Library of Python utilities for PacBio Genomes Analysis

Project description

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

Project details

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0.0.6

Sep 12, 2019

This version

0.0.4

Sep 10, 2019

0.0.3

Sep 10, 2019

0.0.2

Sep 10, 2019

0.0.2.dev0 pre-release

Sep 10, 2019

0.0.1

Sep 10, 2019

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