Merge pull request #230 from SynBioDex/Johan-Guillen-strand-path

Delete "strand" argument in SeqFeature() due to deprecation and update Complexity Scores expected from IDT
SynBioDex · Feb 23, 2024 · 1534f77 · 1534f77
2 parents b04970b + bfa328e
commit 1534f77
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diff --git a/sbol_utilities/sbol3_genbank_conversion.py b/sbol_utilities/sbol3_genbank_conversion.py
@@ -840,7 +840,7 @@ def _handle_features_sbol_to_gb(self, seq_rec: SeqRecord, obj: ComponentGenBankE
                 # create sequence feature object with label qualifier
                 # TODO: create issue for presence of genbank file with features without the "label" qualifier
                 # TODO: feat_strand value ambiguous in case of multiple locations?
-                feature = SeqFeature(location=feat_loc_object, strand=feat_strand, type=feat_role)
+                feature = SeqFeature(location=feat_loc_object, type=feat_role)
                 feature.loc_positions = feat_loc_positions
                 if isinstance(obj_feat, self.FeatureGenBankExtension):
                     keys = sorted(obj_feat.qualifier_key, key=lambda x: int(x.split(":", 1)[0]))

diff --git a/test/test_files/Comparison_file_Complexity_Scores.nt b/test/test_files/Comparison_file_Complexity_Scores.nt
@@ -6,7 +6,7 @@
 <http://igem.org/IDT_complexity_score/Complexity_Report_20230516T194547Z_a2efceb0> <http://www.w3.org/ns/prov#endedAtTime> "2023-05-16T19:45:47+00:00"^^<http://www.w3.org/2001/XMLSchema#dateTime> .
 <http://sbolstandard.org/testfiles/X2018_Interlab_Devices_BBa_I20270/Measure1> <http://sbols.org/v3#displayId> "Measure1" .
 <http://sbolstandard.org/testfiles/X2018_Interlab_Devices_BBa_I20270/Measure1> <http://sbols.org/v3#type> <http://edamontology.org/data_1259> .
-<http://sbolstandard.org/testfiles/X2018_Interlab_Devices_BBa_I20270/Measure1> <http://www.ontology-of-units-of-measure.org/resource/om-2/hasNumericalValue> "11.7"^^<http://www.w3.org/2001/XMLSchema#double> .
+<http://sbolstandard.org/testfiles/X2018_Interlab_Devices_BBa_I20270/Measure1> <http://www.ontology-of-units-of-measure.org/resource/om-2/hasNumericalValue> "13.2"^^<http://www.w3.org/2001/XMLSchema#double> .
 <http://sbolstandard.org/testfiles/X2018_Interlab_Devices_BBa_I20270/Measure1> <http://www.ontology-of-units-of-measure.org/resource/om-2/hasUnit> <http://www.ontology-of-units-of-measure.org/resource/om-2/NumberUnit> .
 <http://sbolstandard.org/testfiles/X2018_Interlab_Devices_BBa_I20270/Measure1> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://sbols.org/v3#Identified> .
 <http://sbolstandard.org/testfiles/X2018_Interlab_Devices_BBa_I20270/Measure1> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.ontology-of-units-of-measure.org/resource/om-2/Measure> .
@@ -19,7 +19,7 @@
 <http://sbolstandard.org/testfiles/X2018_Interlab_Devices_BBa_I20270> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://sbols.org/v3#Sequence> .
 <http://sbolstandard.org/testfiles/X2018_Interlab_Devices_BBa_R0040/Measure1> <http://sbols.org/v3#displayId> "Measure1" .
 <http://sbolstandard.org/testfiles/X2018_Interlab_Devices_BBa_R0040/Measure1> <http://sbols.org/v3#type> <http://edamontology.org/data_1259> .
-<http://sbolstandard.org/testfiles/X2018_Interlab_Devices_BBa_R0040/Measure1> <http://www.ontology-of-units-of-measure.org/resource/om-2/hasNumericalValue> "53.7"^^<http://www.w3.org/2001/XMLSchema#double> .
+<http://sbolstandard.org/testfiles/X2018_Interlab_Devices_BBa_R0040/Measure1> <http://www.ontology-of-units-of-measure.org/resource/om-2/hasNumericalValue> "54.0"^^<http://www.w3.org/2001/XMLSchema#double> .
 <http://sbolstandard.org/testfiles/X2018_Interlab_Devices_BBa_R0040/Measure1> <http://www.ontology-of-units-of-measure.org/resource/om-2/hasUnit> <http://www.ontology-of-units-of-measure.org/resource/om-2/NumberUnit> .
 <http://sbolstandard.org/testfiles/X2018_Interlab_Devices_BBa_R0040/Measure1> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://sbols.org/v3#Identified> .
 <http://sbolstandard.org/testfiles/X2018_Interlab_Devices_BBa_R0040/Measure1> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.ontology-of-units-of-measure.org/resource/om-2/Measure> .
@@ -32,7 +32,7 @@
 <http://sbolstandard.org/testfiles/X2018_Interlab_Devices_BBa_R0040> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://sbols.org/v3#Sequence> .
 <http://sbolstandard.org/testfiles/X2018_Interlab_Devices_J364000/Measure1> <http://sbols.org/v3#displayId> "Measure1" .
 <http://sbolstandard.org/testfiles/X2018_Interlab_Devices_J364000/Measure1> <http://sbols.org/v3#type> <http://edamontology.org/data_1259> .
-<http://sbolstandard.org/testfiles/X2018_Interlab_Devices_J364000/Measure1> <http://www.ontology-of-units-of-measure.org/resource/om-2/hasNumericalValue> "8.3"^^<http://www.w3.org/2001/XMLSchema#double> .
+<http://sbolstandard.org/testfiles/X2018_Interlab_Devices_J364000/Measure1> <http://www.ontology-of-units-of-measure.org/resource/om-2/hasNumericalValue> "9.9"^^<http://www.w3.org/2001/XMLSchema#double> .
 <http://sbolstandard.org/testfiles/X2018_Interlab_Devices_J364000/Measure1> <http://www.ontology-of-units-of-measure.org/resource/om-2/hasUnit> <http://www.ontology-of-units-of-measure.org/resource/om-2/NumberUnit> .
 <http://sbolstandard.org/testfiles/X2018_Interlab_Devices_J364000/Measure1> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://sbols.org/v3#Identified> .
 <http://sbolstandard.org/testfiles/X2018_Interlab_Devices_J364000/Measure1> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.ontology-of-units-of-measure.org/resource/om-2/Measure> .