added test and docstring for #5053

Bio/SeqIO/SnapGeneIO.py

@@ -214,6 +214,14 @@ def _parse_primers_packet(length, data, record):
     A Primers packet is similar to a Features packet but specifically
     stores primer binding features. The data is a XML string starting
     with a 'Primers' root node.
+
+    Within the Primers packet, a primer can have multiple BindingSite
+    elements. However, not all of them are shown to the user when the file is
+    opened SnapGene. This seems to depend on the HybridizationParams element, which
+    stores a minimal hybridization length and Tm. When a SnapGene file is parsed,
+    `primer_bind` features that do not meet the hybridization parameters are dropped,
+    since they are not shown to the user when the file is opened in SnapGene.
+    For more details, see #5053.
     """
     xml = parseString(data.decode("UTF-8"))
     min_match_length = 0

Tests/test_SeqIO_SnapGene.py

@@ -260,6 +260,17 @@ class TestSnapGene(unittest.TestCase):
                 if "segments" in exp_feat:
                     self._check_feature_segments(exp_feat["segments"], read_feat)
 
+    def test_filter_with_hybridization_params(self):
+        """Ensure only releveant `primer_bind` features from SnapGene files are retained in
+        the `SeqRecord`. See the docstring of `_parse_primers_packet` for more details.
+        """
+        record = SeqIO.read("SnapGene/sample-hybridization-params.dna", "snapgene")
+        count_primer_features = 0
+        for feature in record.features:
+            if "XhoI-hht2(US)-Fwd" in feature.qualifiers["label"]:
+                count_primer_features += 1
+        self.assertEqual(count_primer_features, 1)
+
 
 class TestCorruptedSnapGene(unittest.TestCase):
     def setUp(self):