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Change variant display name format: Add exon, remove hgvs #3

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Change variant display name format: Add exon, remove hgvs #3

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4 changes: 2 additions & 2 deletions varseq_hl7.py
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Original file line number Diff line number Diff line change
Expand Up @@ -219,7 +219,7 @@ def get_variant_display_name(self, variant):
molecular_cons = self.get_consequence(variant)
if molecular_cons == "Nonsense":
molecular_cons = "Nonsense Variant"
return f"{variant['geneName']} {pdot}{variant['cDot']} {molecular_cons}"
return f"{variant['geneName']} {variant['location']} {molecular_cons}"

def get_tumor_variant_obxs(self, variant, variant_idx):
ref, alt = variant["refAlt"].split("/")
Expand All @@ -240,7 +240,7 @@ def get_tumor_variant_obxs(self, variant, variant_idx):
create_obx_segment("7400052", variant["proteinId"]),
create_obx_segment("51958-7", f"{variant['transcriptName']}^{variant['transcriptName']}^RefSeq-T"), # Transcript Reference Sequence
create_obx_segment("48000-4", self.get_chrom(variant)), # Chromosome
create_obx_segment("48006-1", '^' + self.get_consequence(variant)),
create_obx_segment("48006-1", '^' + self.get_consequence(variant)), # Molecular Consequence
create_obx_segment("69547-8", ref), # Genomic Reference Allele
create_obx_segment("69551-0", alt), # Genomic Alternate Allele
create_obx_segment("81254-5", f"{start}^{stop}"), # Genomic Allele Start-End
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