Library of Python utilities that I needed so many times
Project description
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 thanXM_
.
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 thanNM_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)
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