Fix BLAT-incompatible target names in multi-target score sets

BLAT automatically removes certain characters from query names, including removing all characters after a space.
If the BLAT result name does not match any target genes in the score set, attempt to match based on BLAT's query name shortening patterns.
If multiple matches (could happen if labels are something like "Gene 1" and "Gene 2", in which case both would be shortened to "Gene"), raise an error.

Author: sallybg

src/dcd_mapping/align.py

@@ -4,7 +4,6 @@
 import subprocess
 import tempfile
 from pathlib import Path
-from typing import Any
 from urllib.parse import urlparse
 
 import requests
@@ -167,7 +166,9 @@ def _get_target_sequence_type(metadata: ScoresetMetadata) -> TargetSequenceType
         raise ValueError(msg)
 
 
-def _get_blat_output(metadata: ScoresetMetadata, silent: bool) -> Any:  # noqa: ANN401
+def _get_blat_output(
+    metadata: ScoresetMetadata, silent: bool
+) -> dict[str, QueryResult]:
     """Run a BLAT query and returns a path to the output object.
 
     If unable to produce a valid query the first time, then try a query using ``dnax``
@@ -195,7 +196,6 @@ def _get_blat_output(metadata: ScoresetMetadata, silent: bool) -> Any:  # noqa:
         try:
             output = parse_blat(out_file, "blat-psl")
 
-        # TODO reevaluate this code block - are there cases in mavedb where target sequence type is incorrectly supplied?
         except ValueError:
             target_args = "-q=dnax -t=dnax"
             process_result = _run_blat(target_args, query_file, "/dev/stdout", silent)
@@ -336,13 +336,31 @@ def align(
         # blat names the result id "query" if there is only one query; replace "query" with the target gene name for single-target score sets
         if target_label == "query" and len(scoreset_metadata.target_genes) == 1:
             target_label = list(scoreset_metadata.target_genes.keys())[0]  # noqa: RUF015
-        # NOTE this is a temporary fix that will not work for multi-target score sets!
-        # blat automatically reformats query names.
-        if (
-            target_label not in scoreset_metadata.target_genes
-            and len(scoreset_metadata.target_genes) == 1
-        ):
-            target_label = list(scoreset_metadata.target_genes.keys())[0]  # noqa: RUF015
+        # blat automatically reformats query names, so sometimes they don't match our metadata
+        if target_label not in scoreset_metadata.target_genes:
+            # if single-target score set, don't need to match by name
+            if len(scoreset_metadata.target_genes) == 1:
+                target_label = list(scoreset_metadata.target_genes.keys())[0]  # noqa: RUF015
+            else:
+                # try to match query name to a target gene in the metadata
+                matches = 0
+                for target_gene_name in scoreset_metadata.target_genes:
+                    blat_target_gene_name = (
+                        target_gene_name.split(" ")[0]
+                        .replace("(", "")
+                        .replace(")", "")
+                        .replace(",", "")
+                    )
+                    if blat_target_gene_name == target_label:
+                        target_label = target_gene_name
+                        matches += 1
+                # we may be missing some blat reformatting rules here - if so, this error will be thrown
+                if matches == 0:
+                    msg = f"BLAT result {target_label} does not match any target gene names in scoreset {scoreset_metadata.urn}."
+                    raise AlignmentError(msg)
+                if matches > 1:
+                    # could happen if multiple target genes have the same first word in their label (unlikely)
+                    msg = f"BLAT result {target_label} matches multiple target gene names in scoreset {scoreset_metadata.urn}"
         target_gene = scoreset_metadata.target_genes[target_label]
         alignment_results[target_label] = _get_best_match(blat_result, target_gene)
     return alignment_results