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()