processed_data/go_integration_final_topk2.json')
parser.add_argument('--go_info_path', type=str, default='data/raw_data/go.json')
args = parser.parse_args()
result = analyze_protein_go(args.protein_id, args.protein2gopath, args.go_info_path)
if result["status"] == "success":
print(f"\nProtein {result['protein_id']} GO annotations:")
for anno in result["go_annotations"]:
print(f"\nGO ID: {anno['go_id']}")
print("\nAll related GO ID definitions:")
for go_id, definition in result["all_related_definitions"].items():
print(f"\nGO:{go_id}")
print(f"Definition: {definition}")
else:
print(result["message"]) |