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()
1 maintainer
Metadata
1 maintainer
Release files for pypeta 0.6.9
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Source distribution (sdist)
| File | Size | Uploaded | Provenance | |
|---|---|---|---|---|
| pypeta-0.6.9.tar.gz | 22.0 kB | Without provenance | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| pypeta-0.6.9-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 44.0 kB
Release files / pypeta-0.6.9.tar.gz
| Download URL | pypeta-0.6.9.tar.gz |
|---|---|
| Size | 22.0 kB |
| Tags | Source |
|
SHA-256 checksum How to use checksums |
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|
Release files / pypeta-0.6.9-py3-none-any.whl
| Download URL | pypeta-0.6.9-py3-none-any.whl |
|---|---|
| Size | 21.9 kB |
| Tags | Python 3 |
|
SHA-256 checksum How to use checksums |
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No |
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twine/3.4.1 importlib_metadata/3.10.0 pkginfo/1.7.1 requests/2.25.1 requests-toolbelt/0.9.1 tqdm/4.61.2 CPython/3.8.8
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Security for pypeta 0.6.9
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