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):
    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 ) : 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.
Parse out HGNC symbols from a stream .