scout/parse/panel.py
def parse_gene_panel(path, institute='cust000', panel_id='test', panel_type='clinical', date=datetime.now(), 
                     version=1.0, display_name=None, genes = None):
    """Parse the panel info and return a gene panel

        Args:
            path(str): Path to panel file
            institute(str): Name of institute that owns the panel
            panel_id(str): Panel id
            date(datetime.datetime): Date of creation
            version(float)
            full_name(str): Option to have a long name

        Returns:
            gene_panel(dict)
    """
    LOG.info("Parsing gene panel %s", panel_id)
    gene_panel = {}

    gene_panel['path'] = path
    gene_panel['type'] = panel_type
    gene_panel['date'] = date
    gene_panel['panel_id'] = panel_id
    gene_panel['institute'] = institute
    version = version or 1.0
    gene_panel['version'] = float(version)
    gene_panel['display_name'] = display_name or panel_id

    if not path:
        panel_handle = genes
    else:
        panel_handle = get_file_handle(gene_panel['path'])
    gene_panel['genes'] = parse_genes(gene_lines=panel_handle)

    return gene_panel
def parse_gene_panel(path, institute='cust000', panel_id='test', panel_type='clinical', date=datetime.now(), 
                     version=1.0, display_name=None, genes = None):
    LOG.info("Parsing gene panel %s", panel_id)
    gene_panel = {}

    gene_panel['path'] = path
    gene_panel['type'] = panel_type
    gene_panel['date'] = date
    gene_panel['panel_id'] = panel_id
    gene_panel['institute'] = institute
    version = version or 1.0
    gene_panel['version'] = float(version)
    gene_panel['display_name'] = display_name or panel_id

    if not path:
        panel_handle = genes
    else:
        panel_handle = get_file_handle(gene_panel['path'])
    gene_panel['genes'] = parse_genes(gene_lines=panel_handle)

    return gene_panel
def parse_gene_panel ( path , institute = 'cust000' , panel_id = 'test' , panel_type = 'clinical' , date = datetime . now ( ) , version = 1.0 , display_name = None , genes = None ) : LOG . info ( "Parsing gene panel %s" , panel_id ) gene_panel = { } gene_panel [ 'path' ] = path gene_panel [ 'type' ] = panel_type gene_panel [ 'date' ] = date gene_panel [ 'panel_id' ] = panel_id gene_panel [ 'institute' ] = institute version = version or 1.0 gene_panel [ 'version' ] = float ( version ) gene_panel [ 'display_name' ] = display_name or panel_id if not path : panel_handle = genes else : panel_handle = get_file_handle ( gene_panel [ 'path' ] ) gene_panel [ 'genes' ] = parse_genes ( gene_lines = panel_handle ) return gene_panel
Parse the panel info and return a gene panel

        Args:
            path(str): Path to panel file
            institute(str): Name of institute that owns the panel
            panel_id(str): Panel id
            date(datetime.datetime): Date of creation
            version(float)
            full_name(str): Option to have a long name

        Returns:
            gene_panel(dict)
Parse the panel info and return a gene panel