def config(context, out, vtype, madeline_path): """Create a scout config file.""" mip_case = context.obj["case"] scout_data = mip_case.scout_config(vtype) if madeline_path: scout_data["madeline"] = os.path.abspath(madeline_path) if context.obj["use_family"]: # rename samples to use unique sample ids with family id new_inds = {} for ind_id, ind_data in scout_data["individuals"].items(): new_indid = "{}-{}".format(mip_case.family_id, ind_id) ind_data["name"] = new_indid new_inds[new_indid] = ind_data scout_data["individuals"] = new_inds ini_lines = scout_tools.write_ini(scout_data) click.echo("\n".join(ini_lines).decode("utf-8"), file=out)
def test_write_ini(): data = {'name': 'P.T. Anderson', 'occupation': 'Master'} data_str = scout_tools.write_ini(data) assert len(data_str) == 2 assert ConfigObj(data_str) == data