diff --git a/scripts/aviti_run_parameter_parser.py b/scripts/aviti_run_parameter_parser.py index 1c7a85fc..19bd402a 100644 --- a/scripts/aviti_run_parameter_parser.py +++ b/scripts/aviti_run_parameter_parser.py @@ -162,18 +162,24 @@ def set_run_stats(process, run_dir): for art in process.all_outputs(): if "Lane" in art.name: lane_nbr = int(art.name.split(" ")[1]) - lane_stats = next(d for d in run_stats["LaneStats"] if d["Lane"] == lane_nbr) + lane_stats = next( + d for d in run_stats["LaneStats"] if d["Lane"] == lane_nbr + ) for read in lane_stats["Reads"]: read_key = read["Read"] art.udf[f"Reads PF (M) {read_key}"] = lane_stats["PFCount"] / 1000000 art.udf[f"%PF {read_key}"] = lane_stats["PercentPF"] - art.udf[f"Yield PF (Gb) {read_key}"] = ( - lane_stats["TotalYield"] / 1000000000 - ) + art.udf[f"Yield PF (Gb) {read_key}"] = lane_stats["TotalYield"] / 1000000000 art.udf[f"% Aligned {read_key}"] = read["PhiXAlignmentRate"] - art.udf[f"% Bases >=Q30 {read_key}"] = calculate_mean(read["Cycles"], "PercentQ30") - art.udf[f"% Bases >=Q40 {read_key}"] = calculate_mean(read["Cycles"], "PercentQ40") - art.udf[f"Avg Q Score {read_key}"] = calculate_mean(read["Cycles"], "AverageQScore") + art.udf[f"% Bases >=Q30 {read_key}"] = calculate_mean( + read["Cycles"], "PercentQ30" + ) + art.udf[f"% Bases >=Q40 {read_key}"] = calculate_mean( + read["Cycles"], "PercentQ40" + ) + art.udf[f"Avg Q Score {read_key}"] = calculate_mean( + read["Cycles"], "AverageQScore" + ) art.udf[f"% Error Rate {read_key}"] = calculate_mean( read["Cycles"], "PercentPhixErrorRate" )