def main():
"""Main function
"""
# Get args
parser = build_parser()
try:
args = parser.parse_args()
except:
parser.print_help()
sys.exit(0)
if args.input_glob:
gct_files = glob.glob(args.input_glob)
elif args.input_list:
gct_files = grp.read(args.input_list)
else:
raise Exception('input_glob or input_list must be specified')
gct_list = load_data(gct_files)
setup_logger.setup(verbose=args.verbose)
adj_ds, adj_list = combat_by_group(gct_list,
col_group=args.col_group,
batch_field=args.batch_field,
use_col_group_as_batch=args.use_col_group_as_batch)
save_data(adj_ds, adj_list)
made_gallery = galleries.mk_index(table_headers=headers,
table_tuples=table_info,
outfolder=out_dir,
project_name=proj_name)
if made_gallery:
logger.info("successfully made QC gallery")
index_info.to_csv(os.path.join(out_dir, 'qc_report.txt'), sep='\t')
def main(args, project_name):
# Read in the data
if args.custom_path is not None:
out_dir = args.custom_path
else:
out_dir = os.path.join(base_path, project_name, 'qc/merino')
qc_galleries(out_dir, project_name)
if __name__ == "__main__":
args = build_parser().parse_args(sys.argv[1:])
setup_logger.setup(verbose=args.verbose)
logger.debug("args: {}".format(args))
main(args, project_name=args.project_name)
assert expected_col_id in r.index, (expected_col_id, r.index)
expected_col_id = index_builder(pert_list[2])
assert expected_col_id in r.index, (expected_col_id, r.index)
assert "trt_cp" == r["pert_type"][expected_col_id], r["pert_type"][expected_col_id]
assert 2 == r["random_inclusion"][expected_col_id], r["random_inclusion"][expected_col_id]
assert r["other"][expected_col_id] is None, r["other"][expected_col_id]
assert 2.2 == r["something"][expected_col_id], r["something"][expected_col_id]
assert 3 == r["pert_well"][expected_col_id], r["pert_well"][expected_col_id]
def test_convert_objects_to_metadata_df_for_prism_cell(self):
cell_list = [pm.PrismCell(1, 2, 3, 5), pm.PrismCell(7, 11, 13, 17)]
def index_builder(c):
return c.id
r = pm.convert_objects_to_metadata_df(index_builder, cell_list)
assert r is not None
logger.debug("r: {}".format(r))
assert "pool_id" in r.columns
assert "davepool_id" in r.columns
assert "analyte_id" in r.columns
if __name__ == "__main__":
setup_logger.setup(verbose=True)
unittest.main()