Merge pull request #679 from Lazy-poet/issue/669

add method for computing number of sequences in a query

lib/sequenceserver/blast/job.rb

@@ -21,23 +21,32 @@ def initialize(params)
         else
           validate params
           super do
-            @method    = params[:method]
+            @method = params[:method]
+            @query = params[:sequence]
             @qfile     = store('query.fa', params[:sequence])
             @databases = Database[params[:databases]]
             @advanced  = params[:advanced].to_s.strip
             @options   = @advanced + defaults
             # The following params are for analytics only
             @num_threads = config[:num_threads]
             @query_length = calculate_query_size
+            @number_of_sequences = calculate_number_of_sequences
             @databases_ncharacters_total = calculate_databases_ncharacters_total
           end
         end
       end
 
       # :nodoc:
       # Attributes used by us - should be considered private.
-      attr_reader :advanced
-      attr_reader :databases, :databases_ncharacters_total, :method, :num_threads, :options, :qfile, :query_length
+      attr_reader :advanced,
+                  :databases,
+                  :databases_ncharacters_total,
+                  :method,
+                  :num_threads,
+                  :options,
+                  :qfile,
+                  :query_length,
+                  :number_of_sequences
 
       # :nodoc:
       # Deprecated; see Report#extract_params
@@ -92,6 +101,14 @@ def calculate_query_size
         size
       end
 
+      def calculate_number_of_sequences
+        # splitting the query by ">" starting a new line lets us determine number of sequences
+        sequences = @query.split(/\n\s*>\s*+/)
+        # Remove any empty strings from the split result
+        sequences.reject!(&:empty?)
+        sequences.length
+      end
+
       def validate(params)
         validate_method params[:method]
         validate_sequences params[:sequence]

spec/job_spec.rb

@@ -51,6 +51,34 @@ module SequenceServer
       "corrected\n YUOP POKJ M NAHAA JJHFGF YERTQ                        "
     end
 
+    let(:query_without_symbol) do
+    "MNTLWLSLWDYPGKLPLNFMVFDTKDDLQAAYWRDPYSIPLAVIFEDPQPISQRLIYEIR
+    TNPSYTLPPPPTKLYSAPISCRKNKTGHWMDDILSIKTGESCPVNNYLHSGFLALQMITD
+    ITKIKLENSDVTIPDIKLIMFPKEPYTADWMLAFRVVIPLYMVLALSQFITYLLILIVGE
+    KENKIKEGMKMMGLNDSVF"
+    end
+
+    let(:query_with_symbol) do
+    '>SI2.2.0_13722 locus=Si_gnF.scaffold06207[1925625..1928536].pep_1 quality=100.00
+    MSANRLNVLVTLMLAVALLVTESGNAQVDGYLQFNPKRSAVSSPQKYCGKKLSNALQIIC
+    DGVYNSMFKKSGQDFPPQNKRHIAHRINGNEEESFTTLKSNFLNWCVEVYHRHYRFVFVS
+    EMEMADYPLAYDISPYLPPFLSRARARGMLDGRFAGRRYRRESRGIHEECCINGCTINEL
+    TSYCGP'
+    end
+
+    let(:query_with_and_without_symbol) do
+    "MNTLWLSLWDYPGKLPLNFMVFDTKDDLQAAYWRDPYSIPLAVIFEDPQPISQRLIYEIR
+    TNPSYTLPPPPTKLYSAPISCRKNKTGHWMDDILSIKTGESCPVNNYLHSGFLALQMITD
+    ITKIKLENSDVTIPDIKLIMFPKEPYTADWMLAFRVVIPLYMVLALSQFITYLLILIVGE
+    KENKIKEGMKMMGLNDSVF
+    >SI2.2.0_13722 locus=Si_gnF.scaffold06207[1925625..1928536].pep_1 quality=100.00
+    MSANRLNVLVTLMLAVALLVTESGNAQVDGYLQFNPKRSAVSSPQKYCGKKLSNALQIIC
+    DGVYNSMFKKSGQDFPPQNKRHIAHRINGNEEESFTTLKSNFLNWCVEVYHRHYRFVFVS
+    EMEMADYPLAYDISPYLPPFLSRARARGMLDGRFAGRRYRRESRGIHEECCINGCTINEL
+    TSYCGP
+    "
+    end
+
     # all databases used here are v5 databases included in
     # SequenceServer.init(database_dir: "#{__dir__}/database")
     # [15] = funky ids (nucleotide)
@@ -85,8 +113,43 @@ module SequenceServer
         databases: [Database.ids[15], Database.ids[16], Database.ids[19]],
         method: 'blastn'
       }
-    end
 
+      @params_query_without_symbol ={
+        sequence: query_without_symbol,
+        databases: [Database.ids[17]],
+        method: 'blastp'
+      }
+
+      @params_query_with_symbol ={
+        sequence: query_with_symbol,
+        databases: [Database.ids[17]],
+        method: 'blastp'
+      }
+      @params_query_with_and_without_symbol ={
+        sequence: query_with_and_without_symbol,
+        databases: [Database.ids[17]],
+        method: 'blastp'
+      }
+    end
+    context 'queries not containing a >' do
+        let(:job) {Job.create(@params_query_without_symbol)}
+      it 'should accurately compute number of sequences' do
+        expect(job.number_of_sequences).to eq(1)
+      end 
+    end
+    context 'queries containing a > at the start' do
+        let(:job) {Job.create(@params_query_with_symbol)}
+      it 'should accurately compute number of sequences' do
+        expect(job.number_of_sequences).to eq(1)
+      end 
+    end
+    context 'queries containing a > but not at the start' do
+        let(:job) {Job.create(@params_query_with_and_without_symbol)}
+      it 'should accurately compute number of sequences' do
+        expect(job.number_of_sequences).to eq(2)
+      end 
+    end
+
     context 'with one protein database' do
       let(:test_job1) { Job.create(@params_prot_1db) }
 
@@ -105,7 +168,7 @@ module SequenceServer
       it 'should accurately compute total characters of databases used' do
         expect(test_job2.databases_ncharacters_total).to eql(280_685)
       end
-
+      
       it 'should accurately compute query length' do
         expect(test_job2.query_length).to eq(64)
       end