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Library of Python utilities for PacBio Genomes Analysis

Project description


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)


from pbga import H2DbManager

with H2DbManager("path/to/", 
                 password="sa") as h2:
    with h2.get_connection() as conn:
        with conn.cursor() as cur:
            # do whatever you want
            for i, x in zip(range(5), cur.fetchall()):
                # print first 5 lines 

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