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)
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