Commit a424bef0 authored by Thonier Florian's avatar Thonier Florian Committed by Mathieu Giraud

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

link to #3054
parent 64e23fb6
......@@ -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")
......
!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
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