scout/commands/export/panel.py
def panel(context, panel, build, bed, version):
    """Export gene panels to .bed like format.
    
        Specify any number of panels on the command line
    """
    LOG.info("Running scout export panel")
    adapter = context.obj['adapter']
    # Save all chromosomes found in the collection if panels
    chromosomes_found = set()
    
    if not panel:
        LOG.warning("Please provide at least one gene panel")
        context.abort()

    LOG.info("Exporting panels: {}".format(', '.join(panel)))
    if bed:
        if version:
            version = [version]
        lines = export_panels(
            adapter=adapter, 
            panels=panel, 
            versions=version, 
            build=build,
        )
    else:
        lines = export_gene_panels(
            adapter=adapter, 
            panels=panel, 
            version=version,
            )
    for line in lines:
        click.echo(line)
def panel(context, panel, build, bed, version):
    LOG.info("Running scout export panel")
    adapter = context.obj['adapter']
    # Save all chromosomes found in the collection if panels
    chromosomes_found = set()
    
    if not panel:
        LOG.warning("Please provide at least one gene panel")
        context.abort()

    LOG.info("Exporting panels: {}".format(', '.join(panel)))
    if bed:
        if version:
            version = [version]
        lines = export_panels(
            adapter=adapter, 
            panels=panel, 
            versions=version, 
            build=build,
        )
    else:
        lines = export_gene_panels(
            adapter=adapter, 
            panels=panel, 
            version=version,
            )
    for line in lines:
        click.echo(line)
def panel ( context , panel , build , bed , version ) : LOG . info ( "Running scout export panel" ) adapter = context . obj [ 'adapter' ] # Save all chromosomes found in the collection if panels chromosomes_found = set ( ) if not panel : LOG . warning ( "Please provide at least one gene panel" ) context . abort ( ) LOG . info ( "Exporting panels: {}" . format ( ', ' . join ( panel ) ) ) if bed : if version : version = [ version ] lines = export_panels ( adapter = adapter , panels = panel , versions = version , build = build , ) else : lines = export_gene_panels ( adapter = adapter , panels = panel , version = version , ) for line in lines : click . echo ( line )
Export gene panels to .bed like format.
    
        Specify any number of panels on the command line
Export gene panels to . bed like format . Specify any number of panels on the command line