scout/server/blueprints/variants/controllers.py
def upload_panel(store, institute_id, case_name, stream):
    """Parse out HGNC symbols from a stream."""
    institute_obj, case_obj = institute_and_case(store, institute_id, case_name)
    raw_symbols = [line.strip().split('\t')[0] for line in stream if
                   line and not line.startswith('#')]
    # check if supplied gene symbols exist
    hgnc_symbols = []
    for raw_symbol in raw_symbols:
        if store.hgnc_genes(raw_symbol).count() == 0:
            flash("HGNC symbol not found: {}".format(raw_symbol), 'warning')
        else:
            hgnc_symbols.append(raw_symbol)
    return hgnc_symbols
def upload_panel(store, institute_id, case_name, stream):
    """Parse out HGNC symbols from a stream."""
    institute_obj, case_obj = institute_and_case(store, institute_id, case_name)
    raw_symbols = [line.strip().split('\t')[0] for line in stream if
                   line and not line.startswith('#')]
    # check if supplied gene symbols exist
    hgnc_symbols = []
    for raw_symbol in raw_symbols:
        if store.hgnc_genes(raw_symbol).count() == 0:
            flash("HGNC symbol not found: {}".format(raw_symbol), 'warning')
        else:
            hgnc_symbols.append(raw_symbol)
    return hgnc_symbols
Parse out HGNC symbols from a stream.