[med-svn] [Git][med-team/virulencefinder][upstream] New upstream version 2.0.4

[Nilesh Patra (@nilesh)]

Nilesh Patra pushed to branch upstream at Debian Med / virulencefinder


Commits:
6840870f by Nilesh Patra at 2021-07-06T00:40:24+05:30
New upstream version 2.0.4
- - - - -


1 changed file:

- virulencefinder.py


Changes:

=====================================
virulencefinder.py
=====================================
@@ -412,6 +412,9 @@ for db in results:
             contig_res[contig_id].append([hit["query_start"], hit["query_end"],
                                          bit_score, hit])
 
+    if not contig_res:
+        json_results[db_name][db] = "No hit found"
+
     # Check for overlapping hits, only report the best
     for contig_id, hit_lsts in contig_res.items():
 
@@ -456,8 +459,8 @@ for db in results:
                 function = ""
 
             # Write JSON results dict
-            json_results[db_name][db].update({header: {}})
-            json_results[db_name][db][header] = {
+            json_results[db_name][db].update({contig_id: {}})
+            json_results[db_name][db][contig_id] = {
                 "virulence_gene": gene,
                 "identity": round(identity, 2),
                 "HSP_length": HSP,
@@ -483,7 +486,7 @@ userinput = {"filename(s)": args.infile,
              "method": method,
              "file_format": file_format}
 run_info = {"date": date, "time": time}
-
+json_results=dict(sorted(json_results.items(), key=lambda x: x[0].lower()))
 data[service]["user_input"] = userinput
 data[service]["run_info"] = run_info
 data[service]["results"] = json_results



View it on GitLab: https://salsa.debian.org/med-team/virulencefinder/-/commit/6840870f7051dbc7997ef05b4a5ff7fdae5bc8f3

-- 
View it on GitLab: https://salsa.debian.org/med-team/virulencefinder/-/commit/6840870f7051dbc7997ef05b4a5ff7fdae5bc8f3
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