Add ftdna 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}", rows)
+    csv = send(:"parse_#{genotype.filetype.sub('-', '_')}", rows)
     known_chromosomes = ['MT', 'X', 'Y', (1..22).map(&:to_s)].flatten
     csv.select! do |row|
       # snp name
@@ -166,6 +166,20 @@ class Parsing
     end
   end
 
+  def parse_ftdna_illumina(rows)
+    rows.shift if rows.first.start_with?('RSID')
+    rows.map do |row|
+      fields = row.strip.split(',')
+      [
+        genotype.id,
+        fields[0].gsub('"', ''),
+        fields[1].gsub('"', ''),
+        fields[2].gsub('"', ''),
+        fields[3].gsub('"', '')
+      ]
+    end
+  end
+
   def execute(sql)
     Genotype.connection.execute(sql)
   end

spec/integration/genotype_parsing_and_deleting_spec.rb

@@ -123,4 +123,39 @@ describe 'genotype parsing', sidekiq: :inline do
       end
     end
   end
+
+  context 'ftdna-illumina' do
+    let(:file) { File.open(Rails.root.join('test/data/ftdna-illumina_sample.csv')) }
+    let(:genotype) do
+      create(:genotype, genotype: file, filetype: 'ftdna-illumina')
+    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 = [
+        ['rs3094315', '752566', '1', {}, { 'A' => 0, 'T' => 0, 'G' => 0, 'C' => 0 }, 0, 1],
+        ['rs3131972',  '752721', '1', {}, { 'A' => 0, 'T' => 0, 'G' => 0, 'C' => 0 }, 0, 1],
+        ['rs12562034',  '768448', '1', {}, { 'A' => 0, 'T' => 0, 'G' => 0, 'C' => 0 }, 0, 1],
+        ['rs12124819',  '776546',  '1', {}, { 'A' => 0, 'T' => 0, 'G' => 0, 'C' => 0 }, 0, 1],
+        ['rs11240777',  '798959', '1', {}, { '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(AA GG GG AA AG)
+      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/ftdna-illumina_sample.csv

@@ -0,0 +1,6 @@
+RSID,CHROMOSOME,POSITION,RESULT
+"rs3094315","1","752566","AA"
+"rs3131972","1","752721","GG"
+"rs12562034","1","768448","GG"
+"rs12124819","1","776546","AA"
+"rs11240777","1","798959","AG"