diff --git a/app/ConvertRGIJsonToTSV.py b/app/ConvertRGIJsonToTSV.py index 2797f2c..43c8708 100755 --- a/app/ConvertRGIJsonToTSV.py +++ b/app/ConvertRGIJsonToTSV.py @@ -87,7 +87,8 @@ def run(self): "Nudged", "Note", "Hit_Start", - "Hit_End"]) + "Hit_End", + "Antibiotic"]) if os.path.isfile(self.filepath): with open(self.filepath) as rgi_file: @@ -258,7 +259,9 @@ def run(self): nudged, note, rgi_data[hsp][ordered[0]]["hit_start"], - rgi_data[hsp][ordered[0]]["hit_end"] + rgi_data[hsp][ordered[0]]["hit_end"], + "; ".join(rgi_data[hsp][ordered[0]]["ARO_category"][x]["category_aro_name"] for x in rgi_data[hsp][ordered[0]]["ARO_category"] \ + if rgi_data[hsp][ordered[0]]["ARO_category"][x]["category_aro_class_name"] == 'Antibiotic') ] for key, value in match_dict.items(): writer.writerow(value) @@ -321,7 +324,9 @@ def run(self): nudged, note, rgi_data[hsp][ordered[0]]["hit_start"], - rgi_data[hsp][ordered[0]]["hit_end"] + rgi_data[hsp][ordered[0]]["hit_end"], + "; ".join(rgi_data[hsp][ordered[0]]["ARO_category"][x]["category_aro_name"] for x in rgi_data[hsp][ordered[0]]["ARO_category"] \ + if rgi_data[hsp][ordered[0]]["ARO_category"][x]["category_aro_class_name"] == 'Antibiotic'), ] for key, value in match_dict.items():