Pypeta
pypeta is the python code interface for BGI-PETA database. It provides APIs for login, querying and fetching data.
Installation
From source code.
$ git clone https://github.com/JaylanLiu/pypeta
$ cd pypeta
$ python setup.py install
Example usage
Import libraies:
import pypeta
Login to BGI-PETA database via PETA account:
peta=pypeta.Peta(username='bgi-peta@genomics.cn',password='******')
Or login via token:
peta=pypeta.Peta(token = '******')
Get all visable studies info:
peta.list_visible_studys()
Set target study id and other filters:
peta.select_studys(["chol_nus_2012"])
peta.data_restriction["attributesEqualFilters"]=[]
Also studies and filters can be load from a json file, which can be get from the PETA website:
peta.set_data_restriction_from_json_file('json.txt')
Fetch SNV and InDel data as MAF format:
peta.fetch_mutation_data()
Fetch clinical info as tsv format:
peta.fetch_clinical_data()
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