Final changes to VF that deal with issue openvar/variantValidator#360

openvar · Apr 27, 2022 · 1ab6c10 · 1ab6c10
1 parent 0083bf7
commit 1ab6c10
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Showing 3 changed files with 10 additions and 2 deletions.
diff --git a/.DS_Store b/.DS_Store
diff --git a/VariantFormatter/formatter.py b/VariantFormatter/formatter.py
@@ -74,6 +74,7 @@ def vcf2hgvs_genomic(pseudo_vcf, genome_build, vfo):
             pos = vcf_list[1]
             ref = vcf_list[2]
             alt = vcf_list[3]
+
             # assemble the HGVS genomic description
             ac = chr_dict.to_accession(chrom, genome_build)
             if ac is None:

diff --git a/VariantFormatter/variantformatter.py b/VariantFormatter/variantformatter.py
@@ -64,7 +64,7 @@ def __init__(self, p_vcf, g_hgvs, un_norm_hgvs, hgvs_ref_bases, gen_error, genom
 
         # Warn incorrect m. accession for hg19
         try:
-            if ("NC_012920.1" in str(g_hgvs) or "NC_001807.4" in gen_error) and "hg19" in genome_build:
+            if ("NC_012920.1" in str(g_hgvs)) and "hg19" in genome_build:
                 gen_error = "NC_012920.1 is not associated with genome build hg19, instead use genome build GRCh37"
         except TypeError:
             pass
@@ -189,8 +189,13 @@ def __init__(self, variant_description, genome_build, vfo, transcript_model=None
             # Continuation - No exception
             try:
                 vcf_dictionary = formatter.hgvs_genomic2vcf(hgvs_genomic, self.genome_build, self.vfo)
-                vcf_list = [vcf_dictionary['grc_chr'], vcf_dictionary['pos'], vcf_dictionary['ref'],
+                if vcf_dictionary['grc_chr'] == "NC_001807.4" and genome_build == "hg19":
+                    chr_num = vcf_dictionary['ucsc_chr']
+                else:
+                    chr_num = vcf_dictionary['grc_chr']
+                vcf_list = [chr_num, vcf_dictionary['pos'], vcf_dictionary['ref'],
                             vcf_dictionary['alt']]
+
                 p_vcf = ':'.join(vcf_list)
             except Exception as e:
                 if "Variant span is outside sequence bounds" in str(e):
@@ -206,6 +211,7 @@ def __init__(self, variant_description, genome_build, vfo, transcript_model=None
                 self.genomic_descriptions = gds
                 self.warning_level = 'genomic_variant_warning'
                 return
+
             try:
                 genomic_level = formatter.vcf2hgvs_genomic(p_vcf, self.genome_build, self.vfo)
             except Exception as e:
@@ -434,6 +440,7 @@ def __init__(self, variant_description, genome_build, vfo, transcript_model=None
                 elif self.genomic_descriptions.selected_build == 'hg38' or self.genomic_descriptions.selected_build \
                         == 'GRCh38':
                     build_to = 'GRCh37'
+
                 current_lift = lo.liftover(self.genomic_descriptions.g_hgvs,
                                            self.genomic_descriptions.selected_build,
                                            build_to,