feat!: don't redefine Strand model (#168)

pyproject.toml

@@ -30,7 +30,7 @@ dependencies = [
     "ga4gh.vrs ~=0.8.1",
     "biocommons.seqrepo",
     "gene-normalizer ~=0.1.40-dev1",
-    "cool-seq-tool ~=0.5.0",
+    "cool-seq-tool ~=0.5.1",
 ]
 dynamic=["version"]
 

src/fusor/fusor.py

@@ -6,7 +6,7 @@
 
 from bioutils.accessions import coerce_namespace
 from cool_seq_tool.app import CoolSeqTool
-from cool_seq_tool.schemas import ResidueMode
+from cool_seq_tool.schemas import ResidueMode, Strand
 from ga4gh.core import ga4gh_identify
 from ga4gh.vrs import models
 from ga4gh.vrsatile.pydantic.vrs_models import (
@@ -42,7 +42,6 @@
     MultiplePossibleGenesElement,
     RegulatoryClass,
     RegulatoryElement,
-    Strand,
     StructuralElementType,
     TemplatedSequenceElement,
     TranscriptSegmentElement,

src/fusor/models.py

@@ -4,6 +4,7 @@
 from enum import Enum
 from typing import Any, Literal
 
+from cool_seq_tool.schemas import Strand
 from ga4gh.vrsatile.pydantic import return_value
 from ga4gh.vrsatile.pydantic.vrsatile_models import (
     CURIE,
@@ -248,13 +249,6 @@ def validate_sequence(cls, v):
     )
 
 
-class Strand(str, Enum):
-    """Define possible values for strand"""
-
-    POSITIVE = "+"
-    NEGATIVE = "-"
-
-
 class TemplatedSequenceElement(BaseStructuralElement):
     """Define Templated Sequence Element class.
     A templated sequence is a contiguous genomic sequence found in the gene
@@ -286,7 +280,7 @@ class TemplatedSequenceElement(BaseStructuralElement):
                     },
                     "label": "chr12:44908821-44908822(+)",
                 },
-                "strand": "+",
+                "strand": 1,
             }
         },
     )

src/fusor/nomenclature.py

@@ -1,6 +1,7 @@
 """Provide helper methods for fusion nomenclature generation."""
 
 from biocommons.seqrepo.seqrepo import SeqRepo
+from cool_seq_tool.schemas import Strand
 from ga4gh.vrsatile.pydantic.vrs_models import SequenceLocation
 
 from fusor.exceptions import IDTranslationException
@@ -98,6 +99,7 @@ def templated_seq_nomenclature(element: TemplatedSequenceElement, sr: SeqRepo) -
     :raises ValueError: if location isn't a SequenceLocation or if unable
         to retrieve region or location
     """
+    strand_value = "+" if element.strand == Strand.POSITIVE else "-"
     if element.region and element.region.location:
         location = element.region.location
         if isinstance(location, SequenceLocation):
@@ -111,7 +113,7 @@ def templated_seq_nomenclature(element: TemplatedSequenceElement, sr: SeqRepo) -
                 ]
             except IDTranslationException as e:
                 raise ValueError from e
-            return f"{refseq_id.split(':')[1]}(chr {chrom}):g.{start}_{end}({element.strand.value})"
+            return f"{refseq_id.split(':')[1]}(chr {chrom}):g.{start}_{end}({strand_value})"
         raise ValueError
     raise ValueError
 

tests/conftest.py

@@ -546,7 +546,7 @@ def exhaustive_example(alk_gene_descriptor, braf_gene_descriptor):
                         },
                     },
                 },
-                "strand": "+",
+                "strand": 1,
             },
             {"type": "MultiplePossibleGenesElement"},
         ],
@@ -668,7 +668,7 @@ def fusion_example():
                         },
                     },
                 },
-                "strand": "+",
+                "strand": 1,
             },
             {"type": "MultiplePossibleGenesElement"},
         ],

tests/test_fusor.py

@@ -3,6 +3,7 @@
 import copy
 
 import pytest
+from cool_seq_tool.schemas import Strand
 from ga4gh.vrsatile.pydantic.vrsatile_models import GeneDescriptor, LocationDescriptor
 
 from fusor.exceptions import FUSORParametersException
@@ -186,7 +187,7 @@ def templated_sequence_element():
                 },
             },
         },
-        "strand": "+",
+        "strand": 1,
     }
     return TemplatedSequenceElement(**params)
 
@@ -209,7 +210,7 @@ def templated_sequence_element_ensg():
                 },
             },
         },
-        "strand": "-",
+        "strand": -1,
     }
     return TemplatedSequenceElement(**params)
 
@@ -234,7 +235,7 @@ def templated_sequence_element_custom_id():
                 },
             },
         },
-        "strand": "+",
+        "strand": 1,
     }
     return TemplatedSequenceElement(**params)
 
@@ -808,12 +809,12 @@ def test_templated_sequence_element(
 ):
     """Test that templated sequence element works correctly"""
     tsg = fusor_instance.templated_sequence_element(
-        100, 150, "NC_000001.11", "+", residue_mode="residue"
+        100, 150, "NC_000001.11", Strand.POSITIVE, residue_mode="residue"
     )
     assert tsg.model_dump() == templated_sequence_element.model_dump()
 
     tsg = fusor_instance.templated_sequence_element(
-        99, 150, "NC_000001.11", "+", residue_mode="inter-residue"
+        99, 150, "NC_000001.11", Strand.POSITIVE, residue_mode="inter-residue"
     )
     assert tsg.model_dump() == templated_sequence_element.model_dump()
 
@@ -826,22 +827,26 @@ def test_templated_sequence_element(
         100,
         150,
         "NC_000001.11",
-        "+",
+        Strand.POSITIVE,
         add_location_id=True,
         seq_id_target_namespace="ga4gh",
     )
     assert tsg.model_dump() == expected
 
     tsg = fusor_instance.templated_sequence_element(
-        140719329, 140719400, "ENSG00000157764", "-"
+        140719329, 140719400, "ENSG00000157764", Strand.NEGATIVE
     )
     assert tsg.model_dump() == templated_sequence_element_ensg.model_dump()
 
     # test untranslateable sequence ID
     # adds "ensembl" namespace but unable to translate to ga4gh digest ID
     expected = copy.deepcopy(templated_sequence_element_ensg.model_dump())
     tsg = fusor_instance.templated_sequence_element(
-        140719329, 140719400, "ENSG00000157764", "-", seq_id_target_namespace="ga4gh"
+        140719329,
+        140719400,
+        "ENSG00000157764",
+        Strand.NEGATIVE,
+        seq_id_target_namespace="ga4gh",
     )
     assert tsg.model_dump() == expected
 
@@ -852,7 +857,7 @@ def test_templated_sequence_element(
         200,
         300,
         "custom_ID__1",
-        "+",
+        Strand.POSITIVE,
         residue_mode="inter-residue",
         seq_id_target_namespace="ga4gh",
     )

tests/test_models.py

@@ -3,6 +3,7 @@
 import copy
 
 import pytest
+from cool_seq_tool.schemas import Strand
 from pydantic import ValidationError
 
 from fusor.models import (
@@ -231,12 +232,12 @@ def templated_sequence_elements(location_descriptors):
     return [
         {
             "type": "TemplatedSequenceElement",
-            "strand": "+",
+            "strand": 1,
             "region": location_descriptors[5],
         },
         {
             "type": "TemplatedSequenceElement",
-            "strand": "-",
+            "strand": -1,
             "region": location_descriptors[4],
         },
     ]
@@ -552,7 +553,7 @@ def assert_genomic_region_test_element(test):
         expected values.
         """
         assert test.type == "TemplatedSequenceElement"
-        assert test.strand.value == "+"
+        assert test.strand == Strand.POSITIVE
         assert test.region.id == "chr12:p12.1-p12.2"
         assert test.region.type == "LocationDescriptor"
         assert test.region.location.species_id == "taxonomy:9606"
@@ -585,7 +586,7 @@ def assert_genomic_region_test_element(test):
     # test enum validation
     with pytest.raises(ValidationError) as exc_info:
         assert TemplatedSequenceElement(
-            type="GeneElement", region=location_descriptors[0], strand="+"
+            type="GeneElement", region=location_descriptors[0], strand=Strand.POSITIVE
         )
     msg = "Input should be <FUSORTypes.TEMPLATED_SEQUENCE_ELEMENT: 'TemplatedSequenceElement'>"
     check_validation_error(exc_info, msg)