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