Merge pull request #1122 from griffithlab/variant-tsv

Update Variant TSV exporter to include new variant types

server/app/tsv_formatters/variant_tsv_formatter.rb

@@ -3,18 +3,33 @@ def self.objects
     Variant.joins(molecular_profiles: [:evidence_items])
       .includes(:variant_groups, :variant_types, :hgvs_descriptions, :variant_aliases, :feature)
       .where("evidence_items.status = 'accepted'")
-      .where(features: { feature_instance_type: 'Features::Gene'})
       .distinct
   end
 
   def self.headers
-    [
+    shared_headers = [
       'variant_id',
       'variant_civic_url',
-      'gene',
-      'entrez_id',
+      'feature_type',
+      'feature_id',
+      'feature_name',
+      'feature_civic_url',
       'variant',
+      'variant_aliases',
+      'is_flagged',
       'variant_groups',
+      'variant_types',
+      'single_variant_molecular_profile_id',
+      'last_review_date',
+    ]
+
+    shared_headers + gene_headers + factor_headers + fusion_headers
+  end
+
+  def self.gene_headers
+    [
+      'gene',
+      'entrez_id',
       'chromosome',
       'start',
       'stop',
@@ -23,29 +38,40 @@ def self.headers
       'representative_transcript',
       'ensembl_version',
       'reference_build',
-      'chromosome2',
-      'start2',
-      'stop2',
-      'representative_transcript2',
-      'variant_types',
       'hgvs_descriptions',
-      'last_review_date',
       'allele_registry_id',
       'clinvar_ids',
-      'variant_aliases',
-      'is_flagged',
-      'single_variant_molecular_profile_id'
     ]
   end
 
-  def self.row_from_object(variant)
+  def self.factor_headers 
     [
-      variant.id,
-      LinkAdaptors::Variant.new(variant).permalink_path(include_domain: true),
+      'ncit_id'
+    ]
+  end
+
+  def self.fusion_headers
+    [
+      '5_prime_partner_status',
+      '5_prime_partner',
+      '3_prime_partner_status',
+      '3_prime_partner',
+      'vicc_compliant_name',
+      '5_prime_transcript',
+      '5_prime_end_exon',
+      '5_prime_exon_offset',
+      '5_prime_exon_offset_direction',
+      '3_prime_transcript',
+      '3_prime_start_exon',
+      '3_prime_exon_offset',
+      '3_prime_exon_offset_direction',
+    ]
+  end
+
+  def self.create_gene_row(variant)
+    row = [
       variant.feature.name,
       variant.feature.feature_instance.entrez_id,
-      variant.name,
-      variant.variant_groups.map(&:name).join(','),
       variant.chromosome,
       variant.start,
       variant.stop,
@@ -54,19 +80,78 @@ def self.row_from_object(variant)
       variant.representative_transcript,
       variant.ensembl_version,
       variant.reference_build,
-      variant.chromosome2,
-      variant.start2,
-      variant.stop2,
-      variant.representative_transcript2,
-      variant.variant_types.map(&:name).join(','),
       variant.hgvs_descriptions.map(&:description).join(','),
-      variant.updated_at,
       variant.allele_registry_id,
       variant.clinvar_entries.map(&:clinvar_id).join(','),
+    ]
+    row += Array.new(factor_headers.size)
+    row += Array.new(fusion_headers.size)
+    return row
+  end
+
+  def self.create_factor_row(variant)
+    row = Array.new(gene_headers.size)
+    row += [
+      variant.ncit_id
+    ]
+    row += Array.new(fusion_headers.size)
+    return row
+  end
+
+  def self.create_fusion_row(variant)
+    fusion_feature = variant.feature.feature_instance
+    five_prime_coords = variant.five_prime_end_exon_coordinates
+    three_prime_coords = variant.three_prime_start_exon_coordinates
+
+    row = Array.new(gene_headers.size)
+    row += Array.new(factor_headers.size)
+    row += [
+      fusion_feature.five_prime_partner_status,
+      fusion_feature.five_prime_gene&.name,
+      fusion_feature.three_prime_partner_status,
+      fusion_feature.three_prime_gene&.name,
+      variant.vicc_compliant_name,
+      five_prime_coords&.representative_transcript,
+      five_prime_coords&.exon,
+      five_prime_coords&.exon_offset,
+      five_prime_coords&.exon_offset_direction,
+      three_prime_coords&.representative_transcript,
+      three_prime_coords&.exon,
+      three_prime_coords&.exon_offset,
+      three_prime_coords&.exon_offset_direction,
+    ]
+    return row
+  end
+
+  def self.row_from_object(variant)
+    shared_cols = [
+      variant.id,
+      LinkAdaptors::Variant.new(variant).permalink_path(include_domain: true),
+      variant.feature.feature_instance_type.demodulize,
+      variant.feature.id,
+      variant.feature.name,
+      LinkAdaptors::Feature.new(variant.feature).permalink_path(include_domain: true),
+      variant.name,
       variant.variant_aliases.map(&:name).join(','),
       variant.flagged,
-      variant.single_variant_molecular_profile_id
+      variant.variant_groups.map(&:name).join(','),
+      variant.variant_types.map(&:name).join(','),
+      variant.single_variant_molecular_profile_id,
+      variant.updated_at,
     ]
+
+    variant_cols = case variant
+    when Variants::GeneVariant
+      create_gene_row(variant)
+    when Variants::FactorVariant
+      create_factor_row(variant)
+    when Variants::FusionVariant
+      create_fusion_row(variant)
+    else
+      raise StandardError.new("Unknown variant type for TSV export: #{variant.class}")
+    end
+
+    shared_cols + variant_cols
   end
 
   def self.file_name