scout/parse/matchmaker.py
def omim_terms(case_obj):
    """Extract all OMIM phenotypes available for the case
    Args:
        case_obj(dict): a scout case object
    Returns:
        disorders(list): a list of OMIM disorder objects
    """
    LOG.info("Collecting OMIM disorders for case {}".format(case_obj.get('display_name')))
    disorders = []

    case_disorders = case_obj.get('diagnosis_phenotypes') # array of OMIM terms
    if case_disorders:
        for disorder in case_disorders:
            disorder_obj = {
                "id" : ':'.join([ 'MIM', str(disorder)])
            }
            disorders.append(disorder_obj)
    return disorders
def omim_terms(case_obj):
    """Extract all OMIM phenotypes available for the case
    Args:
        case_obj(dict): a scout case object
    Returns:
        disorders(list): a list of OMIM disorder objects
    """
    LOG.info("Collecting OMIM disorders for case {}".format(case_obj.get('display_name')))
    disorders = []

    case_disorders = case_obj.get('diagnosis_phenotypes') # array of OMIM terms
    if case_disorders:
        for disorder in case_disorders:
            disorder_obj = {
                "id" : ':'.join([ 'MIM', str(disorder)])
            }
            disorders.append(disorder_obj)
    return disorders
def omim_terms ( case_obj ) : LOG . info ( "Collecting OMIM disorders for case {}" . format ( case_obj . get ( 'display_name' ) ) ) disorders = [ ] case_disorders = case_obj . get ( 'diagnosis_phenotypes' ) # array of OMIM terms if case_disorders : for disorder in case_disorders : disorder_obj = { "id" : ':' . join ( [ 'MIM' , str ( disorder ) ] ) } disorders . append ( disorder_obj ) return disorders
Extract all OMIM phenotypes available for the case
    Args:
        case_obj(dict): a scout case object
    Returns:
        disorders(list): a list of OMIM disorder objects
Extract all OMIM phenotypes available for the case Args : case_obj ( dict ) : a scout case object Returns : disorders ( list ) : a list of OMIM disorder objects