BGI-PETA data APIs
Project description
# 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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