Add IYG parsing

app/workers/parsing.rb

@@ -55,7 +55,7 @@ class Parsing
     rows = File.readlines(genotype.genotype.path)
       .reject { |line| line.start_with?('#') } # Skip comments
     stats[:rows_without_comments] = rows.length
-    csv = send(:"parse_#{genotype.filetype.sub('-', '_')}", rows)
+    csv = send(:"parse_#{genotype.filetype.sub('-', '_').downcase}", rows)
     known_chromosomes = ['MT', 'X', 'Y', (1..22).map(&:to_s)].flatten
     csv.select! do |row|
       # snp name
@@ -180,6 +180,37 @@ class Parsing
     end
   end
 
+  def parse_iyg(rows)
+    db_snp_names = {
+      "MT-T3027C" => "rs199838004", "MT-T4336C" => "rs41456348",
+      "MT-G4580A" => "rs28357975", "MT-T5004C" => "rs41419549",
+      "MT-C5178a" => "rs28357984", "MT-A5390G" => "rs41333444",
+      "MT-C6371T" => "rs41366755", "MT-G8697A" => "rs28358886",
+      "MT-G9477A" => "rs2853825", "MT-G10310A" => "rs41467651",
+      "MT-A10550G" => "rs28358280", "MT-C10873T" => "rs2857284",
+      "MT-C11332T" => "rs55714831", "MT-A11947G" => "rs28359168",
+      "MT-A12308G" => "rs2853498", "MT-A12612G" => "rs28359172",
+      "MT-T14318C" => "rs28357675", "MT-T14766C" => "rs3135031",
+      "MT-T14783C" => "rs28357680"
+    }
+    rows.map do |row|
+      snp_name, local_genotype = row.split("\t")
+      if snp_name.start_with?('MT')
+        position = snp_name[/[0-9]+/]
+        chromosome = 'MT'
+      else
+        position = chromosome = '1'
+      end
+      [
+        genotype.id,
+        db_snp_names.fetch(snp_name, snp_name),
+        chromosome,
+        position,
+        local_genotype.strip
+      ]
+    end
+  end
+
   def execute(sql)
     Genotype.connection.execute(sql)
   end

spec/integration/genotype_parsing_and_deleting_spec.rb

@@ -158,4 +158,40 @@ describe 'genotype parsing', sidekiq: :inline do
       end
     end
   end
+
+  context 'IYG' do
+    let(:file) { File.open(Rails.root.join('test/data/iyg_sample.csv')) }
+    let(:genotype) do
+      create(:genotype, genotype: file, filetype: 'IYG')
+    end
+
+    it 'parse ancestry data', truncate: true do
+      # Snp
+      snp_data = Snp.all.map do |s|
+        [s.name, s.position, s.chromosome, s.genotype_frequency,
+         s.allele_frequency, s.ranking, s.user_snps_count]
+      end.sort_by { |s| s[0] }
+
+      expected = [
+        ['rs2131925', '1', '1', {}, { 'A' => 0, 'T' => 0, 'G' => 0, 'C' => 0 }, 0, 1],
+        ['rs2815752', '1', '1', {}, { 'A' => 0, 'T' => 0, 'G' => 0, 'C' => 0 }, 0, 1],
+        ['rs10924081', '1', '1', {}, { 'A' => 0, 'T' => 0, 'G' => 0, 'C' => 0 }, 0, 1],
+        ['rs199838004', '3027',  'MT', {}, { 'A' => 0, 'T' => 0, 'G' => 0, 'C' => 0 }, 0, 1],
+        ['rs41456348', '4336', 'MT', {}, { 'A' => 0, 'T' => 0, 'G' => 0, 'C' => 0 }, 0, 1]
+      ]
+
+      expect(snp_data).to match_array(expected)
+
+      # UserSnp
+      user_snps = UserSnp.all
+      user_snp_genotypes = user_snps.map(&:local_genotype)
+      expected_genotypes = %w(GT AA AA T T)
+      expect(user_snp_genotypes).to eq(expected_genotypes)
+      user_snps.each do |s|
+        expect(s.genotype_id).to eq(genotype.id)
+        expect(Snp.pluck(:name)).to include(s.snp_name)
+      end
+    end
+  end
+
 end

test/data/iyg_sample.csv

@@ -0,0 +1,5 @@
+rs2131925	GT
+rs2815752	AA
+rs10924081	AA
+MT-T3027C	T
+MT-T4336C	T