Fix pfam description annotation

Merck · Oct 1, 2019 · 4a6d6de · 4a6d6de
1 parent 8a64366
commit 4a6d6de
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Showing 2 changed files with 4 additions and 2 deletions.
diff --git a/deepbgc/pipeline/pfam.py b/deepbgc/pipeline/pfam.py
@@ -94,6 +94,7 @@ def annotate(self):
 
         # Read descriptions from Pfam clan TSV
         pfam_descriptions = self._get_pfam_descriptions()
+        print('DESCRIPTIONS: {}'.format(pfam_descriptions))
 
         # Extract all matched domain hits
         num = 0
@@ -117,7 +118,8 @@ def annotate(self):
                     'locus_tag': [query.id],
                     'database': [PFAM_DB_VERSION],
                 }
-                description = pfam_descriptions.get(pfam_id)
+                short_pfam_id = pfam_id.rsplit('.', maxsplit=1)[0]
+                description = pfam_descriptions.get(short_pfam_id)
                 if description:
                     qualifiers['description'] = [description]
                 pfam = SeqFeature(

diff --git a/test/integration/pipeline/test_integration_pfam.py b/test/integration/pipeline/test_integration_pfam.py
@@ -29,6 +29,6 @@ def test_integration_pfam_annotator(tmpdir):
     assert pfam.qualifiers.get('db_xref') == ['PF00005.26']
     assert pfam.qualifiers.get('locus_tag') == ['AAK73498.1']
     assert pfam.qualifiers.get('description') == ['ABC transporter']
-    assert pfam.qualifiers.get('database') == ['Pfam-A.31.0.hmm']
+    assert pfam.qualifiers.get('database') == ['31.0']
 
     assert_sorted_features(record)