This commit allows mito genes (currently ensembl only) to validate as tx

VariantValidator/modules/format_converters.py

@@ -1695,6 +1695,8 @@ def mitochondrial(variant, validator):
     Check whether the variant is mitochondrial, ensure the correct reference
     sequence type is used, and retain the mitochondrial HGVS object.
     """
+    logger.info(f"Checking whether {variant.quibble} is mitochondrial")
+
     mitochondrial_accessions = ('NC_012920.1', 'NC_001807.4')
 
     if (
@@ -1787,6 +1789,8 @@ def mitochondrial(variant, validator):
             validator.select_transcripts
         )
 
+        logger.info(f"Mitochondrial transcripts: {rel_var}")
+
         # Retain the mitochondrial HGVS object.
         variant.hgvs_genomic = hgvs_mito
 

VariantValidator/modules/mappers.py

@@ -1075,6 +1075,8 @@ def final_tx_to_multiple_genomic(variant, validator, tx_variant, liftover_level=
     mapping_options = variant.map_dat.mapping_options(variant.hgvs_coding.ac,hdp=validator.hdp)
     mapping_options = sorted(mapping_options, key=itemgetter(1))
 
+    logger.info(f'Mapping options for {variant.hgvs_coding.ac}: {mapping_options}')
+
     for alt_chr in mapping_options:
         if liftover_level is None:
             multi_list.append(variant.genomic_g.ac)
@@ -1087,11 +1089,14 @@ def final_tx_to_multiple_genomic(variant, validator, tx_variant, liftover_level=
                 multi_list.append(alt_chr[1])
 
     for alt_chr in multi_list:
-        logger.debug("Trying to do final gap mapping with %s", alt_chr)
+        logger.info("Trying to do final gap mapping with %s", alt_chr)
 
         # Loop out NCBI36 refs
         if alt_chr.startswith('NC_') and not alt_chr.startswith('NC_000'):
-            continue
+            if alt_chr == 'NC_012920.1' or alt_chr == 'NC_001807.4':
+                pass
+            else:
+                continue
 
         try:
             # Re set ori

VariantValidator/modules/vvMixinConverters.py

@@ -2410,6 +2410,12 @@ def relevant_transcripts(
         """
         Automatically maps genomic positions onto all overlapping transcripts.
         """
+
+        logger.info(f"Mapping {hgvs_genomic} to relevant transcripts with alt_aln_method {alt_aln_method}")
+
+        if hgvs_genomic.type == 'm':
+            hgvs_genomic.type = 'g'
+
         # The two region queries differ by one base at each boundary.
         # Combine both to avoid missing transcripts at either end.
         rts_list = self.hdp.get_tx_for_region(
@@ -2419,6 +2425,8 @@ def relevant_transcripts(
             hgvs_genomic.posedit.pos.end.base - 1
         )
 
+        logger.info(f"rts_list: {rts_list}")
+
         rts_dict = {
             tx_dat['tx_ac']: tx_dat['alt_strand']
             for tx_dat in rts_list
@@ -2431,6 +2439,8 @@ def relevant_transcripts(
             hgvs_genomic.posedit.pos.end.base
         )
 
+        logger.info(f"rts_list_2: {rts_list_2}")
+
         for tx_dat in rts_list_2:
             rts_dict[tx_dat['tx_ac']] = tx_dat['alt_strand']
 
@@ -2447,6 +2457,8 @@ def relevant_transcripts(
         ):
             rts = self.transcript_filter(rts, select_transcripts)
 
+        logger.info(f"rts: {rts}")
+
         # Prepare insertion as a forced delins for mappings where HGVS insertion
         # handling otherwise fails.
         hgvs_genomic_forced_delins = None
@@ -2522,7 +2534,8 @@ def relevant_transcripts(
                     tx_ac
                 )
 
-            except vvhgvs.exceptions.HGVSError:
+            except vvhgvs.exceptions.HGVSError as e:
+                logger.info(f"HGVS error: {e}")
                 curr_genomic = (
                     hgvs_genomic_forced_delins
                     if hgvs_genomic_forced_delins is not None
@@ -2534,7 +2547,8 @@ def relevant_transcripts(
                         curr_genomic,
                         tx_ac
                     )
-                except vvhgvs.exceptions.HGVSError:
+                except vvhgvs.exceptions.HGVSError as e:
+                    logger.info(f"HGVS error: {e}")
                     continue
 
             except Exception as err:

VariantValidator/modules/vvMixinCore.py

@@ -750,13 +750,13 @@ def validate(self,
 
                     # COLLECT gene symbol, name and ACCESSION INFORMATION
                     # Gene symbol
-                    if my_variant.reftype != ':g.':
+                    if my_variant.reftype != ':g.' and my_variant.reftype != ':m.':
                         toskip = self._get_transcript_info(my_variant)
                         if toskip:
                             continue
 
                     # Now start mapping from genome to transcripts
-                    if my_variant.reftype == ':g.':
+                    if my_variant.reftype == ':g.' or my_variant.reftype == ':m.':
                         try:
                             toskip = mappers.gene_to_transcripts(my_variant, self, select_transcripts_dict, batch_list)
                         except IndexError:
@@ -976,13 +976,15 @@ def validate(self,
                                                                           self,
                                                                           hgvs_tx_variant,
                                                                           liftover_level=liftover_level)
+                    logger.info(f"multi_gen_vars: {multi_gen_vars}")
 
                 else:
                     # HGVS genomic in the absence of a transcript variant
                     if hgvs_genomic_variant:
                         multi_gen_vars = [hgvs_genomic_variant]
                     else:
                         multi_gen_vars = []
+
                 # Dictionaries of genomic loci
                 alt_genomic_dicts = []
                 primary_genomic_dicts = {}
@@ -1024,12 +1026,15 @@ def validate(self,
                         if 'NC_000' not in alt_gen_var.ac and 'NC_012920.1' not in alt_gen_var.ac and \
                                 'NC_001807.4' not in alt_gen_var.ac:
                             continue
-                        primary =True
+                        primary = True
                     elif 'NC_' not in alt_gen_var.ac and par is False:
                         pass
                     elif 'NC_000023' in alt_gen_var.ac and par is True:
                         primary =True
                     if primary:
+                        # Restore mito type
+                        if alt_gen_var.ac == "NC_012920.1" or alt_gen_var.ac == "NC_001807.4":
+                            alt_gen_var.type = "m"
                         for genome_build in vcf_dict['chrs_by_genome']:
                             primary_genomic_dicts[genome_build] = {
                                 'hgvs_genomic_description': alt_gen_var,

tests/variantvalidator/test_inputs_ensembl.py

@@ -629,6 +629,13 @@ def test_variant14(self):
         #     'hgvs_genomic_description': 'NC_000016.10:g.2049574del',
         #     'vcf': {'chr': '16', 'pos': '2049571', 'ref': 'TC', 'alt': 'T'}}
 
+    def test_regression_mito(self):
+        variant = 'NC_012920.1(MT-ND4):m.11232T>C'  # ENST00000340539.5 contains 3 fewer bases between NC_000002.11
+        results = self.vv.validate(variant, 'GRCh38', 'all', transcript_set="ensembl").format_as_dict(test=True)
+        print(results)
+        assert "ENST00000361381.2:c.473T>C" in results.keys()
+        assert results["ENST00000361381.2:c.473T>C"]["primary_assembly_loci"]["grch38"]["hgvs_genomic_description"] == "NC_012920.1:m.11232T>C"
+
 
 # Copyright (C) 2016-2026 VariantValidator Contributors
 # This file is part of VariantValidator and is distributed under the

tests/variantvalidator/test_mappers.py

@@ -1227,7 +1227,7 @@ def test_all_liftover_accepts_nc_nt_nw(self):
 
     def test_old_ncbi_reference_is_skipped(self):
         self.variant.map_dat.mapping_options.return_value = [
-            ("NM_000001.1", "NC_001807.4", "splign"),
+            ("NM_000001.1", "NC_001807.3", "splign"),
         ]
 
         result = final_tx_to_multiple_genomic(