Bump up year in license, save BGC ids in GBK file.

Merck · Mar 8, 2019 · bafba1d · bafba1d
1 parent 82d4dba
commit bafba1d
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diff --git a/LICENSE b/LICENSE
@@ -1,6 +1,6 @@
 The MIT License
 
-Copyright © 2018 Merck Sharp & Dohme Corp. a subsidiary of Merck & Co., Inc., Kenilworth, NJ, USA."
+Copyright © 2019 Merck Sharp & Dohme Corp. a subsidiary of Merck & Co., Inc., Kenilworth, NJ, USA."
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

diff --git a/deepbgc/pipeline/detector.py b/deepbgc/pipeline/detector.py
@@ -110,7 +110,7 @@ def run(self, record):
         for cluster_proteins in clusters:
             start = cluster_proteins[0].location.start
             end = cluster_proteins[-1].location.end
-            candidate_id = '{}({}-{})'.format(record.id, int(start), int(end))
+            candidate_id = '{}_{}-{}.1'.format(record.id, int(start), int(end))
 
             if self.min_nucl > 1:
                 nucl_length = end - start

diff --git a/deepbgc/util.py b/deepbgc/util.py
@@ -149,8 +149,11 @@ def extract_cluster_record(cluster_feature, record):
     """
 
     cluster_record = cluster_feature.extract(record)
-    # TODO set cluster ID
-    # cluster_record.id = cluster.qualifiers.get('bgc_candidate_id', ['unknown_cluster_id'])[0]
+    cluster_record.id = cluster_feature.qualifiers.get('bgc_candidate_id', ['unknown_cluster_id'])[0]
+    cluster_record.description = ''
+    cluster_record.annotations['source'] = record.annotations.get('source', '')
+    cluster_record.annotations['organism'] = record.annotations.get('organism', '')
+
     proteins_by_id = get_proteins_by_id(get_protein_features(cluster_record))
     # Remove pfams with protein not fully inside cluster borders (therefore not present in cluster_record)
     cluster_record.features = [f for f in cluster_record.features