244 lines
7.9 KiB
Python
244 lines
7.9 KiB
Python
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"""
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Pfam API 客户端
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Pfam 是一个蛋白质家族数据库，基于隐马尔可夫模型 (HMM)
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URL: https://pfam.xfam.org/
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API: https://xfam.wordpress.com/2020/07/08/pfam-33-1-is-available/
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"""
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import requests
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import time
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from typing import Dict, List, Optional, Any, Tuple
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from dataclasses import dataclass
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@dataclass
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class PfamEntry:
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"""Pfam 条目"""
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accession: str
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name: str
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description: str
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clan: Optional[str] = None
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domain_architecture: Optional[List[str]] = None
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class PfamClient:
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"""
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Pfam 数据库客户端
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用于查询蛋白质家族信息、HMM 模型、结构域架构
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"""
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# Pfam REST API (通过 EBI)
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BASE_URL = "https://www.ebi.ac.uk/interpro/api"
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PFAM_URL = "https://pfam.xfam.org"
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def __init__(self, rate_limit: float = 0.5):
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"""
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初始化客户端
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Args:
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rate_limit: 请求间隔（秒）
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"""
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self.rate_limit = rate_limit
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self.last_request_time = 0
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self.session = requests.Session()
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self.session.headers.update({
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'User-Agent': 'bbav20311/1.0 (Research Tool)',
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'Accept': 'application/json'
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})
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def _rate_limited_request(self, url: str, **kwargs) -> requests.Response:
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"""带速率限制的请求"""
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elapsed = time.time() - self.last_request_time
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if elapsed < self.rate_limit:
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time.sleep(self.rate_limit - elapsed)
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response = self.session.get(url, **kwargs)
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self.last_request_time = time.time()
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return response
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def search_protein(self, protein_id: str) -> List[PfamEntry]:
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"""
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搜索蛋白质的结构域
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Args:
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protein_id: 蛋白质 ID（UniProt ID）
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Returns:
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Pfam 条目列表
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"""
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url = f"{self.BASE_URL}/entry/pfam/protein/uniprot/{protein_id}"
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try:
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response = self._rate_limited_request(url)
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response.raise_for_status()
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data = response.json()
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entries = []
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for result in data.get('results', []):
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entry = PfamEntry(
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accession=result.get('metadata', {}).get('accession', ''),
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name=result.get('metadata', {}).get('name', ''),
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description=result.get('metadata', {}).get('description', ''),
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clan=result.get('metadata', {}).get('clan', {}).get('accession') if result.get('metadata', {}).get('clan') else None
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)
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entries.append(entry)
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return entries
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except requests.exceptions.RequestException as e:
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print(f"[WARN] Pfam API request failed: {e}")
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return []
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def get_family_info(self, pfam_acc: str) -> Optional[Dict[str, Any]]:
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"""
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获取 Pfam 家族详细信息
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Args:
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pfam_acc: Pfam 登录号（如 PF03110）
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Returns:
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家族详细信息
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"""
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url = f"{self.BASE_URL}/entry/pfam/{pfam_acc}"
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try:
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response = self._rate_limited_request(url)
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response.raise_for_status()
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data = response.json()
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metadata = data.get('metadata', {})
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return {
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'accession': metadata.get('accession'),
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'name': metadata.get('name'),
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'description': metadata.get('description'),
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'clan': metadata.get('clan', {}).get('accession') if metadata.get('clan') else None,
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'clan_name': metadata.get('clan', {}).get('name') if metadata.get('clan') else None,
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'go_terms': metadata.get('go_terms', []),
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'interpro': metadata.get('interpro', {}),
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'protein_count': data.get('proteins', {}).get('total', 0),
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'structure_count': data.get('structures', {}).get('total', 0),
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}
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except requests.exceptions.RequestException as e:
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print(f"[WARN] Pfam API request failed: {e}")
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return None
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def search_by_keyword(self, keyword: str, page_size: int = 20) -> List[Dict[str, Any]]:
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"""
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按关键词搜索 Pfam 家族
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Args:
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keyword: 搜索关键词
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page_size: 每页结果数
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Returns:
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搜索结果列表
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"""
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url = f"{self.BASE_URL}/entry/pfam"
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params = {
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'search': keyword,
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'page_size': page_size,
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}
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try:
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response = self._rate_limited_request(url, params=params)
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response.raise_for_status()
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data = response.json()
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results = []
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for result in data.get('results', []):
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metadata = result.get('metadata', {})
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results.append({
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'accession': metadata.get('accession'),
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'name': metadata.get('name'),
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'description': metadata.get('description'),
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'clan': metadata.get('clan', {}).get('accession') if metadata.get('clan') else None,
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})
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return results
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except requests.exceptions.RequestException as e:
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print(f"[WARN] Pfam API request failed: {e}")
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return []
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def get_hmm_model(self, pfam_acc: str) -> Optional[str]:
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"""
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获取 HMM 模型（如果可用）
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Args:
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pfam_acc: Pfam 登录号
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Returns:
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HMM 模型字符串
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"""
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# Pfam HMM 模型通常需要从 FTP 或特定端点下载
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# 这里返回下载链接
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return f"https://pfam.xfam.org/family/{pfam_acc}/hmm"
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def get_clan_info(self, clan_acc: str) -> Optional[Dict[str, Any]]:
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"""
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获取 Clan（超家族）信息
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Args:
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clan_acc: Clan 登录号（如 CL0016）
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Returns:
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Clan 信息
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"""
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url = f"{self.BASE_URL}/entry/pfam/clan/{clan_acc}"
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try:
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response = self._rate_limited_request(url)
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response.raise_for_status()
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data = response.json()
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return {
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'accession': data.get('metadata', {}).get('accession'),
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'name': data.get('metadata', {}).get('name'),
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'description': data.get('metadata', {}).get('description'),
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'member_families': [f.get('accession') for f in data.get('members', [])],
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}
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except requests.exceptions.RequestException as e:
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print(f"[WARN] Pfam API request failed: {e}")
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return None
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def analyze_protein_domains(self, protein_sequence: str) -> Dict[str, Any]:
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"""
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分析蛋白质序列的结构域
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注意：这需要提交到 Pfam 搜索（可能需要网页界面）
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Args:
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protein_sequence: 蛋白质序列
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Returns:
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结构域分析结果
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"""
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# Pfam 序列搜索通常通过网页表单或 InterProScan
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# 这里返回搜索链接
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return {
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'search_url': 'https://www.ebi.ac.uk/jdispatcher/pfa/iprscan5',
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'note': 'Use InterProScan for sequence analysis',
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'sequence_length': len(protein_sequence),
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}
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# 使用示例
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if __name__ == "__main__":
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client = PfamClient()
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# 搜索 SBP 家族
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results = client.search_by_keyword("SBP")
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print(f"Found {len(results)} Pfam families")
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# 获取 PF03110 (SBP) 详细信息
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info = client.get_family_info("PF03110")
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if info:
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print(f"Family: {info['name']}")
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print(f"Description: {info['description']}")
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print(f"Protein count: {info['protein_count']}")
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