生物信息-004-Biopython从NCBI搜索和取回数据库记录

Entrez模块

Entrez提供了链向在NCBI服务器的esearch和efetch工具的连接

---

列出Entrez模块的方法和属性

#!/usr/bin/env python# -*- coding: utf-8 -*-__author__ = 'sunchengquan'__mail__ = '[e-mail]'from Bio import Entrezs = dir(Entrez)print(s)运行结果：['_HTTPError', '__builtins__', '__cached__', '__doc__', '__file__', '__loader__', '__name__', '__package__', '__path__', '__spec__', '_as_bytes', '_binary_to_string_handle', '_construct_cgi', '_construct_params', '_encode_options', '_open', '_update_ecitmatch_variables', '_urlencode', '_urlopen', 'ecitmatch', 'efetch', 'egquery', 'einfo', 'elink', 'email', 'epost', 'esearch', 'espell', 'esummary', 'parse', 'print_function', 'read', 'time', 'tool', 'warnings']

---

Entrez数据库提供了什么

#!/usr/bin/env python# -*- coding: utf-8 -*-__author__ = 'sunchengquan'__mail__ = '[e-mail]'#从Entrez数据库得到信息，使用Entrez.einfo()函数from Bio import Entrez#email属性把邮箱地址告诉NCBI（可选）Entrez.email = '[e-mail]'handle = Entrez.einfo()info = Entrez.read(handle)print(info)运行结果：{'DbList': ['pubmed', 'protein', 'nuccore', 'ipg', 'nucleotide', 'nucgss', 'nucest', 'structure', 'sparcle', 'genome', 'annotinfo', 'assembly', 'bioproject', 'biosample', 'blastdbinfo', 'books', 'cdd', 'clinvar', 'clone', 'gap', 'gapplus', 'grasp', 'dbvar', 'gene', 'gds', 'geoprofiles', 'homologene', 'medgen', 'mesh', 'ncbisearch', 'nlmcatalog', 'omim', 'orgtrack', 'pmc', 'popset', 'probe', 'proteinclusters', 'pcassay', 'biosystems', 'pccompound', 'pcsubstance', 'pubmedhealth', 'seqannot', 'snp', 'sra', 'taxonomy', 'biocollections', 'unigene', 'gencoll', 'gtr']}#给定一个数据库名字作为Entrez.einfo()的参数#则可以得到关于这个数据库的信息from Bio import EntrezEntrez.email = '[e-mail]'handle = Entrez.einfo(db ='pubmed')info = Entrez.read(handle)#print(info)#print(info['DbInfo'])print(info.keys())print(info['DbInfo']['Description'])运行结果：dict_keys(['DbInfo'])PubMed bibliographic record

---

多于一个术语搜索Pubmed，用AND/OR组合关键词

#!/usr/bin/env python# -*- coding: utf-8 -*-__author__ = 'sunchengquan'__mail__ = '[e-mail]'from Bio import EntrezEntrez.email = '[e-mail]'handle = Entrez.esearch(db='pubmed',term='PyCogent AND RNA')record = Entrez.read(handle)print(record['IdList'])运行结果：['18230758']#验证在NCBI网站pumed用关键词‘PyCogent AND RNA’检索

#!/usr/bin/env python# -*- coding: utf-8 -*-__author__ = 'sunchengquan'__mail__ = '[e-mail]'from Bio import EntrezEntrez.email = '[e-mail]'handle = Entrez.esearch(db='pubmed',term='PyCogent OR RNA')record = Entrez.read(handle)print(record['Count'])运行结果：961515

#可选参数retmax最大返回数目，可以用来设置查询文本的最大检索数目from Bio import EntrezEntrez.email = '[e-mail]'handle = Entrez.esearch(db='pubmed',term='PyCogent or RAN',retmax=3)record = Entrez.read(handle)print(record['IdList'])运行结果：['29192776', '29191911', '29191431']

---

用GenBank格式检索和解析核酸数据库条目

#!/usr/bin/env python# -*- coding: utf-8 -*-__author__ = 'sunchengquan'__mail__ = '[e-mail]'from Bio import Entrez# search sequences by a combination of keywordsEntrez.email = '[e-mail]'handle = Entrez.esearch(db='nucleotide',term='Homo sapiens AND mRNA AND Mapk')records = Entrez.read(handle)print(records['Count'])top3_records = records['IdList'][0:3]print(top3_records)# retriveve the sequences by their GI number#多个ID必须用一个逗号隔开的GI号的字符串gi_list = ','.join(top3_records)print(gi_list)#文件格式retmode必须设置成xmlhandle = Entrez.efetch(db='nucleotide',id=gi_list,rettype='gb',retmode='xml')records = Entrez.read(handle)print(len(records))print(records[0].keys())print(records[0]['GBSeq_organism'])运行结果：2855['385298702', '373938425', '239046737']385298702,373938425,2390467373dict_keys(['GBSeq_locus', 'GBSeq_length', 'GBSeq_strandedness', 'GBSeq_moltype', 'GBSeq_topology', 'GBSeq_division', 'GBSeq_update-date', 'GBSeq_create-date', 'GBSeq_definition', 'GBSeq_primary-accession', 'GBSeq_accession-version', 'GBSeq_other-seqids', 'GBSeq_keywords', 'GBSeq_source', 'GBSeq_organism', 'GBSeq_taxonomy', 'GBSeq_references', 'GBSeq_comment', 'GBSeq_primary', 'GBSeq_feature-table', 'GBSeq_sequence'])Homo sapiens

---

用关键词搜索NCBI蛋白质数据库条目

#!/usr/bin/env python# -*- coding: utf-8 -*-__author__ = 'sunchengquan'__mail__ = '[e-mail]'from Bio import Entrez# search sequences by a combination of keywordsEntrez.email = '[e-mail]'handle = Entrez.esearch(db='protein',term='Human AND cancer AND p21')records = Entrez.read(handle)print(records['Count'])id_list = records['IdList'][0:3]#retrieve sequencesid_list = ','.join(id_list)print(id_list)handle = Entrez.efetch(db='protein',id=id_list,rettype='fasta',retmode='xml')records = Entrez.read(handle)print(records[0].keys())print(records[0]['TSeq_defline'])运行结果：1320161377472,161377470,161377468dict_keys(['TSeq_seqtype', 'TSeq_gi', 'TSeq_accver', 'TSeq_taxid', 'TSeq_orgname', 'TSeq_defline', 'TSeq_length', 'TSeq_sequence'])cyclin-A1 isoform c [Homo sapiens]