#46 - get_tx_info should properly handle alt_ac and alt_aln_method

cdot/hgvs/dataproviders/json_data_provider.py

@@ -8,6 +8,7 @@
 from lazy import lazy
 from hgvs.dataproviders.interface import Interface
 from hgvs.dataproviders.seqfetcher import SeqFetcher
+from hgvs.exceptions import HGVSDataNotAvailableError
 from intervaltree import IntervalTree
 from typing import List
 
@@ -181,15 +182,19 @@ def _get_transcript_info(transcript):
     def get_tx_info(self, tx_ac, alt_ac, alt_aln_method):
         self._check_alt_aln_method(alt_aln_method)
 
-        transcript = self._get_transcript(tx_ac)
-        if not transcript:
-            return None
-
-        tx_info = self._get_transcript_info(transcript)
-        tx_info["tx_ac"] = tx_ac
-        tx_info["alt_ac"] = alt_ac
-        tx_info["alt_aln_method"] = self.NCBI_ALN_METHOD
-        return tx_info
+        if transcript := self._get_transcript(tx_ac):
+            for build_data in transcript["genome_builds"].values():
+                print(f"BUILD DATA: {build_data}")
+                if alt_ac == build_data["contig"]:
+                    tx_info = self._get_transcript_info(transcript)
+                    tx_info["tx_ac"] = tx_ac
+                    tx_info["alt_ac"] = alt_ac
+                    tx_info["alt_aln_method"] = self.NCBI_ALN_METHOD
+                    return tx_info
+
+        raise HGVSDataNotAvailableError(
+            f"No tx_info for (tx_ac={tx_ac},alt_ac={alt_ac},alt_aln_method={alt_aln_method})"
+        )
 
     def get_tx_mapping_options(self, tx_ac):
         mapping_options = []

tests/test_json_data_provider.py

@@ -5,6 +5,7 @@
 
 import hgvs
 from hgvs.assemblymapper import AssemblyMapper
+from hgvs.exceptions import HGVSDataNotAvailableError
 
 from cdot.hgvs.dataproviders.json_data_provider import JSONDataProvider
 
@@ -86,6 +87,17 @@ def test_get_gene_info(self):
         }
         self.assertEqual(gene_info, expected)
 
+    def test_get_tx_info(self):
+        # We only have data for GRCh37 but none for 38
+
+        # Make sure 37 works
+        tx_info = self.json_data_provider.get_tx_info("NM_001637.3", "NC_000007.13", "splign")
+        print(tx_info)
+
+        # Make sure 38 fails
+        with self.assertRaises(HGVSDataNotAvailableError):
+            tx_info = self.json_data_provider.get_tx_info("NM_001637.3", "NC_000007.14", "splign")
+
 
 if __name__ == '__main__':
     unittest.main()