scout/commands/load/exons.py
def exons(context, build):
    """Load exons into the scout database"""
    
    adapter = context.obj['adapter']
    
    start = datetime.now()
    # Test if there are any exons loaded
    
    nr_exons = adapter.exons(build=build).count()
    if nr_exons:
        LOG.warning("Dropping all exons ")
        adapter.drop_exons(build=build)
        LOG.info("Exons dropped")
    
    # Load the exons
    ensembl_exons = fetch_ensembl_exons(build=build)
    load_exons(adapter, ensembl_exons, build)

    adapter.update_indexes()
    
    LOG.info("Time to load exons: {0}".format(datetime.now() - start))
def exons(context, build):
    adapter = context.obj['adapter']
    
    start = datetime.now()
    # Test if there are any exons loaded
    
    nr_exons = adapter.exons(build=build).count()
    if nr_exons:
        LOG.warning("Dropping all exons ")
        adapter.drop_exons(build=build)
        LOG.info("Exons dropped")
    
    # Load the exons
    ensembl_exons = fetch_ensembl_exons(build=build)
    load_exons(adapter, ensembl_exons, build)

    adapter.update_indexes()
    
    LOG.info("Time to load exons: {0}".format(datetime.now() - start))
def exons ( context , build ) : adapter = context . obj [ 'adapter' ] start = datetime . now ( ) # Test if there are any exons loaded nr_exons = adapter . exons ( build = build ) . count ( ) if nr_exons : LOG . warning ( "Dropping all exons " ) adapter . drop_exons ( build = build ) LOG . info ( "Exons dropped" ) # Load the exons ensembl_exons = fetch_ensembl_exons ( build = build ) load_exons ( adapter , ensembl_exons , build ) adapter . update_indexes ( ) LOG . info ( "Time to load exons: {0}" . format ( datetime . now ( ) - start ) )
Load exons into the scout database
Load exons into the scout database