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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)

Use Jannovar VariantEffects

We can access values of Jannovar VariantEffect enum:

import pbga.effects as pe 

ve = pe.VARIANT_EFFECTS #  get tuple with all variant effects

p = pe.get_priority('MISSENSE_VARIANT') # returns 21

Quick setup of Python logging framework

Setting up of Python logging framework might be tedious. Here's a small helper function:

from pbga.utils import setup_logging

# set level to INFO, create a `main.log` file use nice log message format  
setup_logging()  

Limitations

  • tested with python>=3.6.8

Project details


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