Metadata-Version: 2.1
Name: pbga
Version: 0.0.2
Summary: Library of Python utilities for PacBio Genomes Analysis
Home-page: https://github.com/TheJacksonLaboratory/PBGA-python-toolkit
Author: Daniel Danis
Author-email: daniel.gordon.danis@gmail.com
License: GPLv3
Description: # PBGA
        
        PacBio Genome Analysis Python toolkit.
        
        ## Install
        
        The code is available at PyPi, therefore you can install it with pip.
        
        ```bash
        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:
        ```python
        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)
        
        ```
        
Keywords: bioinformatics genomics
Platform: UNKNOWN
Description-Content-Type: text/markdown
