PBGA

PacBio Genome Analysis Python toolkit.

Install

The code is available at PyPi, therefore you can install it with pip.

pip install pbga

Connect to PBGA database

The PBGA database is a H2 database, therefore primarily meant to be used with Java. We can connect to the database from Python, if:

Java is installed on the local machine
the local machine runs UNIX-like OS (sorry, Windows users)

Then:

from pbga import H2DbManager

with H2DbManager("path/to/sv_database.mv.db", 
                 user="sa", 
                 password="sa") as h2:
    with h2.get_connection() as conn:
        with conn.cursor() as cur:
            # do whatever you want
            cur.execute('SELECT * FROM PBGA.CLINGEN_TRIPLOSENSITIVITY;')
            for i, x in zip(range(5), cur.fetchall()):
                # print first 5 lines 
                print(x)

Limitations

tested with python>=3.6.8

Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Source Distribution

pbga-0.0.4.tar.gz (2.1 MB view details)

Uploaded Sep 10, 2019 Source

Built Distributions

If you're not sure about the file name format, learn more about wheel file names.

The dropdown lists show the available interpreters, ABIs, and platforms. Enable javascript to be able to filter the list of wheel files.

pbga-0.0.4-py3.6.egg (2.1 MB view details)

Uploaded Sep 10, 2019 Egg

pbga-0.0.4-py3-none-any.whl (2.1 MB view details)

Uploaded Sep 10, 2019 Python 3

File details

Details for the file pbga-0.0.4.tar.gz.

File metadata

Download URL: pbga-0.0.4.tar.gz
Upload date: Sep 10, 2019
Size: 2.1 MB
Tags: Source
Uploaded using Trusted Publishing? No
Uploaded via: twine/1.13.0 pkginfo/1.5.0.1 requests/2.22.0 setuptools/41.0.1 requests-toolbelt/0.9.1 tqdm/4.32.1 CPython/3.7.3

File hashes

Hashes for pbga-0.0.4.tar.gz
Algorithm	Hash digest
SHA256	`5fb88eb043585d00e0ae716a791eb9e61520178df554d78ca39ec414394ca11c`
MD5	`b3d8f969727a094e321893def7db26d4`
BLAKE2b-256	`c0d8340326aef2b4fd134e1b98e063eb9f4dd7e71a9cbf828d42fb8fb3122c01`

See more details on using hashes here.

File details

Details for the file pbga-0.0.4-py3.6.egg.

File metadata

Download URL: pbga-0.0.4-py3.6.egg
Upload date: Sep 10, 2019
Size: 2.1 MB
Tags: Egg
Uploaded using Trusted Publishing? No
Uploaded via: twine/1.13.0 pkginfo/1.5.0.1 requests/2.22.0 setuptools/41.0.1 requests-toolbelt/0.9.1 tqdm/4.32.1 CPython/3.7.3

File hashes

Hashes for pbga-0.0.4-py3.6.egg
Algorithm	Hash digest
SHA256	`a11efac67b4f96cd4dea466675320a3d057d966aba036af355ee4a104b2824b9`
MD5	`2623c7f2902fc77434149d6db614acaa`
BLAKE2b-256	`aba46dc6510c708419a2bbf0b48047526c815bbe90cc2d8b8cf0f010cb491186`

See more details on using hashes here.

File details

Details for the file pbga-0.0.4-py3-none-any.whl.

File metadata

Download URL: pbga-0.0.4-py3-none-any.whl
Upload date: Sep 10, 2019
Size: 2.1 MB
Tags: Python 3
Uploaded using Trusted Publishing? No
Uploaded via: twine/1.13.0 pkginfo/1.5.0.1 requests/2.22.0 setuptools/41.0.1 requests-toolbelt/0.9.1 tqdm/4.32.1 CPython/3.7.3

File hashes

Hashes for pbga-0.0.4-py3-none-any.whl
Algorithm	Hash digest
SHA256	`c5588994cb2b3110f40447985574938ec0f577a64f06e44daeaf90f93c617ce8`
MD5	`4d1d15f13f11d7bb0d6482c00dbf6c3e`
BLAKE2b-256	`21239b5661987686b653ceb5ff3262f20ec1646011b12aedf670921f328dd058`