From 10a4357fe112ab0106f2572509de7a074b4096d6 Mon Sep 17 00:00:00 2001
From: Jeremy Arbesfeld <jarbesfeld@gmail.com>
Date: Thu, 14 Nov 2024 09:52:10 -0500
Subject: [PATCH] Add try_longest_compatible

---
 .../mappers/exon_genomic_coords.py            | 21 ++++++++++++++++---
 1 file changed, 18 insertions(+), 3 deletions(-)

diff --git a/src/cool_seq_tool/mappers/exon_genomic_coords.py b/src/cool_seq_tool/mappers/exon_genomic_coords.py
index 6e3c006..fd22ab8 100644
--- a/src/cool_seq_tool/mappers/exon_genomic_coords.py
+++ b/src/cool_seq_tool/mappers/exon_genomic_coords.py
@@ -416,6 +416,7 @@ async def genomic_to_tx_segment(
         seg_end_genomic: int | None = None,
         transcript: str | None = None,
         get_nearest_transcript_junction: bool = False,
+        try_longest_compatible: bool = True,
         gene: str | None = None,
     ) -> GenomicTxSegService:
         """Get transcript segment data for genomic data, lifted over to GRCh38.
@@ -461,6 +462,8 @@ async def genomic_to_tx_segment(
             following the breakpoint for the 3' end. For the negative strand, adjacent
             is defined as the exon following the breakpoint for the 5' end and the exon
             preceding the breakpoint for the 3' end.
+        :param try_longest_compatible: ``True`` if should try longest compatible remaining
+            if mane transcript was not compatible. ``False`` otherwise.
         :param gene: A valid, case-sensitive HGNC symbol. Must be given if no ``transcript``
             value is provided.
         :param coordinate_type: Coordinate type for ``seg_start_genomic`` and
@@ -489,6 +492,7 @@ async def genomic_to_tx_segment(
                 transcript=transcript,
                 gene=gene,
                 get_nearest_transcript_junction=get_nearest_transcript_junction,
+                try_longest_compatible=try_longest_compatible,
                 is_seg_start=True,
             )
             if start_tx_seg_data.errors:
@@ -509,6 +513,7 @@ async def genomic_to_tx_segment(
                 transcript=transcript,
                 gene=gene,
                 get_nearest_transcript_junction=get_nearest_transcript_junction,
+                try_longest_compatible=try_longest_compatible,
                 is_seg_start=False,
             )
             if end_tx_seg_data.errors:
@@ -739,6 +744,7 @@ async def _genomic_to_tx_segment(
         transcript: str | None = None,
         gene: str | None = None,
         get_nearest_transcript_junction: bool = False,
+        try_longest_compatible: bool = True,
         is_seg_start: bool = True,
     ) -> GenomicTxSeg:
         """Given genomic data, generate a boundary for a transcript segment.
@@ -766,6 +772,8 @@ async def _genomic_to_tx_segment(
             following the breakpoint for the 3' end. For the negative strand, adjacent
             is defined as the exon following the breakpoint for the 5' end and the exon
             preceding the breakpoint for the 3' end.
+        :param try_longest_compatible: ``True`` if should try longest compatible remaining
+            if mane transcript was not compatible. ``False`` otherwise.
         :param is_seg_start: ``True`` if ``genomic_pos`` is where the transcript segment starts.
             ``False`` if ``genomic_pos`` is where the transcript segment ends.
         :return: Data for a transcript segment boundary (inter-residue coordinates)
@@ -806,9 +814,16 @@ async def _genomic_to_tx_segment(
                 ):
                     transcript = mane_transcripts[0]["RefSeq_nuc"]
                 else:
-                    transcript = await self._select_optimal_transcript(
-                        genomic_pos, genomic_ac, gene
-                    )
+                    if try_longest_compatible:
+                        transcript = await self._select_optimal_transcript(
+                            genomic_pos, genomic_ac, gene
+                        )
+                    else:
+                        return GenomicTxSeg(
+                            errors=[
+                                "A MANE transcript either does not exist or was not found in UTA. Please set `try_longest_compatible` to ``True`` to re-run"
+                            ]
+                        )
             tx_exons = await self._get_all_exon_coords(
                 tx_ac=transcript, genomic_ac=genomic_ac
             )