Library of Python utilities for PacBio Genomes Analysis

Project description

PBGA

PacBio Genome Analysis Python toolkit.

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)

Project details

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0.0.6

Sep 12, 2019

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

This version

0.0.1

Sep 10, 2019

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