Metadata-Version: 2.1
Name: ddgen
Version: 0.0.3
Summary: Library of Python utilities that I needed so many times
Home-page: https://github.com/ielis/ddgen
Author: Daniel Danis
Author-email: daniel.gordon.danis@gmail.com
License: GPLv3
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 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`.
        
        ```python
        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:
        ```python
        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)
        ```
        
Keywords: bioinformatics genomics
Platform: UNKNOWN
Description-Content-Type: text/markdown
