def parse_transcript_ids(transcript_ids_filename):
    """
    If user has provided a file with Ensembl transcript ids, parse these to a list.
    """

    with open(transcript_ids_filename, 'r') as transcript_ids_file:
        transcript_ids_list = transcript_ids_file.read().splitlines()
        transcript_ids_list = [x for x in transcript_ids_list if len(x)>0]

    return transcript_ids_list