Add is_exonic field to transcript segment output

Author: jarbesfeld

src/cool_seq_tool/mappers/exon_genomic_coords.py

@@ -65,6 +65,7 @@ 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_config = ConfigDict(
         json_schema_extra={
@@ -79,6 +80,7 @@ class TxSegment(BaseModelForbidExtra):
                     },
                     "end": 154192135,
                 },
+                "is_exonic": True,
             }
         }
     )
@@ -136,6 +138,7 @@ def check_errors(cls, values: dict) -> dict:  # noqa: N805
                         },
                         "end": 154192135,
                     },
+                    "is_exonic": True,
                 },
                 "errors": [],
             }
@@ -202,6 +205,7 @@ def add_meta_check_errors(cls, values: dict) -> dict:  # noqa: N805
                         },
                         "end": 154192135,
                     },
+                    "is_exonic": True,
                 },
                 "seg_end": {
                     "exon_ord": 7,
@@ -214,6 +218,7 @@ def add_meta_check_errors(cls, values: dict) -> dict:  # noqa: N805
                         },
                         "start": 154170399,
                     },
+                    "is_exonic": True,
                 },
             }
         }
@@ -894,7 +899,9 @@ async def _genomic_to_tx_segment(
 
         # Check if breakpoint occurs on an exon.
         # If not, determine the adjacent exon given the selected transcript
+        is_exonic = True
         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,
@@ -925,6 +932,7 @@ async def _genomic_to_tx_segment(
         if err_msg:
             return GenomicTxSeg(errors=[err_msg])
 
+        #print(is_exonic)
         return GenomicTxSeg(
             gene=gene,
             genomic_ac=genomic_ac,
@@ -934,6 +942,7 @@ async def _genomic_to_tx_segment(
                 exon_ord=exon_num,
                 offset=offset,
                 genomic_location=genomic_location,
+                is_exonic=is_exonic,
             ),
         )
 

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: