cool-seq-tool 0.14.3__py3-none-any.whl → 0.14.4__py3-none-any.whl

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.dist-info → cool_seq_tool-0.14.4.dist-info}/METADATA

@@ -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.dist-info → cool_seq_tool-0.14.4.dist-info}/RECORD

@@ -6,7 +6,7 @@ cool_seq_tool/handlers/__init__.py,sha256=KalQ46vX1MO4SJz2SlspKoIRy1n3c3Vp1t4Y2p
 cool_seq_tool/handlers/seqrepo_access.py,sha256=lRzPc8V0eZJTlefbHuVKeZTEC8-KcyPzpqX7vx3amu8,9118
 cool_seq_tool/mappers/__init__.py,sha256=tavpwkNogg_nF1J_kb6Q9jk7ezqdRz063v7BMZ4koLM,390
 cool_seq_tool/mappers/alignment.py,sha256=kWgYssM8YL-Z13H9GdpL77P7simNcbxltAs9YDXHE54,9640
-cool_seq_tool/mappers/exon_genomic_coords.py,sha256=t36NhWo2Rl84dgZY6qO7XFmGpfisjAqC-1ZOTRZxWvg,44757
+cool_seq_tool/mappers/exon_genomic_coords.py,sha256=fV4LyrpHPLRrx6AtV15g93q5XCH3i-y3Wj9tl-Cg8mM,45845
 cool_seq_tool/mappers/feature_overlap.py,sha256=X5UFClaH6ixRsO2fDLxqjywp-Z0bvNx4uzgBICy394U,9758
 cool_seq_tool/mappers/liftover.py,sha256=lltx9zxfkrb5PHtJlKp3a39JCwPP4e0Zft-mQc1jXL8,3367
 cool_seq_tool/mappers/mane_transcript.py,sha256=IluiLBxPQoY-CxkpqpjEBcMlHvrNLa34wdKdQxtKgDY,54613
@@ -18,8 +18,8 @@ cool_seq_tool/sources/__init__.py,sha256=51QiymeptF7AeVGgV-tW_9f4pIUr0xtYbyzpvHO
 cool_seq_tool/sources/mane_transcript_mappings.py,sha256=C5puIA1xuEzBaSvs8VtSxVb2OIDGUg5no8v6Ma2QSdw,6597
 cool_seq_tool/sources/transcript_mappings.py,sha256=903RKTMBO2rbKh6iTQ1BEWnY4C7saBFMPw2_4ATuudg,10054
 cool_seq_tool/sources/uta_database.py,sha256=zzRzmYuybqzEg7zeuQjhK46SPK5GfbiWWNRGNJju8AI,36197
-cool_seq_tool-0.14.3.dist-info/licenses/LICENSE,sha256=IpqC9A-tZW7XXXvCS8c4AVINqkmpxiVA-34Qe3CZSjo,1072
-cool_seq_tool-0.14.3.dist-info/METADATA,sha256=C-8jHyitpgW7cvaBDKtjfa8ClFsTil9X7yStIY73y3I,6535
-cool_seq_tool-0.14.3.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-cool_seq_tool-0.14.3.dist-info/top_level.txt,sha256=cGuxdN6p3y16jQf6hCwWhE4OptwUeZPm_PNJlPb3b0k,14
-cool_seq_tool-0.14.3.dist-info/RECORD,,
+cool_seq_tool-0.14.4.dist-info/licenses/LICENSE,sha256=IpqC9A-tZW7XXXvCS8c4AVINqkmpxiVA-34Qe3CZSjo,1072
+cool_seq_tool-0.14.4.dist-info/METADATA,sha256=gPz48irXCwNUecTcgpKrdrHiBhi8R_Is55S2UYs9Qtk,6535
+cool_seq_tool-0.14.4.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+cool_seq_tool-0.14.4.dist-info/top_level.txt,sha256=cGuxdN6p3y16jQf6hCwWhE4OptwUeZPm_PNJlPb3b0k,14
+cool_seq_tool-0.14.4.dist-info/RECORD,,