pear_structured_log; return now percentage of reads merge/discarded/assembled

link to #3054

tools/pear_structured_log.py

@@ -86,14 +86,16 @@ def pear_converter(fileIn, fileOut):
     ### Warnings
     json_data["warning"] = []
     # assembled reads
-    percentage_not_assembled = int(json_data["reads"]["reads_not_assembled_number"]) / json_data["reads"]["reads_total_number"]
+    percentage_assembled = int(json_data["reads"]["reads_assembled_number"])*100 / json_data["reads"]["reads_total_number"]
+    json_data["reads"]["percentage_assembled"] = percentage_assembled
+    percentage_not_assembled = int(json_data["reads"]["reads_not_assembled_number"])*100 / json_data["reads"]["reads_total_number"]
     json_data["reads"]["percentage_not_assembled"] = percentage_not_assembled
     if percentage_not_assembled > 50.00 : 
       json_data["warning"].append("Very few reads assembled")
     elif percentage_not_assembled > 20.00 : 
       json_data["warning"].append("Few reads assembled")
     # discarded reads
-    percentage_discarded     = json_data["reads"]["reads_discarded_number"]     / json_data["reads"]["reads_total_number"]
+    percentage_discarded     = json_data["reads"]["reads_discarded_number"]*100     / json_data["reads"]["reads_total_number"]
     json_data["reads"]["percentage_discarded"] = percentage_discarded
     if percentage_discarded > 10.00 : 
       json_data["warning"].append("High level of discarded reads")

tools/tests/should-get-tests/pear_structured_log.should-get

+!LAUNCH: python ../../pear_structured_log.py -i pear_log.log
+
+$ Clone id-1 has a different number of reads 
+1:Not the same number or reads: id-1
+
+$ Clone id-2 is not in the second file
+1:[-] .* Clone not present: .* id-2
+
+$ Clone id-3 is not in the first file
+1:[+] .* Clone not present: .* id-3