""" PlantCARE API 客户端 PlantCARE 是一个植物顺式作用调控元件数据库 URL: http://bioinformatics.psb.ugent.be/webtools/plantcare/html/ """ import requests import time from typing import Dict, List, Optional, Any from dataclasses import dataclass from pathlib import Path @dataclass class CisElement: """顺式作用元件""" name: str sequence: str function: str position: Optional[int] = None strand: Optional[str] = None class PlantCAREClient: """ PlantCARE 数据库客户端 用于查询启动子区域的顺式作用调控元件 """ BASE_URL = "http://bioinformatics.psb.ugent.be/webtools/plantcare/html/" def __init__(self, rate_limit: float = 1.0): """ 初始化客户端 Args: rate_limit: 请求间隔（秒），避免过载服务器 """ self.rate_limit = rate_limit self.last_request_time = 0 self.session = requests.Session() self.session.headers.update({ 'User-Agent': 'bbav20311/1.0 (Research Tool)' }) def _rate_limited_request(self, method: str, url: str, **kwargs) -> requests.Response: """带速率限制的请求""" elapsed = time.time() - self.last_request_time if elapsed < self.rate_limit: time.sleep(self.rate_limit - elapsed) response = self.session.request(method, url, **kwargs) self.last_request_time = time.time() return response def search_elements(self, sequence: str, element_type: Optional[str] = None) -> List[CisElement]: """ 搜索顺式作用元件 Args: sequence: DNA 序列（启动子区域） element_type: 元件类型过滤（如 "light", "hormone", "stress"） Returns: 顺式作用元件列表 """ # PlantCARE 网页版没有公开 REST API # 这里实现基于本地数据库的查询或网页解析 # 实际使用时可能需要本地部署 PlantCARE 数据库 # 模拟返回（实际应替换为真实查询） elements = self._parse_sequence_for_elements(sequence) if element_type: elements = [e for e in elements if element_type.lower() in e.function.lower()] return elements def _parse_sequence_for_elements(self, sequence: str) -> List[CisElement]: """ 解析序列中的顺式作用元件 基于 PlantCARE 已知元件模式进行匹配 """ # PlantCARE 常见元件数据库（简化版） element_patterns = { 'CAAT-box': {'pattern': 'CCAAT', 'function': 'core promoter element'}, 'TATA-box': {'pattern': 'TATA', 'function': 'core promoter element'}, 'G-box': {'pattern': 'CACGTG', 'function': 'light responsive'}, 'ABRE': {'pattern': 'ACGTGG', 'function': 'abscisic acid responsive'}, 'W-box': {'pattern': 'TTGAC', 'function': 'WRKY binding site'}, 'WUN-motif': {'pattern': 'AAATTTCCT', 'function': 'wound responsive'}, 'MYB-binding': {'pattern': 'CNGTT', 'function': 'MYB transcription factor binding'}, 'MYC-binding': {'pattern': 'CACATG', 'function': 'MYC transcription factor binding'}, 'GT-1 motif': {'pattern': 'GGTTAA', 'function': 'light responsive'}, 'I-box': {'pattern': 'GATAA', 'function': 'light responsive'}, } elements = [] sequence_upper = sequence.upper() for name, info in element_patterns.items(): pattern = info['pattern'] # 支持简并碱基 import re pattern_regex = pattern.replace('N', '[ATCG]') for match in re.finditer(pattern_regex, sequence_upper): elements.append(CisElement( name=name, sequence=sequence[match.start():match.end()], function=info['function'], position=match.start(), strand='+' )) return elements def get_element_details(self, element_name: str) -> Optional[Dict[str, Any]]: """ 获取元件详细信息 Args: element_name: 元件名称（如 "G-box"） Returns: 元件详细信息字典 """ # 本地元件数据库 element_db = { 'CAAT-box': { 'name': 'CAAT-box', 'consensus': 'CCAAT', 'function': 'Core promoter element, enhances transcription efficiency', 'factors': ['CTF/NF1', 'CCAAT-binding factors'], 'references': ['Mantovani, 1999'], }, 'TATA-box': { 'name': 'TATA-box', 'consensus': 'TATA(A/T)A(A/T)', 'function': 'Core promoter element, transcription start site selection', 'factors': ['TBP (TATA-binding protein)'], 'references': ['Smale & Kadonaga, 2003'], }, 'G-box': { 'name': 'G-box', 'consensus': 'CACGTG', 'function': 'Light-responsive element, also involved in ABA signaling', 'factors': ['bZIP transcription factors', 'HY5'], 'references': ['Menkens et al., 1995'], }, 'ABRE': { 'name': 'ABRE', 'consensus': 'ACGTGG/TC', 'function': 'Abscisic acid responsive element', 'factors': ['bZIP/ABF transcription factors'], 'references': ['Nakashima & Yamaguchi-Shinozaki, 2013'], }, 'W-box': { 'name': 'W-box', 'consensus': 'TTGAC(C/T)', 'function': 'WRKY transcription factor binding site, defense response', 'factors': ['WRKY transcription factors'], 'references': ['Eulgem et al., 2000'], }, } return element_db.get(element_name) def analyze_promoter(self, promoter_sequence: str, upstream_length: int = 1500) -> Dict[str, Any]: """ 全面分析启动子区域 Args: promoter_sequence: 启动子序列 upstream_length: 上游长度（默认1500bp） Returns: 分析结果字典 """ elements = self.search_elements(promoter_sequence) # 分类统计 categories = {} for elem in elements: category = self._categorize_element(elem) if category not in categories: categories[category] = [] categories[category].append(elem) return { 'total_elements': len(elements), 'categories': {k: len(v) for k, v in categories.items()}, 'elements_by_category': categories, 'core_promoter_elements': [e for e in elements if 'core promoter' in e.function], 'regulatory_elements': [e for e in elements if 'responsive' in e.function or 'binding' in e.function], 'sequence_length': len(promoter_sequence), } def _categorize_element(self, element: CisElement) -> str: """对元件进行分类""" function_lower = element.function.lower() if 'core promoter' in function_lower: return 'core_promoter' elif 'light' in function_lower: return 'light_responsive' elif 'hormone' in function_lower or 'acid' in function_lower: return 'hormone_responsive' elif 'stress' in function_lower or 'wound' in function_lower: return 'stress_responsive' elif 'binding' in function_lower: return 'tf_binding' else: return 'other' # 使用示例 if __name__ == "__main__": client = PlantCAREClient() # 测试序列 # 测试序列 test_seq = "ATGCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCG" # 搜索元件 elements = client.search_elements(test_seq) print(f"Found {len(elements)} cis-elements") for elem in elements: print(f" - {elem.name}: {elem.sequence} ({elem.function})")