v5.4.1

Resolved bug in saving QC scores to csv

Author: fsalbeez

analyze_run.py

@@ -121,7 +121,7 @@
 
 ## Set up structure of the output folder - simplify into RESUTLS, QUALITY CONTROL, R&D
 # make an output folder in your path's wd if it hasn't been made already
-output_folder = f'output_{barcode_assignment}_[{CLI_arg[1]}]_v{software_version}'
+output_folder = f'output_{barcode_assignment}_{CLI_arg[1]}_v{software_version}'
 if not os.path.exists(output_folder):
     os.makedirs(output_folder)
 

threshold.py

@@ -87,7 +87,6 @@ def raw_thresholder(self, unique_crRNA_assays, assigned_only, t13_df, CLI_thresh
             norm_thresholds_df = raw_thresholds_df.loc['NTC Threshold'] / ntc_mean_df
             raw_thresholds_df = pd.concat([raw_thresholds_df, norm_thresholds_df], ignore_index=True, axis=0)
             raw_thresholds_df.index = ['NTC Mean', 'NTC Standard Deviation', 'NTC 3*SD', 'NTC Threshold', 'Normalized NTC Threshold']
-
 
         else:
             print("Consult ReadME and input appropriate command-line arguments to specify thresholding method.")