biomart 0.9.2

它将做什么：

• 显示biomart服务器的所有数据库
• 显示Biomart数据库的所有数据集
• 显示biomart数据集的属性和筛选器
• 以python dict格式运行查询，并以tsv格式返回biomart响应。

它不会做什么：

• 以json、xml等格式处理并返回结果。

用法

导入biomart模块

from biomart import BiomartServer

连接到Biomart服务器

server = BiomartServer( "http://www.biomart.org/biomart" )

# if you are behind a proxy
import os
server.http_proxy = os.environ.get('http_proxy', 'http://my_http_proxy.org')

# set verbose to True to get some messages
server.verbose = True

与Biomart服务器交互

# show server databases
server.show_databases() # uses pprint behind the scenes

# show server datasets
server.show_datasets() # uses pprint behind the scenes

# use the 'uniprot' dataset
uniprot = server.datasets['uniprot']

# show all available filters and attributes of the 'uniprot' dataset
uniprot.show_filters()  # uses pprint
uniprot.show_attributes()  # uses pprint

运行搜索

# run a search with the default attributes - equivalent to hitting "Results" on the web interface.
# this will return a lot of data.
response = uniprot.search()
response = uniprot.search( header = 1 ) # if you need the columns header

# response format is TSV
for line in response.iter_lines():
  line = line.decode('utf-8')
  print(line.split("\t"))

# run a count - equivalent to hitting "Count" on the web interface
response = uniprot.count()
print(response.text)

# run a search with custom filters and default attributes.
response = uniprot.search({
  'filters': {
      'accession': 'Q9FMA1'
  }
}, header = 1 )

response = uniprot.search({
  'filters': {
      'accession': ['Q9FMA1', 'Q8LFJ9']  # ID-list specified accessions
  }
}, header = 1 )

# run a search with custom filters and attributes (no header)
response = uniprot.search({
  'filters': {
      'accession': ['Q9FMA1', 'Q8LFJ9']
  },
  'attributes': [
      'accession', 'protein_name'
  ]
})

快捷函数：直接连接到biomart数据集 这段代码很短，但可能需要很长的时间，因为模块需要获取所有服务器的数据库才能找到数据集。

from biomart import BiomartDataset

interpro = BiomartDataset( "http://www.biomart.org/biomart", name = 'entry' )

response = interpro.search({
  'filters': { 'entry_id': 'IPR027603' },
  'attributes': [ 'entry_name', 'abstract' ]
})