v5.2.2

Author: fsalbeez

README.md

@@ -2,7 +2,7 @@
 CARMEN is a diagnostic tool designed for surveillance purposes. Below are the instructions to complete your CARMEN analysis. 
 
 ## Software Version
-When cloning this repository, you will be using software version 5.2.1.
+When cloning this repository, you will be using software version 5.2.2.
 
 ## Overview
 At this point, you have ran the $Standard\ BioTools\ Dynamic\ Array^{TM}$ IFC (integrated fluidic circuit) on the $Standard\ BioTools\ Biomark^{TM}$ instrument and have completed the experimental portion of CARMEN. In running this code, you will be able to complete the data analysis portion of CARMEN and generate both binary positive/negative and quantitative signal output of your diagnostic assay. 

analyze_run.py

@@ -52,7 +52,7 @@
 
 ######################################################################################################################################################
 # assign software version
-software_version = '5.2.1'
+software_version = '5.2.2'
 
 ######################################################################################################################################################
 # data loading

redcap_builder.py

@@ -97,7 +97,10 @@ def merge_group(group, bbp_P1_assays, bbp_P2_assays, rvp_assays):
         ### strip all _ and asterisks from the column names
         for i, col in enumerate(redcap_t13_hit_binary_output.columns):
             if not re.search(r'rnasep', col, re.IGNORECASE):
-                new_col = re.split(r'[_*]', col)[0] # remove _ and * from all col names for assays
+                new_col = re.split(r'[*]', col)[0] # remove _ and * from all col names for assays
+                new_col = "_".join(new_col.split("_")[:-1])
+                    #record_id = record_id.split("_")[:-1] 
+                    #record_id = "_".join(record_id) 
                 redcap_t13_hit_binary_output.columns.values[i] = new_col
             if  re.search(r'rnasep', col, re.IGNORECASE):
                 new_col = re.split(r'[*]', col)[0] # we don't want to remove the _P1 or _RVP or _P2 part from RNASEP column header