quorum 0.5.2 → 0.6.0

data/spec/dummy/quorum/lib/search_tools/blast.rb

@@ -1,452 +0,0 @@
-$LOAD_PATH.unshift(File.expand_path("../../", __FILE__))
-
-require 'bio-blastxmlparser'
-require 'logger'
-
-module Quorum
-  module SearchTools
-    #
-    # Blast Search Tool
-    #
-    class Blast
-
-      class QuorumJob < ActiveRecord::Base
-        self.table_name = "quorum_jobs"
-
-        has_one :quorum_blastn_job,
-          :foreign_key => "job_id"
-        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,
-          :foreign_key => "blastx_job_id"
-
-        has_one :quorum_tblastn_job,
-          :foreign_key => "job_id"
-        has_many :quorum_tblastn_job_reports,
-          :foreign_key => "tblastn_job_id"
-
-        has_one :quorum_blastp_job,
-          :foreign_key => "job_id"
-        has_many :quorum_blastp_job_reports,
-          :foreign_key => "blastp_job_id"
-      end
-
-      class QuorumBlastnJob < ActiveRecord::Base
-        self.table_name = "quorum_blastn_jobs"
-        belongs_to :quorum_job
-        has_many :quorum_blastn_job_reports
-      end
-
-      class QuorumBlastnJobReport < ActiveRecord::Base
-        self.table_name = "quorum_blastn_job_reports"
-        belongs_to :quorum_blastn_job
-      end
-
-      class QuorumBlastxJob < ActiveRecord::Base
-        self.table_name = "quorum_blastx_jobs"
-        belongs_to :quorum_job
-        has_many :quorum_blastx_job_reports
-      end
-
-      class QuorumBlastxJobReport < ActiveRecord::Base
-        self.table_name = "quorum_blastx_job_reports"
-        belongs_to :quorum_blastx_job
-      end
-
-      class QuorumTblastnJob < ActiveRecord::Base
-        self.table_name = "quorum_tblastn_jobs"
-        belongs_to :quorum_job
-        has_many :quorum_tblastn_job_reports
-      end
-
-      class QuorumTblastnJobReport < ActiveRecord::Base
-        self.table_name = "quorum_tblastn_job_reports"
-        belongs_to :quorum_tblastn_job
-      end
-
-      class QuorumBlastpJob < ActiveRecord::Base
-        self.table_name = "quorum_blastp_jobs"
-        belongs_to :quorum_job
-        has_many :quorum_blastp_job_reports
-      end
-
-      class QuorumBlastpJobReport < ActiveRecord::Base
-        self.table_name = "quorum_blastp_job_reports"
-        belongs_to :quorum_blastp_job
-      end
-
-      private
-
-      def initialize(args)
-        @algorithm       = args[:search_tool]
-        @id              = args[:id]
-        @log_directory   = args[:log_directory]
-        @tmp             = args[:tmp_directory]
-        @search_database = args[:search_database]
-        @threads         = args[:threads]
-
-        @logger = Quorum::Logger.new(@log_directory)
-
-        begin
-          @job = QuorumJob.find(@id)
-        rescue Exception => e
-          @logger.log("ActiveRecord", e.message, 1)
-        end
-
-        @na_sequence = @job.na_sequence
-        @aa_sequence = @job.aa_sequence
-
-        ## Create for method invocation ##
-        @job_association        = "quorum_#{@algorithm}_job".to_sym
-        @job_report_association = "quorum_#{@algorithm}_job_reports".to_sym
-
-        @filter                = @job.method(@job_association).call.filter
-        @expectation           = @job.method(@job_association).call.expectation
-        @max_score             = @job.method(@job_association).call.max_score
-        @min_score             = @job.method(@job_association).call.min_bit_score
-        @gapped_alignments     = @job.method(@job_association).call.gapped_alignments
-        @gap_opening_penalty   = @job.method(@job_association).call.gap_opening_penalty
-        @gap_extension_penalty = @job.method(@job_association).call.gap_extension_penalty
-
-        @db = @job.method(@job_association).call.blast_dbs.split(';')
-        @db.map! { |d| File.join(@search_database, d) }
-        @db = @db.join(' ')
-
-        @hash      = create_hash(@job.sequence)
-        @tmp_files = File.join(@tmp, @hash) << "*"
-      end
-
-      #
-      # Create a unique hash plus timestamp.
-      #
-      def create_hash(sequence)
-        Digest::MD5.hexdigest(sequence).to_s + "-" + Time.now.to_f.to_s
-      end
-
-      #
-      # Blastn command
-      #
-      def generate_blastn_cmd
-        blastn = "blastn " <<
-        "-db \"#{@db}\" " <<
-        "-query #{@na_fasta} " <<
-        "-outfmt 5 " <<
-        "-num_threads #{@threads} " <<
-        "-evalue #{@expectation} " <<
-        "-max_target_seqs #{@max_score} " <<
-        "-out #{@out} "
-        if @gapped_alignments
-          blastn << "-gapopen #{@gap_opening_penalty} "
-          blastn << "-gapextend #{@gap_extension_penalty} "
-        else
-          blastn << "-ungapped "
-        end
-        blastn << "-dust yes " if @filter
-        blastn
-      end
-
-      #
-      # Blastx command
-      #
-      def generate_blastx_cmd
-        blastx = "blastx " <<
-        "-db \"#{@db}\" " <<
-        "-query #{@na_fasta} " <<
-        "-outfmt 5 " <<
-        "-num_threads #{@threads} " <<
-        "-evalue #{@expectation} " <<
-        "-max_target_seqs #{@max_score} " <<
-        "-out #{@out} "
-        if @gapped_alignments
-          blastx << "-gapopen #{@gap_opening_penalty} "
-          blastx << "-gapextend #{@gap_extension_penalty} "
-        else
-          blastx << "-ungapped "
-        end
-        blastx << "-seg yes " if @filter
-        blastx
-      end
-
-      #
-      # Tblastn command
-      #
-      def generate_tblastn_cmd
-        tblastn = "tblastn " <<
-        "-db \"#{@db}\" " <<
-        "-query #{@aa_fasta} " <<
-        "-outfmt 5 " <<
-        "-num_threads #{@threads} " <<
-        "-evalue #{@expectation} " <<
-        "-max_target_seqs #{@max_score} " <<
-        "-out #{@out} "
-        if @gapped_alignments
-          tblastn << "-gapopen #{@gap_opening_penalty} "
-          tblastn << "-gapextend #{@gap_extension_penalty} "
-          tblastn << "-comp_based_stats D "
-        else
-          tblastn << "-ungapped "
-          tblastn << "-comp_based_stats F "
-        end
-        tblastn << "-seg yes " if @filter
-        tblastn
-      end
-
-      #
-      # Blastp command
-      #
-      def generate_blastp_cmd
-        blastp = "blastp " <<
-        "-db \"#{@db}\" " <<
-        "-query #{@aa_fasta} " <<
-        "-outfmt 5 " <<
-        "-num_threads #{@threads} " <<
-        "-evalue #{@expectation} " <<
-        "-max_target_seqs #{@max_score} " <<
-        "-out #{@out} "
-        if @gapped_alignments
-          blastp << "-gapopen #{@gap_opening_penalty} "
-          blastp << "-gapextend #{@gap_extension_penalty} "
-          blastp << "-comp_based_stats D "
-        else
-          blastp << "-ungapped "
-          blastp << "-comp_based_stats F "
-        end
-        blastp << "-seg yes " if @filter
-        blastp
-      end
-
-      #
-      # Generate Blast Command
-      #
-      def generate_blast_cmd
-        @cmd = ""
-
-        @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")
-        File.new(@out, "w")
-
-        case @algorithm
-        when "blastn"
-          @cmd << generate_blastn_cmd
-        when "blastx"
-          @cmd << generate_blastx_cmd
-        when "tblastn"
-          @cmd << generate_tblastn_cmd
-        when "blastp"
-          @cmd << generate_blastp_cmd
-        end
-      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.
-      #
-      def format_hit(str)
-        hit_display_id  = ""
-        hit_def = ""
-
-        hit = str.split(" ", 2)
-        if hit.length < 2
-          hit_display_id  = hit.first
-          hit_def = "None"
-        else
-          hit_display_id  = hit.first
-          hit_def = hit.last
-        end
-
-        return hit_display_id, hit_def
-      end
-
-      #
-      # Save Blast Job Report
-      #
-      # Hsps are only reported if a query hit against the Blast db.
-      # Only save the @data if bit_score exists and it's > the user
-      # defined minimum score.
-      #
-      # Set the attribute results to true for downstream processes.
-      #
-      def save_hsp_results
-        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
-
-          job_report = @job.method(@job_report_association).call.build(@data)
-
-          unless job_report.save!
-            @logger.log(
-              "ActiveRecord",
-              "Unable to save #{@algorithm} results to database.",
-              1,
-              @tmp_files
-            )
-          end
-        end
-      end
-
-      #
-      # Save empty Blast Job Report
-      #
-      # Set the attribute results to false for downstream processes.
-      #
-      def save_empty_results
-        job_report = @job.method(@job_report_association).call.build(
-          "#{@algorithm}_job_id" => @job.method(@job_association).call.job_id,
-          "results"              => false
-        )
-        unless job_report.save!
-          @logger.log(
-            "ActiveRecord",
-            "Unable to save #{@algorithm} results to database.",
-            1,
-            @tmp_files
-          )
-        end
-        @logger.log(
-          "NCBI Blast",
-          "#{@algorithm} report empty.",
-          0,
-          @tmp_files
-        )
-      end
-
-      #
-      # Parse and save Blast results.
-      #
-      # Parse the Blast XML output and save results.
-      #
-      def parse_and_save_results
-        @results = false # Did the xml contain results?
-
-        if File.size(@out) > 0
-          report = Bio::Blast::XmlIterator.new(@out)
-          report.to_enum.each do |iteration|
-
-            @data = {}
-
-            @data[:query]     = iteration.query_def.split(" ").first
-            @data[:query_len] = iteration.query_len
-
-            iteration.each do |hit|
-              @data[:hit_display_id], @data[:hit_def] = format_hit(hit.hit_def)
-
-              @data[:hit_id]        = hit.hit_id
-              @data[:hit_accession] = hit.accession
-              @data[:hit_len]       = hit.len
-
-              hit.each do |hsp|
-                @data[:hsp_num]     = hsp.hsp_num
-                @data[:bit_score]   = hsp.bit_score
-                @data[:score]       = hsp.score
-                @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
-                @data[:hit_frame]   = hsp.hit_frame
-                @data[:identity]    = hsp.identity
-                @data[:positive]    = hsp.positive
-                @data[:gaps]        = hsp.gaps
-                @data[:align_len]   = hsp.align_len
-                @data[:qseq]        = hsp.qseq
-                @data[:hseq]        = hsp.hseq
-                @data[:midline]     = hsp.midline
-
-                if @data[:bit_score] &&
-                  (@data[:bit_score].to_i > @min_score.to_i)
-                  @results = true
-                  save_hsp_results
-                end
-
-              end
-            end
-          end
-        end
-
-        save_empty_results unless @results
-      end
-
-      #
-      # Group record ids of hsps belonging to the same query and hit_accession.
-      #
-      def add_hps_groups_to_reports
-        groups = {}
-
-        query_hit_acc = @job.method(
-          @job_report_association
-        ).call.select("DISTINCT query, hit_accession")
-
-        # Populate the hash of hashes with correct query and hit_accession.
-        query_hit_acc.each do |q|
-          groups[q.query] = {}
-        end
-        query_hit_acc.each do |q|
-          groups[q.query][q.hit_accession] = []
-        end
-
-        # Group record ids.
-        reports = @job.method(@job_report_association).call.order("id ASC")
-        reports.each do |r|
-          if groups[r.query][r.hit_accession]
-            groups[r.query][r.hit_accession] << r.id
-          end
-        end
-
-        # Save hsp_group as a comma delimited string.
-        reports.each do |r|
-          if groups[r.query][r.hit_accession]
-            if groups[r.query][r.hit_accession].length > 1
-              r.hsp_group = groups[r.query][r.hit_accession].join(",")
-              unless r.save!
-                @logger.log(
-                  "ActiveRecord",
-                  "Unable to save #{@algorithm} results to database.",
-                  1,
-                  @tmp_files
-                )
-              end
-            end
-          end
-        end
-      end
-
-      #
-      # Remove tmp files.
-      #
-      def remove_tmp_files
-        `rm #{@tmp_files}` if @tmp_files
-      end
-
-      public
-
-      #
-      # Execute Blast on a given dataset.
-      #
-      def execute_blast
-        generate_blast_cmd
-        @logger.log("NCBI Blast", @cmd)
-        system(@cmd)
-
-        # Wrap these methods in a transaction to prevent premature return.
-        @job.method(@job_report_association).call.transaction do
-          parse_and_save_results
-          add_hps_groups_to_reports
-        end
-
-        remove_tmp_files
-      end
-
-    end
-  end
-end