feat: Add tx_status field in TranscriptSegment output

src/cool_seq_tool/mappers/exon_genomic_coords.py

@@ -14,6 +14,7 @@
     CoordinateType,
     ServiceMeta,
     Strand,
+    TranscriptPriority,
 )
 from cool_seq_tool.sources.mane_transcript_mappings import ManeTranscriptMappings
 from cool_seq_tool.sources.uta_database import GenomicAlnData, UtaDatabase
@@ -113,6 +114,9 @@ class GenomicTxSeg(BaseModelForbidExtra):
     )
     genomic_ac: StrictStr | None = Field(None, description="RefSeq genomic accession.")
     tx_ac: StrictStr | None = Field(None, description="RefSeq transcript accession.")
+    tx_status: TranscriptPriority | None = Field(
+        None, description="Transcript priority for RefSeq transcript accession"
+    )
     strand: Strand | None = Field(
         None, description="The strand that the transcript accession exists on."
     )
@@ -144,6 +148,7 @@ def check_errors(cls, values: dict) -> dict:  # noqa: N805
                 "gene": "TPM3",
                 "genomic_ac": "NC_000001.11",
                 "tx_ac": "NM_152263.3",
+                "tx_status": "longest_compatible_remaining",
                 "strand": -1,
                 "seg": {
                     "exon_ord": 0,
@@ -172,6 +177,9 @@ class GenomicTxSegService(BaseModelForbidExtra):
     )
     genomic_ac: StrictStr | None = Field(None, description="RefSeq genomic accession.")
     tx_ac: StrictStr | None = Field(None, description="RefSeq transcript accession.")
+    tx_status: TranscriptPriority | None = Field(
+        None, description="Transcript priority for RefSeq transcript accession"
+    )
     strand: Strand | None = Field(
         None, description="The strand that the transcript exists on."
     )
@@ -211,6 +219,7 @@ def add_meta_check_errors(cls, values: dict) -> dict:  # noqa: N805
                 "gene": "TPM3",
                 "genomic_ac": "NC_000001.11",
                 "tx_ac": "NM_152263.3",
+                "tx_status": "longest_compatible_remaining",
                 "strand": -1,
                 "seg_start": {
                     "exon_ord": 0,
@@ -431,6 +440,7 @@ async def tx_segment_to_genomic(
             gene=gene,
             genomic_ac=genomic_ac,
             tx_ac=transcript,
+            tx_status=self.mane_transcript_mappings.get_transcript_status(transcript),
             strand=strand,
             seg_start=seg_start,
             seg_end=seg_end,
@@ -522,6 +532,7 @@ async def genomic_to_tx_segment(
             params["gene"] = start_tx_seg_data.gene
             params["genomic_ac"] = start_tx_seg_data.genomic_ac
             params["tx_ac"] = start_tx_seg_data.tx_ac
+            params["tx_status"] = start_tx_seg_data.tx_status
             params["strand"] = start_tx_seg_data.strand
             params["seg_start"] = start_tx_seg_data.seg
         else:
@@ -557,6 +568,7 @@ async def genomic_to_tx_segment(
                 params["gene"] = end_tx_seg_data.gene
                 params["genomic_ac"] = end_tx_seg_data.genomic_ac
                 params["tx_ac"] = end_tx_seg_data.tx_ac
+                params["tx_status"] = end_tx_seg_data.tx_status
                 params["strand"] = end_tx_seg_data.strand
 
             params["seg_end"] = end_tx_seg_data.seg
@@ -962,6 +974,7 @@ async def _genomic_to_tx_segment(
             gene=gene,
             genomic_ac=genomic_ac,
             tx_ac=transcript,
+            tx_status=self.mane_transcript_mappings.get_transcript_status(transcript),
             strand=strand,
             seg=TxSegment(
                 exon_ord=exon_num,

src/cool_seq_tool/sources/mane_transcript_mappings.py

@@ -8,7 +8,7 @@
 import polars as pl
 
 from cool_seq_tool.resources.data_files import DataFile, get_data_file
-from cool_seq_tool.schemas import ManeGeneData
+from cool_seq_tool.schemas import ManeGeneData, TranscriptPriority
 
 _logger = logging.getLogger(__name__)
 
@@ -85,6 +85,22 @@ def get_mane_from_transcripts(self, transcripts: list[str]) -> list[dict]:
             return []
         return mane_rows.to_dicts()
 
+    def get_transcript_status(self, tx_ac: str) -> TranscriptPriority:
+        """Get MANE status for a transcript
+
+        :param tx_ac: A RefSeq transcript accession
+        :return: A TranscriptPriority object
+        """
+        mane_info = self.get_mane_from_transcripts([tx_ac])
+        if not mane_info:
+            return TranscriptPriority.LONGEST_COMPATIBLE_REMAINING
+        mane_info = mane_info[0]["MANE_status"]
+        return (
+            TranscriptPriority.MANE_SELECT
+            if mane_info == "MANE Select"
+            else TranscriptPriority.MANE_PLUS_CLINICAL
+        )
+
     def get_mane_data_from_chr_pos(
         self, alt_ac: str, start: int, end: int
     ) -> list[dict]:

tests/mappers/test_exon_genomic_coords.py

@@ -172,6 +172,7 @@ def tpm3_exon1():
         "gene": "TPM3",
         "genomic_ac": "NC_000001.11",
         "tx_ac": "NM_152263.3",
+        "tx_status": "longest_compatible_remaining",
         "strand": -1,
         "seg": {
             "exon_ord": 0,
@@ -197,6 +198,7 @@ def tpm3_exon8():
         "gene": "TPM3",
         "genomic_ac": "NC_000001.11",
         "tx_ac": "NM_152263.3",
+        "tx_status": "longest_compatible_remaining",
         "strand": -1,
         "seg": {
             "exon_ord": 7,
@@ -222,6 +224,7 @@ def tpm3_exon1_g(tpm3_exon1):
         "gene": tpm3_exon1.gene,
         "genomic_ac": tpm3_exon1.genomic_ac,
         "tx_ac": tpm3_exon1.tx_ac,
+        "tx_status": tpm3_exon1.tx_status,
         "strand": tpm3_exon1.strand,
         "seg_start": tpm3_exon1.seg,
     }
@@ -235,6 +238,7 @@ def tpm3_exon8_g(tpm3_exon8):
         "gene": tpm3_exon8.gene,
         "genomic_ac": tpm3_exon8.genomic_ac,
         "tx_ac": tpm3_exon8.tx_ac,
+        "tx_status": tpm3_exon8.tx_status,
         "strand": tpm3_exon8.strand,
         "seg_end": tpm3_exon8.seg,
     }
@@ -248,6 +252,7 @@ def tpm3_exon1_exon8(tpm3_exon1, tpm3_exon8):
         "gene": tpm3_exon8.gene,
         "genomic_ac": tpm3_exon8.genomic_ac,
         "tx_ac": tpm3_exon8.tx_ac,
+        "tx_status": tpm3_exon8.tx_status,
         "strand": tpm3_exon8.strand,
         "seg_start": tpm3_exon1.seg,
         "seg_end": tpm3_exon8.seg,
@@ -269,6 +274,7 @@ def tpm3_exon1_exon8_offset(tpm3_exon1, tpm3_exon8):
         "gene": "TPM3",
         "genomic_ac": "NC_000001.11",
         "tx_ac": "NM_152263.3",
+        "tx_status": "longest_compatible_remaining",
         "strand": -1,
         "seg_start": tpm3_exon1_cpy.seg,
         "seg_end": tpm3_exon8_cpy.seg,
@@ -283,6 +289,7 @@ def mane_braf():
         "gene": "BRAF",
         "genomic_ac": "NC_000007.14",
         "tx_ac": "NM_004333.6",
+        "tx_status": "mane_select",
         "strand": -1,
         "seg_start": {
             "exon_ord": 5,
@@ -321,6 +328,7 @@ def wee1_exon2_exon11():
         "gene": "WEE1",
         "genomic_ac": "NC_000011.10",
         "tx_ac": "NM_003390.3",
+        "tx_status": "longest_compatible_remaining",
         "strand": 1,
         "seg_start": {
             "exon_ord": 1,
@@ -359,6 +367,7 @@ def mane_wee1_exon2_exon11():
         "gene": "WEE1",
         "genomic_ac": "NC_000011.10",
         "tx_ac": "NM_003390.4",
+        "tx_status": "mane_select",
         "strand": 1,
         "seg_start": {
             "exon_ord": 1,
@@ -397,6 +406,7 @@ def ntrk1_exon10_exon17():
         "gene": "NTRK1",
         "genomic_ac": "NC_000001.11",
         "tx_ac": "NM_002529.3",
+        "tx_status": "longest_compatible_remaining",
         "strand": 1,
         "seg_start": {
             "exon_ord": 9,
@@ -435,6 +445,7 @@ def zbtb10_exon3_end():
         "gene": "ZBTB10",
         "genomic_ac": "NC_000008.11",
         "tx_ac": "NM_001105539.3",
+        "tx_status": "mane_select",
         "strand": 1,
         "seg_start": None,
         "seg_end": {
@@ -461,6 +472,7 @@ def zbtb10_exon5_start():
         "gene": "ZBTB10",
         "genomic_ac": "NC_000008.11",
         "tx_ac": "NM_001105539.3",
+        "tx_status": "mane_select",
         "strand": 1,
         "seg_start": {
             "exon_ord": 4,
@@ -487,6 +499,7 @@ def tpm3_exon6_end():
         "gene": "TPM3",
         "genomic_ac": "NC_000001.11",
         "tx_ac": "NM_152263.4",
+        "tx_status": "mane_select",
         "strand": -1,
         "seg_start": None,
         "seg_end": {
@@ -513,6 +526,7 @@ def tpm3_exon5_start():
         "gene": "TPM3",
         "genomic_ac": "NC_000001.11",
         "tx_ac": "NM_152263.4",
+        "tx_status": "mane_select",
         "strand": -1,
         "seg_start": {
             "exon_ord": 4,
@@ -539,6 +553,7 @@ def gusbp3_exon2_end():
         "gene": "GUSBP3",
         "genomic_ac": "NC_000005.10",
         "tx_ac": "NR_027386.2",
+        "tx_status": "longest_compatible_remaining",
         "strand": -1,
         "seg_start": None,
         "seg_end": {
@@ -565,6 +580,7 @@ def eln_grch38_intronic():
         "gene": "ELN",
         "genomic_ac": "NC_000007.14",
         "tx_ac": "NM_000501.4",
+        "tx_status": "mane_select",
         "strand": 1,
         "seg_start": {
             "exon_ord": 0,
@@ -603,6 +619,7 @@ def gusbp3_exon5_start():
         "gene": "GUSBP3",
         "genomic_ac": "NC_000005.10",
         "tx_ac": "NR_027386.2",
+        "tx_status": "longest_compatible_remaining",
         "strand": -1,
         "seg_start": {
             "exon_ord": 4,
@@ -645,6 +662,7 @@ def genomic_tx_seg_service_checks(actual, expected=None, is_valid=True):
         assert actual.gene == expected.gene
         assert actual.genomic_ac == expected.genomic_ac
         assert actual.tx_ac == expected.tx_ac
+        assert actual.tx_status == expected.tx_status
         assert actual.strand == expected.strand
 
         for seg_attr in ["seg_start", "seg_end"]:
@@ -676,6 +694,7 @@ def genomic_tx_seg_service_checks(actual, expected=None, is_valid=True):
         assert actual.gene is None
         assert actual.genomic_ac is None
         assert actual.tx_ac is None
+        assert actual.tx_status is None
         assert actual.strand is None
         assert actual.seg_start is None
         assert actual.seg_end is None
@@ -720,6 +739,7 @@ def genomic_tx_seg_checks(actual, expected=None, is_valid=True):
         assert actual.gene == expected.gene
         assert actual.genomic_ac == expected.genomic_ac
         assert actual.tx_ac == expected.tx_ac
+        assert actual.tx_status == expected.tx_status
         assert actual.strand == expected.strand
 
         expected_seg = expected.seg
@@ -747,6 +767,7 @@ def genomic_tx_seg_checks(actual, expected=None, is_valid=True):
         assert actual.gene is None
         assert actual.genomic_ac is None
         assert actual.tx_ac is None
+        assert actual.tx_status is None
         assert actual.strand is None
         assert actual.seg is None
         assert len(actual.errors) > 0

tests/sources/test_mane_transcript_mappings.py

@@ -5,7 +5,7 @@
 import polars as pl
 import pytest
 
-from cool_seq_tool.schemas import ManeGeneData
+from cool_seq_tool.schemas import ManeGeneData, TranscriptPriority
 
 
 @pytest.fixture(scope="module")
@@ -168,6 +168,15 @@ def test_get_mane_from_transcripts(
     assert resp == []
 
 
+def test_get_transcript_status(test_mane_transcript_mappings):
+    """Test that get_transcript_status works correctly"""
+    actual = test_mane_transcript_mappings.get_transcript_status("NM_152263.4")
+    assert actual == TranscriptPriority.MANE_SELECT
+
+    actual = test_mane_transcript_mappings.get_transcript_status("NM_152263.3")
+    assert actual == TranscriptPriority.LONGEST_COMPATIBLE_REMAINING
+
+
 def test_get_mane_data_from_chr_pos(
     test_mane_transcript_mappings, braf_select, braf_plus_clinical
 ):