cool-seq-tool 0.14.3__tar.gz → 0.14.4__tar.gz

{cool_seq_tool-0.14.3 → cool_seq_tool-0.14.4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: cool_seq_tool
-Version: 0.14.3
+Version: 0.14.4
 Summary: Common Operation on Lots of Sequences Tool
 Author: Kori Kuzma, James Stevenson, Katie Stahl, Alex Wagner
 License: MIT License

{cool_seq_tool-0.14.3 → cool_seq_tool-0.14.4}/src/cool_seq_tool/mappers/exon_genomic_coords.py

@@ -65,6 +65,27 @@ class TxSegment(BaseModelForbidExtra):
     genomic_location: SequenceLocation = Field(
         ..., description="The genomic position of a transcript segment."
     )
+    is_exonic: bool = Field(
+        default=True, description="If the position occurs on an exon"
+    )
+
+    @model_validator(mode="before")
+    def check_seg_pos(cls, values: dict) -> dict:  # noqa: N805
+        """Ensure that only one of `start` or `end` is set in the
+        genomic_location field
+
+        :param values: The values in the TxSegment class
+        :raises ValueError: If `start` and `end` are both set in
+            `genomic_location`
+        :return: Values in model
+        """
+        loc = values.get("genomic_location")
+        start = getattr(loc, "start", None)
+        end = getattr(loc, "end", None)
+        if start and end:
+            err_msg = "Only one of `start` or `end` may be set as this describes the start or end of a transcript segment"
+            raise ValueError(err_msg)
+        return values
 
     model_config = ConfigDict(
         json_schema_extra={
@@ -79,6 +100,7 @@ class TxSegment(BaseModelForbidExtra):
                     },
                     "end": 154192135,
                 },
+                "is_exonic": True,
             }
         }
     )
@@ -136,6 +158,7 @@ class GenomicTxSeg(BaseModelForbidExtra):
                         },
                         "end": 154192135,
                     },
+                    "is_exonic": True,
                 },
                 "errors": [],
             }
@@ -202,6 +225,7 @@ class GenomicTxSegService(BaseModelForbidExtra):
                         },
                         "end": 154192135,
                     },
+                    "is_exonic": True,
                 },
                 "seg_end": {
                     "exon_ord": 7,
@@ -214,6 +238,7 @@ class GenomicTxSegService(BaseModelForbidExtra):
                         },
                         "start": 154170399,
                     },
+                    "is_exonic": True,
                 },
             }
         }
@@ -895,6 +920,7 @@ class ExonGenomicCoordsMapper:
         # Check if breakpoint occurs on an exon.
         # If not, determine the adjacent exon given the selected transcript
         if not self._is_exonic_breakpoint(genomic_pos, tx_exons):
+            is_exonic = False
             exon_num = self._get_adjacent_exon(
                 tx_exons_genomic_coords=tx_exons,
                 strand=strand,
@@ -902,6 +928,7 @@ class ExonGenomicCoordsMapper:
                 end=genomic_pos if not is_seg_start else None,
             )
         else:
+            is_exonic = True
             exon_data = await self.uta_db.get_tx_exon_aln_v_data(
                 transcript,
                 genomic_pos,
@@ -934,6 +961,7 @@ class ExonGenomicCoordsMapper:
                 exon_ord=exon_num,
                 offset=offset,
                 genomic_location=genomic_location,
+                is_exonic=is_exonic,
             ),
         )
 

{cool_seq_tool-0.14.3 → cool_seq_tool-0.14.4}/src/cool_seq_tool.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: cool_seq_tool
-Version: 0.14.3
+Version: 0.14.4
 Summary: Common Operation on Lots of Sequences Tool
 Author: Kori Kuzma, James Stevenson, Katie Stahl, Alex Wagner
 License: MIT License

{cool_seq_tool-0.14.3 → cool_seq_tool-0.14.4}/tests/mappers/test_exon_genomic_coords.py

@@ -184,6 +184,7 @@ def tpm3_exon1():
                 },
                 "end": 154192135,
             },
+            "is_exonic": True,
         },
     }
     return GenomicTxSeg(**params)
@@ -208,6 +209,7 @@ def tpm3_exon8():
                 },
                 "start": 154170399,
             },
+            "is_exonic": True,
         },
     }
     return GenomicTxSeg(**params)
@@ -293,6 +295,7 @@ def mane_braf():
                 },
                 "end": 140801559,
             },
+            "is_exonic": True,
         },
         "seg_end": {
             "exon_ord": 14,
@@ -305,6 +308,7 @@ def mane_braf():
                 },
                 "start": 140753336,
             },
+            "is_exonic": True,
         },
     }
     return GenomicTxSegService(**params)
@@ -438,6 +442,7 @@ def zbtb10_exon3_end():
                 },
                 "end": 80514010,
             },
+            "is_exonic": False,
         },
     }
     return GenomicTxSegService(**params)
@@ -462,6 +467,7 @@ def zbtb10_exon5_start():
                 },
                 "start": 80518580,
             },
+            "is_exonic": False,
         },
         "seg_end": None,
     }
@@ -488,6 +494,7 @@ def tpm3_exon6_end():
                 },
                 "start": 154171410,
             },
+            "is_exonic": False,
         },
     }
     return GenomicTxSegService(**params)
@@ -512,6 +519,7 @@ def tpm3_exon5_start():
                 },
                 "end": 154173080,
             },
+            "is_exonic": False,
         },
         "seg_end": None,
     }
@@ -538,6 +546,7 @@ def gusbp3_exon2_end():
                 },
                 "start": 69680764,
             },
+            "is_exonic": False,
         },
     }
     return GenomicTxSegService(**params)
@@ -562,6 +571,7 @@ def eln_grch38_intronic():
                 },
                 "start": 74028173,
             },
+            "is_exonic": True,
         },
         "seg_end": {
             "exon_ord": 7,
@@ -574,6 +584,7 @@ def eln_grch38_intronic():
                 },
                 "end": 74043599,
             },
+            "is_exonic": False,
         },
     }
     return GenomicTxSegService(**params)
@@ -598,6 +609,7 @@ def gusbp3_exon5_start():
                 },
                 "end": 69645878,
             },
+            "is_exonic": False,
         },
         "seg_end": None,
     }
@@ -648,6 +660,7 @@ def genomic_tx_seg_service_checks(actual, expected=None, is_valid=True):
                 assert (
                     actual_seg.genomic_location.end == expected_seg.genomic_location.end
                 )
+                assert actual_seg.is_exonic == expected_seg.is_exonic
 
         assert actual.errors == expected.errors
     else:
@@ -715,6 +728,7 @@ def genomic_tx_seg_checks(actual, expected=None, is_valid=True):
                 actual_seg.genomic_location.start == expected_seg.genomic_location.start
             )
             assert actual_seg.genomic_location.end == expected_seg.genomic_location.end
+            assert actual_seg.is_exonic == expected_seg.is_exonic
 
         assert actual.errors == expected.errors
     else: