fix: pyliftover.convert_coordinate handling

- This method only returns None when the chromosome is unknown

cool_seq_tool/app.py

@@ -496,13 +496,13 @@ async def _set_genomic_data(self, params: Dict, strand: int,
                        f"{params['chr']}"
 
             chromosome_number, assembly = descr
-            liftover_data = self.uta_db.get_liftover(
+            liftover_pos = self.uta_db.get_liftover(
                 chromosome_number, params["pos"], Assembly.GRCH38)
-            if liftover_data is None:
+            if liftover_pos is None:
                 return f"Position {params['pos']} does not exist on " \
                        f"chromosome {chromosome_number}"
 
-            params["pos"] = liftover_data[1]
+            params["pos"] = liftover_pos
             params["chr"] = grch38_ac
 
         tx_exons = await self._structure_exons(params["transcript"], alt_ac=grch38_ac)

cool_seq_tool/data_sources/mane_transcript.py

@@ -723,15 +723,15 @@ async def g_to_grch38(self, ac: str, start_pos: int,
         if liftover_start_i is None:
             return None
         else:
-            start_pos = liftover_start_i[1]
+            start_pos = liftover_start_i
 
         if not is_same_pos:
             liftover_end_i = self.uta_db.get_liftover(chromosome, end_pos,
                                                       Assembly.GRCH38)
             if liftover_end_i is None:
                 return None
             else:
-                end_pos = liftover_end_i[1]
+                end_pos = liftover_end_i
         else:
             end_pos = start_pos
 

cool_seq_tool/data_sources/uta_database.py

@@ -975,20 +975,18 @@ async def liftover_to_38(self, genomic_tx_data: Dict) -> None:
         nc_acs = await self.execute_query(query)
         genomic_tx_data["alt_ac"] = nc_acs[0][0]
 
-    def get_liftover(self, chromosome: str, pos: int,
-                     liftover_to_assembly: Assembly) -> Optional[Tuple]:
-        """Get new genome assembly data for a position on a chromosome.
-
-        :param str chromosome: The chromosome number. Must be prefixed with `chr`
-        :param int pos: Position on the chromosome
-        :param Assembly liftover_to_assembly: Assembly to liftover to
-        :return: [Target chromosome, target position, target strand,
-            conversion_chain_score] for assembly
+    def get_liftover(
+        self, chromosome: str, pos: int, liftover_to_assembly: Assembly
+    ) -> Optional[int]:
+        """Get new genome assembly position for a given position on a chromosome. Does
+        not validate if position exists on lifted over accession, this must be done
+        separately.
+
+        :param chromosome: The chromosome number. Must be prefixed with `chr`
+        :param pos: Position on the chromosome
+        :param liftover_to_assembly: Assembly to liftover to
+        :return: Target position for assembly
         """
-        if not chromosome.startswith("chr"):
-            logger.warning("`chromosome` must be prefixed with chr")
-            return None
-
         if liftover_to_assembly == Assembly.GRCH38:
             liftover = self.liftover_37_to_38.convert_coordinate(chromosome, pos)
         elif liftover_to_assembly == Assembly.GRCH37:
@@ -997,11 +995,24 @@ def get_liftover(self, chromosome: str, pos: int,
             logger.warning(f"{liftover_to_assembly} assembly not supported")
             liftover = None
 
-        if liftover is None or len(liftover) == 0:
-            logger.warning(f"{pos} does not exist on {chromosome}")
-            return None
+        if liftover is None:
+            # If chromosome is completely unknown to the LiftOver, None is returned
+            # from pyliftover
+            logger.warning(f"Unknown chromosome: {chromosome}")
         else:
-            return liftover[0]
+            len_liftover = len(liftover)
+            if len_liftover == 1:
+                liftover = liftover[0][1]
+            elif len_liftover == 0:
+                liftover = pos
+            else:
+                logger.warning(
+                    f"Multiple liftover results found for {chromosome} {pos}: "
+                    f"{liftover}. Selecting first liftover"
+                )
+                liftover = liftover[0][1]
+
+        return liftover
 
     def _set_liftover(self, genomic_tx_data: Dict, key: str, chromosome: str,
                       liftover_to_assembly: Assembly) -> None:
@@ -1027,7 +1038,7 @@ def _set_liftover(self, genomic_tx_data: Dict, key: str, chromosome: str,
                            f"{genomic_tx_data[key][1]} on {chromosome}")
             return None
 
-        genomic_tx_data[key] = liftover_start_i[1], liftover_end_i[1]
+        genomic_tx_data[key] = liftover_start_i, liftover_end_i
 
     async def p_to_c_ac(self, p_ac: str) -> List[str]:
         """Return c. accession from p. accession.

cool_seq_tool/version.py

@@ -1 +1 @@
-__version__ = "0.1.14-dev0"
+__version__ = "0.1.14-dev1"

tests/unit/test_uta_database.py

@@ -278,10 +278,11 @@ async def test_liftover_to_38(test_db, genomic_tx_data):
 def test_get_liftover(test_db):
     """Test that get_liftover works correctly."""
     resp = test_db.get_liftover("chr7", 140453136, "GRCh38")
-    assert resp == ("chr7", 140753336, "+", 14633688187)
+    assert resp == 140753336
 
+    # pos out of index, this method does not validate
     resp = test_db.get_liftover("chr17", 140453136, "GRCh38")
-    assert resp is None
+    assert resp == 140453136
 
     # not prefixed w chr
     resp = test_db.get_liftover("7", 140453136, "GRCh38")