feat!: use materialized view for tx-exon alignment lookup (#462)

close #461 

* Use the equivalent materialized view for this lookup. It's a small
speedup but it only took a few minutes to fix (I think the view just
exists as a referent for building the materialized view)
* Rename methods regarding "tx_exon_aln_v" to just "tx_exon_aln", since
the Python user doesn't really care that it's a view or a materialized
view or whatever, they just need the "tx-exon aln" part. Hopefully this
isn't too annoying to change wherever else it's used but if it is, this
part could be walked back

Author: jsstevenson

src/cool_seq_tool/mappers/exon_genomic_coords.py

@@ -639,7 +639,7 @@ async def _get_all_exon_coords(
         if genomic_ac:
             query = f"""
                 SELECT DISTINCT ord, tx_start_i, tx_end_i, alt_start_i, alt_end_i, alt_strand
-                FROM {self.uta_db.schema}.tx_exon_aln_v
+                FROM {self.uta_db.schema}.tx_exon_aln_mv
                 WHERE tx_ac = '{tx_ac}'
                 AND alt_aln_method = 'splign'
                 AND alt_ac = '{genomic_ac}'
@@ -648,7 +648,7 @@ async def _get_all_exon_coords(
         else:
             query = f"""
                 SELECT DISTINCT ord, tx_start_i, tx_end_i, alt_start_i, alt_end_i, alt_strand
-                FROM {self.uta_db.schema}.tx_exon_aln_v as t
+                FROM {self.uta_db.schema}.tx_exon_aln_mv as t
                 INNER JOIN {self.uta_db.schema}._seq_anno_most_recent as s
                 ON t.alt_ac = s.ac
                 WHERE s.descr = ''
@@ -890,7 +890,7 @@ async def _genomic_to_tx_segment(
                     # Run if gene is for a noncoding transcript
                     query = f"""
                         SELECT DISTINCT tx_ac
-                        FROM {self.uta_db.schema}.tx_exon_aln_v
+                        FROM {self.uta_db.schema}.tx_exon_aln_mv
                         WHERE hgnc = '{gene}'
                         AND alt_ac = '{genomic_ac}'
                         """  # noqa: S608
@@ -955,7 +955,7 @@ async def _genomic_to_tx_segment(
             )
         else:
             is_exonic = True
-            exon_data = await self.uta_db.get_tx_exon_aln_v_data(
+            exon_data = await self.uta_db.get_tx_exon_aln_data(
                 transcript,
                 genomic_pos,
                 genomic_pos,
@@ -1035,7 +1035,7 @@ async def _validate_genomic_breakpoint(
                 SELECT
                 MIN(alt_start_i) AS min_start,
                 MAX(alt_end_i) AS max_end
-                FROM {self.uta_db.schema}.tx_exon_aln_v
+                FROM {self.uta_db.schema}.tx_exon_aln_mv
                 WHERE tx_ac = '{tx_ac}'
                 AND alt_ac = '{genomic_ac}'
             )
@@ -1060,7 +1060,7 @@ async def _get_tx_ac_gene(
         """
         query = f"""
             SELECT DISTINCT hgnc
-            FROM {self.uta_db.schema}.tx_exon_aln_v
+            FROM {self.uta_db.schema}.tx_exon_aln_mv
             WHERE tx_ac = '{tx_ac}'
             ORDER BY hgnc
             LIMIT 1;

src/cool_seq_tool/mappers/mane_transcript.py

@@ -234,7 +234,7 @@ async def _liftover_to_38(self, genomic_tx_data: GenomicTxMetadata) -> None:
 
         query = f"""
             SELECT DISTINCT alt_ac
-            FROM {self.uta_db.schema}.tx_exon_aln_v
+            FROM {self.uta_db.schema}.tx_exon_aln_mv
             WHERE tx_ac = '{genomic_tx_data.tx_ac}';
             """  # noqa: S608
         nc_acs = await self.uta_db.execute_query(query)
@@ -462,15 +462,15 @@ async def _g_to_c(
         :param ensembl_c_ac: Ensembl transcript accession
         :param alt_ac: Genomic accession
         :param found_result: ``True`` if found result, so do not need to query
-            tx_exon_aln_v table. This is because the user did not need to liftover.
-            ``False`` if need to get result from tx_exon_aln_v table.
+            tx_exon_aln_mv table. This is because the user did not need to liftover.
+            ``False`` if need to get result from tx_exon_aln_mv table.
         :return: Transcript data
         """
         if found_result:
             tx_g_pos = g.alt_pos_range
             tx_pos_range = g.tx_pos_range
         else:
-            result = await self.uta_db.get_tx_exon_aln_v_data(
+            result = await self.uta_db.get_tx_exon_aln_data(
                 refseq_c_ac,
                 g.alt_pos_change_range[0],
                 g.alt_pos_change_range[1],
@@ -820,7 +820,7 @@ def _get_protein_rep(
             if alt_ac is None:
                 alt_ac = row["alt_ac"]
 
-            found_tx_exon_aln_v_result = False
+            found_tx_exon_aln_result = False
             if is_p_or_c_start_anno:
                 # Go from c -> g annotation (liftover as well)
                 g = await self._c_to_g(tx_ac, (c_start_pos, c_end_pos))
@@ -832,7 +832,7 @@ def _get_protein_rep(
                     annotation_layer=AnnotationLayer.GENOMIC,
                     alt_ac=alt_ac,
                 )
-                found_tx_exon_aln_v_result = True
+                found_tx_exon_aln_result = True
             if not g:
                 continue
 
@@ -842,7 +842,7 @@ def _get_protein_rep(
                 g=g,
                 refseq_c_ac=tx_ac,
                 status=TranscriptPriority.LONGEST_COMPATIBLE_REMAINING,
-                found_result=found_tx_exon_aln_v_result,
+                found_result=found_tx_exon_aln_result,
             )
 
             if not lcr_c_data:

src/cool_seq_tool/sources/uta_database.py

@@ -44,7 +44,7 @@ class DbConnectionArgs(BaseModelForbidExtra):
 
 
 class GenomicAlnData(BaseModelForbidExtra):
-    """Represent genomic alignment data from UTA tx_exon_aln_v view"""
+    """Represent genomic alignment data from UTA tx_exon_aln_mv view"""
 
     hgnc: StrictStr = Field(..., description="HGNC gene symbol.")
     ord: StrictInt = Field(..., description="Exon number. 0-based.")
@@ -61,7 +61,7 @@ class GenomicAlnData(BaseModelForbidExtra):
 
 
 class TxExonAlnData(GenomicAlnData):
-    """Represent data from UTA tx_exon_aln_v view"""
+    """Represent data from UTA tx_exon_aln_mv view"""
 
     tx_ac: StrictStr = Field(..., description="Transcript accession.")
     tx_start_i: StrictInt = Field(
@@ -285,7 +285,7 @@ async def get_alt_ac_start_or_end(
         query = f"""
             SELECT T.hgnc, T.alt_ac, T.alt_start_i, T.alt_end_i, T.alt_strand, T.ord
             FROM {self.schema}._cds_exons_fp_v as C
-            JOIN {self.schema}.tx_exon_aln_v as T ON T.tx_ac = C.tx_ac
+            JOIN {self.schema}.tx_exon_aln_mv as T ON T.tx_ac = C.tx_ac
             WHERE T.tx_ac = '{tx_ac}'
             {gene_query}
             AND {tx_exon_start} BETWEEN T.tx_start_i AND T.tx_end_i
@@ -394,15 +394,15 @@ async def gene_exists(self, gene: str) -> bool:
         return result[0][0]
 
     async def transcript_exists(self, transcript: str) -> bool:
-        """Return whether or not a transcript exists in the UTA ``tx_exon_aln_v`` table
+        """Return whether or not a transcript exists in the UTA ``tx_exon_aln_mv`` table
 
         :param transcript: A transcript accession
         :return: ``True`` if transcript exists in UTA, ``False`` if not
         """
         query = f"""
             SELECT EXISTS(
                 SELECT tx_ac
-                FROM {self.schema}.tx_exon_aln_v
+                FROM {self.schema}.tx_exon_aln_mv
                 WHERE tx_ac = '{transcript}'
             );
             """  # noqa: S608
@@ -439,7 +439,7 @@ async def get_ac_descr(self, ac: str) -> str | None:
             result = None
         return result
 
-    async def get_tx_exon_aln_v_data(
+    async def get_tx_exon_aln_data(
         self,
         tx_ac: str,
         start_pos: int,
@@ -448,7 +448,9 @@ async def get_tx_exon_aln_v_data(
         use_tx_pos: bool = True,
         like_tx_ac: bool = False,
     ) -> list[TxExonAlnData]:
-        """Return queried data from tx_exon_aln_v table.
+        """Get alignments between exons and reference sequences.
+
+        This is a direct query against the UTA ``tx_exon_aln_mv`` view.
 
         :param tx_ac: accession on c. coordinate
         :param start_pos: Start position change
@@ -491,7 +493,7 @@ async def get_tx_exon_aln_v_data(
         query = f"""
             SELECT hgnc, tx_ac, tx_start_i, tx_end_i, alt_ac, alt_start_i,
                 alt_end_i, alt_strand, alt_aln_method, ord, tx_exon_id, alt_exon_id
-            FROM {self.schema}.tx_exon_aln_v
+            FROM {self.schema}.tx_exon_aln_mv
             {tx_q}
             {alt_ac_q}
             {aln_method}
@@ -543,7 +545,7 @@ async def get_mane_c_genomic_data(
         self, ac: str, alt_ac: str | None, start_pos: int, end_pos: int
     ) -> GenomicTxMetadata | None:
         """Get MANE transcript and genomic data. Used when going from g. to MANE c.
-        representation. This function parses queried data from the tx_exon_aln_v
+        representation. This function parses queried data from the tx_exon_aln_mv
         table, and sorts the queried data by the most recent genomic build
 
         >>> import asyncio
@@ -569,7 +571,7 @@ async def get_mane_c_genomic_data(
         :return: Metadata for MANE genomic and transcript accessions results if
             successful
         """
-        results = await self.get_tx_exon_aln_v_data(
+        results = await self.get_tx_exon_aln_data(
             tx_ac=ac,
             start_pos=start_pos,
             end_pos=end_pos,
@@ -636,7 +638,7 @@ async def get_genomic_tx_data(
             If ``alt_ac`` is provided, it will return the associated assembly.
         :return: Metadata for genomic and transcript accessions
         """
-        results = await self.get_tx_exon_aln_v_data(
+        results = await self.get_tx_exon_aln_data(
             tx_ac,
             pos[0],
             pos[1],
@@ -816,7 +818,7 @@ async def get_transcripts(
             SELECT AA.pro_ac, AA.tx_ac, ALIGN.alt_ac, T.cds_start_i
             FROM {self.schema}.associated_accessions as AA
             JOIN {self.schema}.transcript as T ON T.ac = AA.tx_ac
-            JOIN {self.schema}.tx_exon_aln_v as ALIGN ON T.ac = ALIGN.tx_ac
+            JOIN {self.schema}.tx_exon_aln_mv as ALIGN ON T.ac = ALIGN.tx_ac
             WHERE ALIGN.alt_aln_method = 'splign'
             {gene_cond}
             {alt_ac_cond}
@@ -903,7 +905,7 @@ async def get_transcripts_from_genomic_pos(
         """
         query = f"""
                SELECT distinct tx_ac
-               FROM {self.schema}.tx_exon_aln_v
+               FROM {self.schema}.tx_exon_aln_mv
                WHERE alt_ac = '{alt_ac}'
                AND {g_pos} BETWEEN alt_start_i AND alt_end_i
                AND tx_ac LIKE 'NM_%';

tests/sources/test_uta_database.py

@@ -14,8 +14,8 @@
 
 
 @pytest.fixture(scope="module")
-def tx_exon_aln_v_data():
-    """Create test fixture for tx_aln_v_data test."""
+def tx_exon_aln_data():
+    """Create test fixture for tx_exon_aln_data test."""
     return TxExonAlnData(
         hgnc="BRAF",
         ord=14,
@@ -121,19 +121,19 @@ async def test_get_ac_descr(test_db):
 
 
 @pytest.mark.asyncio
-async def test_get_tx_exon_aln_v_data(test_db, tx_exon_aln_v_data):
-    """Test that get_tx_exon_aln_v_data"""
-    resp = await test_db.get_tx_exon_aln_v_data(
+async def test_get_tx_exon_aln_data(test_db, tx_exon_aln_data):
+    """Test that get_tx_exon_aln_data"""
+    resp = await test_db.get_tx_exon_aln_data(
         "NM_004333.4", 140453136, 140453136, alt_ac="NC_000007.13", use_tx_pos=False
     )
-    assert resp == [tx_exon_aln_v_data]
+    assert resp == [tx_exon_aln_data]
 
-    resp = await test_db.get_tx_exon_aln_v_data(
+    resp = await test_db.get_tx_exon_aln_data(
         "NM_004333.4", 140453136, 140453136, alt_ac=None, use_tx_pos=False
     )
-    assert resp == [tx_exon_aln_v_data]
+    assert resp == [tx_exon_aln_data]
 
-    resp = await test_db.get_tx_exon_aln_v_data(
+    resp = await test_db.get_tx_exon_aln_data(
         "NM_004333.4", 1860, 1860, alt_ac=None, use_tx_pos=True
     )
     assert resp == [
@@ -169,9 +169,9 @@ async def test_get_tx_exon_aln_v_data(test_db, tx_exon_aln_v_data):
 
 
 @pytest.mark.asyncio
-async def test_data_from_result(test_db, tx_exon_aln_v_data, data_from_result):
+async def test_data_from_result(test_db, tx_exon_aln_data, data_from_result):
     """Test that data_from_result works correctly."""
-    resp = test_db.data_from_result(tx_exon_aln_v_data)
+    resp = test_db.data_from_result(tx_exon_aln_data)
     assert resp == data_from_result
 
 
@@ -198,7 +198,7 @@ async def test_mane_c_genomic_data(test_db):
     }
     assert resp == GenomicTxMetadata(**expected_params)
 
-    # Test example where sorting of tx_exon_aln_v is needed
+    # Test example where sorting of tx_exon_aln_mv is needed
     resp = await test_db.get_mane_c_genomic_data(
         "NM_000077.5", "NC_000009.12", 21971186, 21971187
     )