Merge pull request #32 from openvar/develop_2_0

Develop 2 0
openvar · May 12, 2022 · 5973c52 · 5973c52
2 parents 1baf789 + 3796474
commit 5973c52
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Showing 4 changed files with 16 additions and 8 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/simpleVariantFormatter.py b/VariantFormatter/simpleVariantFormatter.py
@@ -55,9 +55,8 @@ def format(batch_input, genome_build, transcript_model=None, specify_transcripts
                 vcf_list = pseudo_vcf.split('-')
                 delimiter = '-'
             if len(vcf_list) != 4:
-                formatted_variants[variant]['errors'].append(
-                    '%s is an unsupported format: For assistance, submit variant description to '
-                    'https://rest.variantvalidator.org') % pseudo_vcf
+                error = '%s is an unsupported format: For assistance, submit variant description to https://rest.variantvalidator.org' % str(pseudo_vcf)
+                formatted_variants[variant]['errors'].append(error)
                 formatted_variants[variant]['flag'] = 'submission_warning'
                 continue
             if ',' in str(vcf_list[-1]):
@@ -71,9 +70,8 @@ def format(batch_input, genome_build, transcript_model=None, specify_transcripts
                 try:
                     format_these.append(variant)
                 except Exception:
-                    formatted_variants[variant]['errors'].append(
-                        '%s is an unsupported format: For assistance, submit variant description to '
-                        'https://rest.variantvalidator.org') % variant
+                    error = '%s is an unsupported format: For assistance, submit variant description to https://rest.variantvalidator.org' % variant
+                    formatted_variants[variant]['errors'].append(error)
                     formatted_variants[variant]['flag'] = 'submission_warning'
                     continue
 

diff --git a/VariantFormatter/variantformatter.py b/VariantFormatter/variantformatter.py
@@ -64,8 +64,10 @@ 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"
+            elif ("NC_001807.4" in str(g_hgvs)) and "GRCh37" in genome_build:
+                gen_error = "NC_001807.4 is not associated with genome build GRCh37, instead use genome build hg19"
         except TypeError:
             pass
 
@@ -189,8 +191,13 @@ 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 +213,7 @@ 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 +442,7 @@ 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,