blast.rb in quorum-0.3.2

- old
+ new

@@ -11,13 +11,13 @@
     class Blast
 
       class QuorumJob < ActiveRecord::Base
         self.table_name = "quorum_jobs"
 
-        has_one :quorum_blastn_job, 
+        has_one :quorum_blastn_job,
           :foreign_key => "job_id"
-        has_many :quorum_blastn_job_reports, 
+        has_many :quorum_blastn_job_reports,
           :foreign_key => "blastn_job_id"
 
         has_one :quorum_blastx_job,
           :foreign_key => "job_id"
         has_many :quorum_blastx_job_reports,
@@ -215,11 +215,11 @@
         @na_fasta = File.join(@tmp, @hash + ".na.fa")
         @aa_fasta = File.join(@tmp, @hash + ".aa.fa")
         File.open(@na_fasta, "w") { |f| f << @na_sequence }
         File.open(@aa_fasta, "w") { |f| f << @aa_sequence }
 
-        @out = File.join(@tmp, @hash + ".out.xml") 
+        @out = File.join(@tmp, @hash + ".out.xml")
         File.new(@out, "w")
 
         case @algorithm
         when "blastn"
           @cmd << generate_blastn_cmd
@@ -231,22 +231,10 @@
           @cmd << generate_blastp_cmd
         end
       end
 
       #
-      # Make the E-value look pretty.
-      #
-      def format_evalue(evalue)
-        evalue = evalue.to_s
-        e      = evalue.slice!(/e.*/)
-        unless e.nil?
-          e = " x 10<sup>" << e.sub(/e/, '') << "</sup>"
-        end
-        evalue.to_f.round(1).to_s << e.to_s 
-      end
-
-      #
       # Format Blast report hit_display_id and hit_def.
       #
       # For added flexibility, Quorum doesn't parse seqids or deflines.
       # Instead, format_hit splits the hit_def on whitespace and
       # reports hit_display_id as the first element and hit_def as the second.
@@ -267,11 +255,11 @@
         return hit_display_id, hit_def
       end
 
       #
       # Parse and save Blast results using bio-blastxmlparser.
-      # Only save Blast results if results.bit_score > @min_score. 
+      # Only save Blast results if results.bit_score > @min_score.
       #
       def parse_and_save_results
         # Helper to avoid having to perform a query.
         saved = false
 
@@ -293,11 +281,11 @@
 
               hit.each do |hsp|
                 @data[:hsp_num]     = hsp.hsp_num
                 @data[:bit_score]   = hsp.bit_score
                 @data[:score]       = hsp.score
-                @data[:evalue]      = format_evalue(hsp.evalue)
+                @data[:evalue]      = hsp.evalue
                 @data[:query_from]  = hsp.query_from
                 @data[:query_to]    = hsp.query_to
                 @data[:hit_from]    = hsp.hit_from
                 @data[:hit_to]      = hsp.hit_to
                 @data[:query_frame] = hsp.query_frame
@@ -309,11 +297,11 @@
                 @data[:hseq]        = hsp.hseq
                 @data[:midline]     = hsp.midline
 
                 # Hsps are only reported if a query hit against the Blast db.
                 # Only save the @data if bit_score exists.
-                if @data[:bit_score] && 
+                if @data[:bit_score] &&
                   (@data[:bit_score].to_i > @min_score.to_i)
                   @data[:results] = true
                   @data["#{@algorithm}_job_id".to_sym] = @job.method(@job_association).call.job_id
                   saved = true
                   # Build a new report for each Hsp.
@@ -408,10 +396,10 @@
 
       #
       # Execute Blast on a given dataset.
       #
       def execute_blast
-        generate_blast_cmd 
+        generate_blast_cmd
         @logger.log("NCBI Blast", @cmd)
         system(@cmd)
         parse_and_save_results
         add_hps_groups_to_reports
         remove_tmp_files