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)
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