ddgen

Library of Python utilities that I needed so many times in the past

Select RefSeq transcript with the highest priority

RefSeq transcripts have following categories:

• NM_, XM_, NR_, XR_

If we have transcripts from multiple sources, we want to select the one coming from the source with highest priority.

E.g. NM_ has higher priority than XM_.

If we have multiple transcripts from a single source, we want to select the one with smaller integer.

E.g. NM_123.4 has higher priority than NM_124.4.

from ddgen.utils import txs

# tx will be `NM_123.4`
tx = txs.prioritize_refseq_transcripts(['NM_123.4', 'NM_124.4', 'XM_100.1'])

Connect to H2 database

The H2 database is a pure Java SQL database, hence it is 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)

In that case:

from ddgen.db 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)

Setup logging

Quick setup of Python built-in logging library:

from ddgen.utils import setup_logging
setup_logging()