diff --git a/VariantValidator/modules/vvMixinCore.py b/VariantValidator/modules/vvMixinCore.py index 152c4ee7..e94b2d23 100644 --- a/VariantValidator/modules/vvMixinCore.py +++ b/VariantValidator/modules/vvMixinCore.py @@ -725,25 +725,27 @@ def validate(self, # Outside the for loop ###################### logger.debug("End of 1st for loop") + # order the rows by_order = sorted(self.batch_list, key=lambda x: x.order) - for variant in by_order: if type(variant.quibble) is str: logger.debug(f"Formatting variant {variant.quibble}") else: - logger.debug("Formatting variant " + variant.quibble.format({'p_3_letter':False})) + logger.debug("Formatting variant " + variant.quibble.format({'p_3_letter': False})) if not variant.write: continue # Genomic sequence variation # Check for gapped delins - if variant.genomic_g and variant.genomic_g.posedit.edit.type == 'delins': + if (variant.genomic_g and variant.genomic_g.posedit.edit.type == 'delins' and + variant.genomic_g.posedit.edit.alt == ""): + logger.info(f"Delins minus an ALT sequence identified {variant.genomic_g}") variant.genomic_g = hgvs_delins_parts_to_hgvs_obj( - variant.genomic_g.ac, - variant.genomic_g.type, - variant.genomic_g.posedit.pos, - '','') + variant.genomic_g.ac, + variant.genomic_g.type, + variant.genomic_g.posedit.pos, + '', '') hgvs_genomic_variant = variant.genomic_g @@ -754,6 +756,7 @@ def validate(self, genomic_accession = hgvs_genomic_variant.ac else: genomic_accession = None + # RefSeqGene variation logger.debug("RefSeqGene variation") refseqgene_variant = variant.genomic_r diff --git a/tests/test_inputs.py b/tests/test_inputs.py index 9723c543..ecbe9866 100644 --- a/tests/test_inputs.py +++ b/tests/test_inputs.py @@ -31262,6 +31262,15 @@ def cnv_del_vcf(self): assert results["intergenic_variant_1"]["primary_assembly_loci"]["grch38"][ "hgvs_genomic_description"] == "NC_000001.11:g.1000000_1005000del" + def issue_786_part_B(self): + # Test that it fails for genome mismatch + results = self.vv.validate('NC_000023.10:g.18908328_18911824delinsGCCTGCAGAG', 'GRCh37', 'all', liftover_level=True).format_as_dict(test=True) + assert 'intergenic_variant_1' in results + assert results["intergenic_variant_1"]["primary_assembly_loci"]["grch37"][ + "hgvs_genomic_description"] == "NC_000023.10:g.18908328_18911824delinsGCCTGCAGAG" + assert results["intergenic_variant_1"]["primary_assembly_loci"]["grch38"][ + "hgvs_genomic_description"] == "NC_000023.11:g.18890210_18893706delinsGCCTGCAGAG" + # # Copyright (C) 2016-2026 VariantValidator Contributors