feat: add BLAT output caching/reusing

src/dcd_mapping/cli.py

@@ -19,7 +19,15 @@
     default=False,
     help="Enable debug logging",
 )
-def cli(urn: str, debug: bool) -> None:
+@click.option(
+    "--cache_align",
+    "-c",
+    is_flag=True,
+    show_default=True,
+    default=False,
+    help="Enable caching for alignment results. Mostly useful for development/debugging.",
+)
+def cli(urn: str, debug: bool, cache_align: bool) -> None:
     """Get VRS mapping on preferred transcript for URN.
 
     For example:
@@ -29,6 +37,7 @@ def cli(urn: str, debug: bool) -> None:
     \f
     :param urn: scoreset URN
     :param debug: if True, enable debug logging
+    :param cache_align: if True, save alignment output and reuse when available
     """  # noqa: D301
     logging.basicConfig(
         filename="dcd-mapping.log",
@@ -41,7 +50,7 @@ def cli(urn: str, debug: bool) -> None:
     else:
         _logger.setLevel(logging.INFO)
     _logger.debug("debug logging enabled")
-    asyncio.run(map_scoreset_urn(urn, silent=False))
+    asyncio.run(map_scoreset_urn(urn, silent=False, cache_align=cache_align))
 
 
 if __name__ == "__main__":

src/dcd_mapping/main.py

@@ -38,17 +38,20 @@ def _save_results(
 
 
 async def map_scoreset(
-    metadata: ScoresetMetadata, records: List[ScoreRow], silent: bool = True
+    metadata: ScoresetMetadata,
+    records: List[ScoreRow],
+    silent: bool = True,
+    cache_align: bool = False,
 ) -> None:
-    """Given information about a MAVE experiment, map to VRS.
+    """Given information about a MAVE experiment, map to VRS and save output as JSON.
 
     :param metadata: salient data gathered from scoreset on MaveDB
     :param records: experiment scoring results
-    :param silent:
-    :return: something (TODO)
+    :param silent: if True, suppress console output
+    :param cache_align: if True, save alignment output and reuse when available
     """
     try:
-        alignment_result = align(metadata, silent, True)
+        alignment_result = align(metadata, silent, cache_align)
     except AlignmentError:
         _logger.error(f"Alignment failed for scoreset {metadata.urn}")
         return None
@@ -71,11 +74,14 @@ async def map_scoreset(
         _save_results(metadata, vrs_results)
 
 
-async def map_scoreset_urn(urn: str, silent: bool = True) -> None:
+async def map_scoreset_urn(
+    urn: str, silent: bool = True, cache_align: bool = False
+) -> None:
     """Perform end-to-end mapping for a scoreset.
 
     :param urn: identifier for a scoreset.
-    :return: something (TODO)
+    :param silent: if True, suppress console output
+    :param cache_align: if True, save alignment output and reuse when available
     """
     try:
         metadata = get_scoreset_metadata(urn)
@@ -85,5 +91,4 @@ async def map_scoreset_urn(urn: str, silent: bool = True) -> None:
         _logger.critical(msg)
         click.echo(f"Error: {msg}")
         return None
-    mapped = await map_scoreset(metadata, records, silent)
-    return mapped  # TODO not sure what this will be
+    await map_scoreset(metadata, records, silent, cache_align)