Move strand argument from SeqFeature to FeatureLocation

This was deprecated in Biopython 1.80 and removed in 1.82.¹ ¹ <https://github.com/biopython/biopython/blob/biopython-182/DEPRECATED.rst>
nextstrain · Dec 26, 2023 · a3df38d · a3df38d
1 parent 05bff35
commit a3df38d
Showing 1 changed file with 1 addition and 2 deletions.
diff --git a/augur/utils.py b/augur/utils.py
@@ -208,8 +208,7 @@ def _read_nuc_annotation_from_gff(record, reference):
         from Bio.SeqFeature import SeqFeature, FeatureLocation
         (name, start, stop) = sequence_regions[0]
         nuc['pragma'] = SeqFeature(
-            FeatureLocation(start, stop),
-            strand=1,
+            FeatureLocation(start, stop, strand=1),
             type='##sequence-region pragma',
             id=name,
         )