def get_list_scafs(file_in):
    """
    Return a list of scaffolds to walk through. Expects each scaffold on its own
    line in the input file.
    """
    scaf_ls = []
    with open(file_in, 'r') as infile:
        for line in infile:
            scaf_ls.append(line.strip())
    return scaf_ls