bio-rocker 0.1.0

checksums.yaml

@@ -0,0 +1,7 @@
+---
+SHA1:
+  metadata.gz: 51e493216ea815f9919322e9b1319f9914d824c7
+  data.tar.gz: 8c7bf556507ef0b11c5f2477fad589a62c016f11
+SHA512:
+  metadata.gz: b57faf770219b8ab364b25f59696852f219a204f22b12be5fb89d7932e0cb10429316e0b7645bf7e7a18c56590a669f605f444e667cb4a9467626db100df0b34
+  data.tar.gz: 47223060bd29a689406067e9bff41352ffa841c8475a25943e83dc6cfc2901ae7ad8f3b8eea1a44c5cfbe0b6fccac45dd1cf493eb0000ed19877f451bf0463e8

data/bin/ROCker

@@ -0,0 +1,180 @@
+#!/usr/bin/env ruby
+#
+# @author Luis M. Rodriguez-R <lmrodriguezr at gmail dot com>
+# @author Luis (Coto) Orellana
+# @license artistic license 2.0
+# @update Jan-22-2015
+#
+
+require 'rocker'
+require 'optparse'
+
+
+#================================[ Options parsing ]
+$t = {
+   'build'   => 'Creates in silico metagenomes and training sets from reference genomes.',
+   'compile' => 'Identifies the most discriminant bit-score per alignment position in a set of sequence.',
+   'filter'  => 'Uses a pre-compiled set of bit-score thresholds to filter a search result.',
+   'search'  => 'Uses a ROCker compilation to identify reads putatively derived from a set of sequences.',
+   'plot'    => 'Generates a graphical representation of the alignment, the thresholds, and the hits.',
+}
+task = (ARGV.size > 0 ? ARGV.shift : '').downcase
+ARGV << '-h' if ARGV.size==0
+
+o = {}
+opts = OptionParser.new do |opt|
+   if $t.keys.include? task
+      opt.banner = "Usage: ROCker.rb #{task} [options]"
+      opt.separator ""
+      opt.separator $t[task]
+      opt.separator ""
+   end
+   case task
+   when 'build'
+      unless ROCker.has_build_gems?
+	 opt.separator "+ UNSATISFIED REQUIREMENTS"
+	 opt.separator "    The building task requires uninstalled gems, please install them executing:"
+	 opt.separator "       gem install rest_client"
+	 opt.separator "       gem install nokogiri"
+	 opt.separator ""
+      end
+      opt.separator "+ BUILDING ARGUMENTS"
+      opt.on("-p", "--positive GI1,GI2,GI3", Array, "Comma-separated list of NCBI GIs corresponding to the 'positive' training set. Required unless -P or -a are used."){ |v| o[:posori]=v }
+      opt.on("-n", "--negative GI1,GI2,GI3", Array, "Comma-separated list of NCBI GIs corresponding to the 'negative' training set. See also -N."){ |v| o[:negative]=v }
+      opt.on("-o", "--baseout PATH", "Prefix for the output files to be generated. Required."){ |v| o[:baseout]=v }
+      opt.on(      "--nucleotides", "If set, it assumes that the input sequences are in nucleotides. By default, proteins are assumed."){ o[:nucl]=true }
+      opt.on("-t", "--threads INT", "Number of threads to use. By default: #{ROCker.default :thr}."){ |v| o[:thr]=v.to_i }
+      opt.separator ""
+      opt.separator "+ ADVANCED BUILDING ARGUMENTS"
+      opt.on("-P", "--positive-file PATH", "File containing the positive set (see -p), one GI per line. If used, -p is not required."){ |v| o[:posfile]=v }
+      opt.on("-N", "--negative-file PATH", "File containing the negative set (see -n), one GI per line."){ |v| o[:negfile]=v }
+      opt.on("-a", "--alignment PATH", "Protein alignment of the reference sequences. The defline must contain GI numbers. If used, -p is not required."){ |v| o[:aln]=v }
+      opt.on("-s", "--seqdepth NUMBER", "Sequencing depth to be used in building the in silico metagenome. By default: '#{ROCker.default :seqdepth}'."){ |v| o[:seqdepth]=v.to_f }
+      opt.on("-v", "--overlap NUMBER", "Minimum overlap with reference gene to tag a read as positive. By default: '#{ROCker.default :minovl}'."){ |v| o[:minovl]=v.to_f }
+      opt.on(      "--genome-frx NUMBER", "Fraction to subsample the positive set genomes to generate the metagenome. By default: #{ROCker.default :genomefrx}"){ |v| o[:genomefrx]=v.to_f }
+      opt.on(      "--per-genus", "If selected, only one genome per genus is used to build the metagenome."){ o[:pergenus]=true }
+      opt.on(      "--per-species", "If selected, only one genome per species is used to build the metagenome."){ o[:perspecies]=true }
+      opt.on(      "--nometagenome", "Do not create metagenome. Implies --noblast. By default, metagenome is created."){ |v| o[:nomg]=v }
+      opt.on(      "--noblast", "Do not execute BLAST. By default, BLAST is executed."){ |v| o[:noblast]=v }
+      opt.on(      "--noalignment", "Do not align reference set. By default, references are aligned."){ |v| o[:noaln]=v }
+      opt.on(      "--nocleanup", "Keep all intermediate files. By default, intermediate files are removed."){ |v| o[:noclean]=v }
+      opt.on(      "--reuse-files", "Re-use existing result files. By default, existing files are ignored."){ |v| o[:reuse]=true }
+      opt.separator ""
+      opt.separator "+ EXTERNAL SOFTWARE OPTIONS"
+      opt.on("-G", "--grinder PATH", "Path to the grinder executable. By default: '#{ROCker.default :grinder}' (in the $PATH)."){ |v| o[:grinder]=v }
+      opt.on("-M", "--muscle PATH", "Path to the muscle executable. By default: '#{ROCker.default :muscle}' (in the $PATH)."){ |v| o[:muscle]=v }
+      opt.on("-B", "--blastbins PATH", "Path to the Blast+ executables. By default: '#{ROCker.default :blastbins}' (in the $PATH)."){ |v| o[:blastbins]=v }
+      opt.on(      "--grinder-cmd STR", "Command calling grinder, where %1$s: grinder bin, %2$s: input, %3$s: seq. depth, %4$s: output.",
+	 "By default: '#{ROCker.default :grindercmd}'."){ |v| o[:grindercmd]=v }
+      opt.on("--muscle-cmd STR", "Command calling muscle, where %1$s: muscle bin, %2$s: input, %3$s: output.",
+	 "By default: '#{ROCker.default :musclecmd}'."){ |v| o[:musclecmd]=v }
+      opt.on("--blast-cmd STR", "Command calling BLAST search, where %1$s: blast bins, %2$s: program, %3$s: input, %4$s: database, %5$s: output, %6$d: threads.",
+	 "By default: '#{ROCker.default :blastcmd}'."){ |v| o[:blastcmd]=v }
+      opt.on("--makedb-cmd STR", "Command calling BLAST format, where %1$s: blast bins, %2$s: dbtype, %3$s: input, %4$s: database.",
+	 "By default: '#{ROCker.default :makedbcmd}'."){ |v| o[:makedbcmd]=v }
+   when 'compile'
+      opt.separator "+ COMPILATION ARGUMENTS"
+      opt.on("-a", "--alignment PATH", "Protein alignment of the reference sequences. Required."){ |v| o[:aln]=v }
+      opt.on("-b", "--ref-blast PATH",
+      		"Tabular BLAST (blastx) of the test reads vs. the reference dataset. Required unless -t exists."){ |v| o[:blast]=v }
+      opt.on("-k", "--rocker PATH", "ROCker file to be created. Required."){ |v| o[:rocker]=v }
+      opt.on(      "--nucleotides", "If set, it assumes that the input sequences are in nucleotides. By default, proteins are assumed."){ o[:nucl]=true }
+      opt.separator ""
+      opt.separator "+ ADVANCED COMPILATION ARGUMENTS"
+      opt.on("-t", "--table PATH", "Formated tabular file to be created (or reused). Required unless -b is provided."){ |v| o[:table]=v }
+      opt.on(      "--min-score NUMBER", "Minimum Bit-Score to consider a hit. By default: #{ROCker.default :minscore}"){ |v| o[:minscore]=v.to_f }
+      opt.on(      "--norefine", "Do not refine windows."){ o[:refine]=false }
+      opt.on("-w", "--window INT", "Initial size of alignment windows (in number of AA columns). By default: #{ROCker.default :win}."){ |v| o[:win]=v.to_i }
+      opt.separator ""
+      opt.separator "+ INPUT/OUTPUT"
+      opt.separator "   o The input alignment (-a) MUST be in FastA format, and the IDs must"
+      opt.separator "     coincide with those from the BLAST (-b)."
+      opt.separator "   o The input BLAST (-b) MUST be in tabular format. True positives must"
+      opt.separator "     contain the string '@%' somewhere in the query ID."
+      opt.separator "   o The table file (-t) should be tab-delimited and contain six columns:"
+      opt.separator "      1. Subject ID."
+      opt.separator "      2. Start of alignment in subject (translated to alignment column)."
+      opt.separator "      3. End of alignment in subject (translated to alignment column)."
+      opt.separator "      4. Bit score."
+      opt.separator "      5. A number indicating if it was a true (1) or a false (0) positive."
+      opt.separator "      6. Mid-point of the alignment in the reference sequence."
+      opt.separator "   o The ROCker file (-k) is a tab-delimited file containing five columns:"
+      opt.separator "      1. First column of the window in the alignment."
+      opt.separator "      2. Last column of the window in the alignment."
+      opt.separator "      3. Number of positives in the window (hits)."
+      opt.separator "      4. Number of true positives in the window."
+      opt.separator "      5. Bit score threshold set for the window."
+      opt.separator "     The file also contains the alignment (commented with #:)."
+      opt.separator ""
+   when 'filter'
+      opt.separator "+ FILTERING ARGUMENTS"
+      opt.on("-k", "--rocker PATH", "ROCker file generated by the compile task (-k). Required."){ |v| o[:rocker]=v }
+      opt.on("-x", "--query-blast PATH", "Tabular BLAST (blastx) of the query reads vs. the reference dataset. Required."){ |v| o[:qblast]=v }
+      opt.on("-o", "--out-blast PATH", "Filtered tabular BLAST to be created. Required."){ |v| o[:oblast]=v }
+   when 'search'
+      opt.on("-k", "--rocker PATH", "ROCker file generated by the compile task (-k). Required."){ |v| o[:rocker]=v }
+      opt.on("-q", "--query PATH", "File containing the query sequences in FastA format. Required."){ |v| o[:query]=v }
+      opt.on("-o", "--out-blast PATH", "Filtered tabular BLAST to be created. Required."){ |v| o[:oblast]=v }
+   when 'plot'
+      opt.separator "+ PLOTTING ARGUMENTS"
+      opt.on("-k", "--rocker PATH", "ROCker file generated by the compile task (-k). Required."){ |v| o[:rocker]=v }
+      opt.on("-b", "--ref-blast PATH",
+      		"Tabular BLAST (blastx) of the test reads vs. the reference dataset. Required unless -t exists."){ |v| o[:blast]=v }
+      opt.on("-o", "--plot-file PATH", "File to be created with the plot. By default: value of -k + '.' + value of -f."){ |v| o[:gout]=v }
+      opt.separator ""
+      opt.separator "+ ADVANCED PLOTTING ARGUMENTS"
+      opt.on("-t", "--table PATH", "Formated tabular file to be created (or reused). Required unless -b is provided."){ |v| o[:table]=v }
+      opt.on(      "--color", "Color alignment by amino acid."){ o[:color]=true }
+      opt.on(      "--min-score NUMBER", "Minimum Bit-Score to consider a hit. By default: #{ROCker.default :minscore}"){ |v| o[:minscore]=v.to_f }
+      opt.on("-s", "--subject SBJ1,SBJ2,...", Array,
+      	"Plot only information regarding this(ese) subject(s). If multiple, separate by comma. By default, all hits are plotted."){ |v| o[:sbj]=v }
+      opt.on("-f", "--plot-format STRING",
+      	"Format of the plot file. Supported values: pdf (default), png, jpeg, and tiff."){ |v| o[:gformat]=v }
+      opt.on("-W", "--width NUMBER", "Width of the plot in inches. By default: #{ROCker.default :width}."){ |v| o[:width]=v.to_f }
+      opt.on("-H", "--height NUMBER", "Height of the plot in inches. By defaule: #{ROCker.default :height}."){ |v| o[:width]=v.to_f }
+   else
+      opt.banner = "Usage: ROCker.rb [task] [options]"
+      opt.separator ""
+      opt.separator "Please specify one of the following tasks:"
+      $t.keys.each{ |t| opt.separator "     #{t}:\t#{$t[t]}" }
+   end
+   opt.separator ""
+   opt.separator "+ GENERAL ARGUMENTS"
+   opt.on("-R", "--path-to-r PATH", "Path to the R executable to be used. By default: '#{ROCker.default :r}'."){ |v| o[:r]=v }
+   opt.on("-q", "--quiet", "Run quietly."){ |v| o[:q]=true }
+   opt.on("-d", "--debug", "Display debugging information."){ |v| o[:debug]=true }
+   opt.on("-h", "--help","Display this screen") do
+      puts opt
+      exit
+   end
+   opt.separator ""
+   unless $t.include? task
+      puts opt
+      exit
+   end
+end
+opts.parse!
+
+
+#================================[ Main ]
+rocker = ROCker.new(o)
+begin
+   case task
+   when 'build'
+      rocker.build!
+   when 'compile'
+      rocker.compile!
+   when 'filter'
+      rocker.filter!
+   when 'search'
+      rocker.search!
+   when 'plot'
+      rocker.plot!
+   end
+rescue => err
+   $stderr.puts "Exception: #{err}\n\n"
+   err.backtrace.each { |l| $stderr.puts l + "\n" }
+   err
+end
+
+

data/lib/rocker.rb

@@ -0,0 +1,503 @@
+#
+# @author Luis M. Rodriguez-R <lmrodriguezr at gmail dot com>
+# @author Luis (Coto) Orellana
+# @license artistic license 2.0
+# @update Jan-22-2015
+#
+
+require 'rocker/blasthit'
+require 'rocker/rocdata'
+
+class ROCker
+   #================================[ Class ]
+   @@EUTILS = 'http://eutils.ncbi.nlm.nih.gov/entrez/eutils'
+   @@DEFAULTS = {
+      # General
+      :q=>false, :r=>'R', :nucl=>false, :debug=>false,
+      # Build
+      :positive=>[], :negative=>[], :thr=>2,:genomefrx=>1.0, :pergenus=>false, :perspecies=>false,
+	 # ext. software
+	 :grinder=>'grinder', :muscle=>'muscle', :blastbins=>'', :seqdepth=>3, :minovl=>0.75,
+	 :grindercmd=>'%1$s -reference_file "%2$s" -cf "%3$f" -base_name "%4$s" -dc \'-~*Nn\' -md "poly4 3e-3 3.3e-8" -mr "95 5" -rd "100 uniform 5"',
+	 :musclecmd=>'%1$s -in "%2$s" -out "%3$s" -quiet',
+	 :blastcmd=>'%1$s%2$s -query "%3$s" -db "%4$s" -out "%5$s" -num_threads %6$d -outfmt 6 -max_target_seqs 1',
+	 :makedbcmd=>'%1$smakeblastdb -dbtype %2$s -in "%3$s" -out "%4$s"',
+      # Compile
+      :refine=>true, :win=>20, :minscore=>0,
+      # Filter
+      :sbj=>[],
+      # Plot
+      :color=>false, :gformat=>'pdf', :width=>9, :height=>9
+   }
+   @@HAS_BUILD_GEMS = nil
+   def self.eutils() @@EUTILS end
+   def self.defaults() @@DEFAULTS end
+   def self.default(k) @@DEFAULTS[k] end
+   def self.has_build_gems?
+      return @@HAS_BUILD_GEMS unless @@HAS_BUILD_GEMS.nil?
+      @@HAS_BUILD_GEMS = TRUE
+      begin
+	 require 'rubygems'
+	 require 'restclient'
+	 require 'nokogiri'
+      rescue LoadError
+	 @@HAS_BUILD_GEMS = FALSE
+      end
+      @@HAS_BUILD_GEMS
+   end
+
+   #================================[ Instance ]
+   attr_reader :o
+   def initialize(opts)
+      @o = ROCker.defaults
+      opts.each{ |k,v| @o[k] = v }
+      RInterface.R_BIN = opts[:r] unless opts[:r].nil?
+   end
+   
+   #================================[ Build ]
+   def build!
+      # Check requirements
+      puts "Testing environment." unless @o[:q]
+      @o[:noblast]=true if @o[:nomg]
+      raise "Unsatisfied requirements, please see the help message (-h)." unless ROCker.has_build_gems?
+      @o[:positive] += @o[:posori] unless @o[:posori].nil?
+      @o[:positive] += File.readlines(@o[:posfile]).map{ |l| l.chomp } unless @o[:posfile].nil?
+      @o[:negative] += File.readlines(@o[:negfile]).map{ |l| l.chomp } unless @o[:negfile].nil?
+      unless @o[:aln].nil?
+         aln = Alignment.new
+	 aln.read_fasta @o[:aln]
+	 @o[:positive] += aln.get_gis
+      end
+      raise "-p or -P are mandatory." if @o[:positive].size==0
+      raise "-o/--baseout is mandatory." if @o[:baseout].nil?
+      if @o[:positive].size == 1 and not @o[:noaln]
+	 warn "\nWARNING: Positive set contains only one sequence, turning off alignment.\n\n"
+	 @o[:noaln] = true
+      end
+      self.bash "#{@o[:grinder]} --version", "-G/--grinder must be executable. Is Grinder installed?" unless @o[:nomg]
+      self.bash "#{@o[:muscle]} -version", "-M/--muscle must be executable. Is Muscle installed?" unless @o[:noaln]
+      self.bash "#{@o[:blastbins]}makeblastdb -version", "-B/--blastbins must contain executables. Is BLAST+ installed?" unless @o[:noblast]
+      # Download genes
+      puts "Downloading gene data." unless @o[:q]
+      f = File.open(@o[:baseout] + '.ref.fasta', 'w')
+      if @o[:posori].nil? and @o[:posfile].nil? and not @o[:aln].nil?
+	 puts "  * re-using aligned sequences as positive set." unless @o[:q]
+	 f.print aln.to_seq_s
+	 @o[:noaln] = true
+      else
+	 puts "  * downloading #{@o[:positive].size} sequence(s) in positive set." unless @o[:q]
+	 $stderr.puts "   # #{@o[:positive]}" if @o[:debug]
+	 ids = Array.new(@o[:positive])
+	 while ids.size>0
+	    f.print efetch({:db=>(@o[:nucl] ? 'nuccore' : 'protein'), :id=>ids.shift(200).join(','), :rettype=>'fasta', :retmode=>'text'})
+	 end
+      end
+      f.close
+      genome_gis = {:positive=>[], :negative=>[]}
+      [:positive, :negative].each do |set|
+         unless @o[set].size==0
+	    puts "  * gathering genomes from #{@o[set].size} #{set.to_s} sequence(s)." unless @o[:q]
+	    $stderr.puts "   # #{@o[set]}" if @o[:debug]
+	    genome_gis[set] = genes2genomes(@o[set], @o[:nucl])
+	 end
+      end
+      raise "No genomes associated with the positive set." if genome_gis[:positive].size==0
+      genome_gis[:positive] = genome_gis[:positive].sample( (genome_gis[:positive].size*@o[:genomefrx]).round ) if @o[:genomefrx]
+      raise "No positive genomes selected for metagenome construction, is --genome-frx too small?" if genome_gis[:positive].empty?
+      all_gis = genome_gis.values.reduce(:+).uniq
+      
+      # Locate genes
+      puts "Analyzing genome data." unless @o[:q]
+      puts "  * downloading and parsing #{genome_gis[:positive].size} XML file(s)." unless @o[:q]
+      $stderr.puts "   # #{genome_gis[:positive]}" if @o[:debug]
+      positive_coords = {}
+      genome_org = {}
+      i = 0
+      genome_gis[:positive].each do |gi|
+	 print "  * scanning #{(i+=1).ordinalize} genome out of #{genome_gis[:positive].size}. \r" unless @o[:q]
+	 $stderr.puts "   # Looking for any of #{@o[:positive]}" if @o[:debug]
+	 genome_file = @o[:baseout] + '.src.' + i.to_s + '.xml'
+	 if @o[:reuse] and File.exist? genome_file
+	    puts "  * reusing existing file: #{genome_file}." unless @o[:q]
+	    ifh = File.open(genome_file, 'r')
+	    doc = Nokogiri::XML( ifh )
+	    ifh.close
+	 else
+	    genome_file=nil unless @o[:noclean]
+	    res = efetch({:db=>'nuccore', :id=>gi, :rettype=>'xml', :retmode=>'text'}, genome_file)
+	    doc = Nokogiri::XML( res )
+	 end
+	 incomplete = true
+	 doc.xpath('//Bioseq-set/Bioseq-set_seq-set/Seq-entry').each do |genome|
+	    genome_gi = genome.at_xpath('./Seq-entry_set/Bioseq-set/Bioseq-set_seq-set/Seq-entry/Seq-entry_seq/Bioseq/Bioseq_id/Seq-id/Seq-id_gi')
+	    if !genome_gi.nil? and gi==genome_gi.content
+	       incomplete = false
+	       positive_coords[gi] ||= []
+	       $stderr.puts "\n   # got #{gi}, scanning" if @o[:debug]
+	       if @o[:pergenus] or @o[:perspecies]
+		  name = genome.at_xpath('./Seq-entry_set/Bioseq-set/Bioseq-set_descr/Seq-descr/Seqdesc/Seqdesc_source/BioSource/BioSource_org/Org-ref/Org-ref_orgname/OrgName/OrgName_name/OrgName_name_binomial/BinomialOrgName')
+		  unless name.nil?
+		     name_g = name.at_xpath('./BinomialOrgName_genus')
+		     name_s = name.at_xpath('./BinomialOrgName_species')
+		     if name_g.nil? or (name_s.nil? and @o[:perspecies])
+		        name = nil
+		     else
+		        name = @o[:perspecies] ? name_g.content + " " + name_s.content :  name_g.content
+		     end
+		  end
+		  if name.nil?
+		     warn "WARNING: Cannot find binomial name of #{gi}, using genome regardless of taxonomy."
+		     name = rand(36**100).to_s(36)
+		  end
+		  break unless genome_org[ name ].nil?
+		  genome_org[ name ] = gi
+	       end
+	       $stderr.puts "   # traversing #{gi}" if @o[:debug]
+	       genome.xpath('./Seq-entry_set/Bioseq-set/Bioseq-set_annot/Seq-annot/Seq-annot_data/Seq-annot_data_ftable/Seq-feat').each do |pr|
+		  pr_gi = pr.at_xpath('./Seq-feat_product/Seq-loc/Seq-loc_whole/Seq-id/Seq-id_gi')
+		  next if pr_gi.nil?
+		  if @o[:positive].include? pr_gi.content
+		     $stderr.puts "   # found #{pr_gi.content}" if @o[:debug]
+		     pr_loc = pr.at_xpath('./Seq-feat_location/Seq-loc/Seq-loc_int/Seq-interval')
+		     if pr_loc.nil?
+			pr_loc = pr.xpath('./Seq-feat_location/Seq-loc/Seq-loc_mix//Seq-loc/Seq-loc_int/Seq-interval')
+			if pr_loc.nil?
+			   warn "WARNING: Impossible to find location of '#{pr_gi.content}' in '#{gi}'."
+			   incomplete = true
+			else
+			   pr_loc.each do |loc_int|
+			      positive_coords[gi] << {
+				 :gi     => pr_gi.content,
+				 :from   => loc_int.at_xpath('./Seq-interval_from').content.to_i,
+				 :to     => loc_int.at_xpath('./Seq-interval_to').content.to_i
+				 #, :strand => loc_int.at_xpath('./Seq-interval_strand/Na-strand/@value').content
+			      }
+			   end
+			end
+		     else
+			positive_coords[gi] << {
+			   :gi     => pr_gi.content,
+			   :from   => pr_loc.at_xpath('./Seq-interval_from').content.to_i,
+			   :to     => pr_loc.at_xpath('./Seq-interval_to').content.to_i
+			   #, :strand => pr_loc.at_xpath('./Seq-interval_strand/Na-strand/@value').content
+			}
+		     end
+		  end
+	       end
+	       break
+	    end
+	 end
+	 doc = nil
+	 warn "WARNING: Cannot find GI '#{gi}'." if incomplete
+      end
+      genome_gis[:positive] = genome_org.values if @o[:pergenus] or @o[:perspecies]
+      all_gis = genome_gis.values.reduce(:+).uniq
+      print "\n" unless @o[:q]
+      missing = @o[:positive] - positive_coords.values.map{ |a| a.map{ |b| b[:gi] } }.reduce(:+)
+      warn "\nWARNING: Cannot find genomic location of sequence(s) #{missing.join(',')}.\n\n" unless missing.size==0 or @o[:genomefrx]<1.0 or @o[:pergenus] or @o[:perspecies]
+      
+      # Download genomes
+      genomes_file = @o[:baseout] + '.src.fasta'
+      if @o[:reuse] and File.exist? genomes_file
+	 puts "  * reusing existing file: #{genomes_file}." unless @o[:q]
+      else
+	 puts "  * downloading #{all_gis.size} genome(s) in FastA." unless @o[:q]
+	 $stderr.puts "   # #{all_gis}" if @o[:debug]
+	 ids = Array.new(all_gis)
+	 ofh = File.open(genomes_file, 'w')
+	 while ids.size>0
+	    ofh.print efetch({:db=>'nuccore', :id=>ids.shift(200).join(','), :rettype=>'fasta', :retmode=>'text'})
+	 end
+	 ofh.close
+      end
+      
+      # Generate metagenome
+      unless @o[:nomg]
+	 puts "Generating in silico metagenome" unless @o[:q]
+	 if @o[:reuse] and File.exist? @o[:baseout] + ".mg.fasta"
+	    puts "  * reusing existing file: #{@o[:baseout]}.mg.fasta." unless @o[:q]
+	 else
+	    all_src = File.readlines("#{@o[:baseout]}.src.fasta").select{ |l| l =~ /^>/ }.size
+	    thrs = [@o[:thr], all_src].min
+	    puts "  * running grinder and tagging positive reads (#{thrs} threads)." unless @o[:q]
+	    $stderr.puts "   # #{positive_coords}" if @o[:debug]
+	    thr_obj = []
+	    seqs_per_thr = (all_src/thrs).ceil
+	    (0 .. (thrs-1)).each do |thr_i|
+	       thr_obj << Thread.new do
+		  Thread.current[:seqs_a] = thr_i*seqs_per_thr + 1
+		  Thread.current[:seqs_b] = [Thread.current[:seqs_a] + seqs_per_thr, all_src].min
+		  # Create sub-fasta
+		  Thread.current[:ofh] = File.open("#{@o[:baseout]}.src.fasta.#{thr_i.to_s}", 'w')
+		  Thread.current[:ifh] = File.open("#{@o[:baseout]}.src.fasta", 'r')
+		  Thread.current[:seq_i] = 0
+		  while Thread.current[:l] = Thread.current[:ifh].gets
+		     Thread.current[:seq_i]+=1 if Thread.current[:l] =~ /^>/
+		     break if Thread.current[:seq_i] > Thread.current[:seqs_b]
+		     Thread.current[:ofh].print Thread.current[:l] if Thread.current[:seq_i] >= Thread.current[:seqs_a]
+		  end
+		  Thread.current[:ifh].close
+		  Thread.current[:ofh].close
+		  bash sprintf(@o[:grindercmd], @o[:grinder], "#{@o[:baseout]}.src.fasta.#{thr_i.to_s}", @o[:seqdepth], "#{@o[:baseout]}.mg.tmp.#{thr_i.to_s}")
+		  # Tag positives
+		  puts "  * tagging positive reads." unless @o[:q]
+		  Thread.current[:ifh] = File.open(@o[:baseout] + ".mg.tmp.#{thr_i.to_s}-reads.fa", 'r')
+		  Thread.current[:ofh] = File.open(@o[:baseout] + ".mg.fasta.#{thr_i.to_s}", 'w')
+		  while Thread.current[:l]=Thread.current[:ifh].gets
+		     Thread.current[:rd] = /^>(?<id>\d+) reference=gi\|(?<gi>\d+)\|.* position=(?<comp>complement\()?(?<from>\d+)\.\.(?<to>\d+)\)? /.match(Thread.current[:l])
+		     unless Thread.current[:rd].nil?
+			Thread.current[:positive] = false
+			positive_coords[Thread.current[:rd][:gi]] ||= []
+			positive_coords[Thread.current[:rd][:gi]].each do |gn|
+			   Thread.current[:left]  = Thread.current[:rd][:to].to_i - gn[:from]
+			   Thread.current[:right] = gn[:to] - Thread.current[:rd][:from].to_i
+			   if (Thread.current[:left]*Thread.current[:right] >= 0) and ([Thread.current[:left], Thread.current[:right]].min/(Thread.current[:rd][:to].to_i-Thread.current[:rd][:from].to_i) >= @o[:minovl])
+			      Thread.current[:positive] = true
+			      break
+			   end
+			end
+			Thread.current[:l] = ">#{Thread.current[:rd][:id]}#{Thread.current[:positive] ? "@%" : ""} ref=#{Thread.current[:rd][:gi]}:#{Thread.current[:rd][:from]}..#{Thread.current[:rd][:to]}#{(Thread.current[:rd][:comp]=='complement(')?'-':'+'}\n"
+		     end
+		     Thread.current[:ofh].print Thread.current[:l]
+		  end
+		  Thread.current[:ofh].close
+		  Thread.current[:ifh].close
+		  Thread.current[:output] = @o[:baseout] + ".mg.fasta.#{thr_i.to_s}"
+	       end # Thread.new do
+	    end # (1 .. thrs).each
+	    # Concatenate results
+	    ofh = File.open(@o[:baseout] + ".mg.fasta", 'w')
+	    thr_obj.each do |t|
+	       t.join
+	       raise "Thread failed without error trace: #{t}" if t[:output].nil?
+	       ifh = File.open(t[:output], 'r')
+	       while l = ifh.gets
+	          ofh.print l
+	       end
+	       ifh.close
+	       File.unlink t[:output]
+	    end
+	    ofh.close
+         end
+      end # unless @o[:nomg]
+      # Align references
+      unless @o[:noaln]
+	 puts "Aligning reference set." unless @o[:q]
+	 if @o[:reuse] and File.exist? "#{@o[:baseout]}.ref.aln"
+	    puts "  * reusing existing file: #{@o[:baseout]}.ref.aln." unless @o[:q]
+	 else
+	    bash sprintf(@o[:musclecmd], @o[:muscle], "#{@o[:baseout]}.ref.fasta", "#{@o[:baseout]}.ref.aln")
+	    puts "  +--\n  | IMPORTANT NOTE: Manually checking the alignment before\n  | the 'compile' step is *strongly* encouraged.\n  +--\n" unless @o[:q]
+	 end
+      end
+      # Run BLAST 
+      unless @o[:noblast]
+	 puts "Running homology search." unless @o[:q]
+	 if @o[:reuse] and File.exist? "#{@o[:baseout]}.ref.blast"
+	    puts "  * reusing existing file: #{@o[:baseout]}.ref.blast." unless @o[:q]
+	 else
+	    puts "  * preparing database." unless @o[:q]
+	    bash sprintf(@o[:makedbcmd], @o[:blastbins], (@o[:nucl]?'nucl':'prot'), "#{@o[:baseout]}.ref.fasta", "#{@o[:baseout]}.ref")
+	    puts "  * running BLAST." unless @o[:q]
+	    bash sprintf(@o[:blastcmd], @o[:blastbins], (@o[:nucl]?'blastn':'blastx'), "#{@o[:baseout]}.mg.fasta", "#{@o[:baseout]}.ref", "#{@o[:baseout]}.ref.blast", @o[:thr])
+	 end
+      end
+      # Clean
+      unless @o[:noclean]
+	 puts "Cleaning." unless @o[:q]
+	 sff  = %w{.src.xml .src.fasta}
+	 sff += %w{.mg.tmp-reads.fa .mg.tmp-ranks.txt} unless @o[:nomg]
+	 sff += %w{.ref.phr .ref.pin .ref.psq} unless @o[:noblast]
+	 sff.each { |sf| File.unlink @o[:baseout] + sf if File.exist? @o[:baseout] + sf }
+      end
+   end # build!
+
+   #================================[ Compile ]
+   def compile!
+      raise "-a/--alignment is mandatory." if @o[:aln].nil?
+      raise "-a/--alignment must exist." unless File.exist? @o[:aln]
+      if @o[:table].nil?
+	 raise "-t/--table is mandatory unless -b is provided." if @o[:blast].nil?
+	 @o[:table] = "#{@o[:blast]}.table"
+      end
+      raise "-b/--blast is mandatory unless -t exists." if @o[:blast].nil? and not File.exist? @o[:table]
+      raise "-k/--rocker is mandatory." if @o[:rocker].nil?
+
+      puts "Testing environment." unless @o[:q]
+      bash "echo '' | #{@o[:r]} --vanilla", "-r/--path-to-r must be executable. Is R installed?"
+      bash "echo \"library('pROC')\" | #{@o[:r]} --vanilla", "Please install the 'pROC' library for R first."
+
+      puts "Reading files." unless @o[:q]
+      puts "  * loading alignment: #{@o[:aln]}." unless @o[:q]
+      aln = Alignment.new
+      aln.read_fasta @o[:aln]
+      
+      if File.exist? @o[:table]
+	 puts "  * reusing existing file: #{@o[:table]}." unless @o[:q]
+      else
+	 puts "  * generating table: #{@o[:table]}." unless @o[:q]
+	 blast2table(@o[:blast], @o[:table], aln, @o[:minscore])
+      end
+
+      puts "Analyzing data." unless @o[:q]
+      puts "  * computing windows." unless @o[:q]
+      data = ROCData.new(@o[:table], aln, @o[:win])
+      data.nucl = @o[:nucl]
+      if @o[:refine]
+	 puts "  * refining windows." unless @o[:q]
+	 warn "Insufficient hits to refine results." unless data.refine! @o[:table]
+      end
+      puts "  * saving ROCker file: #{@o[:rocker]}." unless @o[:q]
+      data.save @o[:rocker]
+   end # compile!
+   
+   #================================[ Filter ]
+   def filter!
+      raise "-k/--rocker is mandatory." if @o[:rocker].nil?
+      raise "-x/--query-blast is mandatory." if @o[:qblast].nil?
+      raise "-o/--out-blast is mandatory." if @o[:oblast].nil?
+      
+      puts "Reading ROCker file." unless @o[:q]
+      data = ROCData.new @o[:rocker]
+
+      puts "Filtering BLAST." unless @o[:q]
+      ih = File.open(@o[:qblast], 'r')
+      oh = File.open(@o[:oblast], 'w')
+      while ln = ih.gets
+	 bh = BlastHit.new(ln, data.aln)
+	 oh.print ln if not(bh.sfrom.nil?) and bh.bits >= data.win_at_col(bh.midpoint).thr
+      end
+      ih.close
+      oh.close
+   end # filter!
+   #================================[ Search ]
+   def search!
+      raise "-k/--rocker is mandatory." if @o[:rocker].nil?
+      raise "Code Under development..."
+      # ToDo
+      # [ ... ]
+   end # search!
+   
+   #================================[ Plot ]
+   def plot!
+      raise "-k/--rocker is mandatory." if o[:rocker].nil?
+      if @o[:table].nil?
+	 raise "-t/--table is mandatory unless -b is provided." if @o[:blast].nil?
+	 @o[:table] = "#{@o[:blast]}.table"
+      end
+      raise "-b/--blast is mandatory unless -t exists." if @o[:blast].nil? and not File.exist? @o[:table]
+
+      puts "Testing environment." unless @o[:q]
+      bash "echo '' | #{@o[:r]} --vanilla", "-r/--path-to-r must be executable. Is R installed?"
+
+      puts "Reading files." unless @o[:q]
+      puts "  * loding ROCker file: #{@o[:rocker]}." unless @o[:q]
+      data = ROCData.new @o[:rocker]
+      if File.exist? @o[:table]
+	 puts "  * reusing existing file: #{@o[:table]}." unless @o[:q]
+      else
+	 puts "  * generating table: #{@o[:table]}." unless @o[:q]
+	 blast2table(@o[:blast], @o[:table], data.aln, @o[:minscore])
+      end
+
+      puts "Plotting hits." unless @o[:q]
+      extra = @o[:gformat]=='pdf' ? "" : ", units='in', res=300"
+      @o[:gout] ||= "#{@o[:rocker]}.#{@o[:gformat]}"
+      data.rrun "#{@o[:gformat]}('#{@o[:gout]}', #{@o[:width]}, #{@o[:height]}#{extra});"
+      data.rrun "layout(c(2,1,3), heights=c(2-1/#{data.aln.size},3,1));"
+      some_thr = data.load_table! @o[:table], @o[:sbj], @o[:minscore]
+      data.rrun "par(mar=c(0,4,0,0.5)+.1);"
+      data.rrun "plot(1, t='n', xlim=c(0.5,#{data.aln.cols}+0.5), ylim=range(x$V4)+c(-0.04,0.04)*diff(range(x$V4)), xlab='', ylab='Bit score', xaxs='i', xaxt='n');"
+      data.rrun "noise <- runif(ncol(x),-.2,.2)"
+      data.rrun "arrows(x0=x$V2, x1=x$V3, y0=x$V4+noise, col=ifelse(x$V5==1, rgb(0,0,.5,.2), rgb(.5,0,0,.2)), length=0);"
+      data.rrun "points(x$V6, x$V4+noise, col=ifelse(x$V5==1, rgb(0,0,.5,.5), rgb(.5,0,0,.5)), pch=19, cex=1/4);"
+
+      puts "Plotting windows." unless @o[:q]
+      if some_thr
+	 data.rrun "arrows(x0=w$V1, x1=w$V2, y0=w$V5, lwd=2, length=0)"
+	 data.rrun "arrows(x0=w$V2[-nrow(w)], x1=w$V1[-1], y0=w$V5[-nrow(w)], y1=w$V5[-1], lwd=2, length=0)"
+      end
+      data.rrun "legend('bottomright',legend=c('Hit span','Hit mid-point','Reference','Non-reference')," +
+	 "lwd=c(1,NA,1,1),pch=c(NA,19,19,19),col=c('black','black','darkblue','darkred'),ncol=4,bty='n')"
+
+      puts "Plotting alignment." unless @o[:q]
+      data.rrun "par(mar=c(0,4,0.5,0.5)+0.1);"
+      data.rrun "plot(1, t='n', xlim=c(0,#{data.aln.cols}),ylim=c(1,#{data.aln.seqs.size}),xlab='',ylab='Alignment',xaxs='i',xaxt='n',yaxs='i',yaxt='n',bty='n');"
+      i = 0
+      data.rrun "clr <- rainbow(26, v=1/2, s=3/4);" if @o[:color]
+      data.aln.seqs.values.each do |s|
+         color = s.aln.split(//).map{|c| c=="-" ? "'grey80'" : (@o[:sbj].include?(s.id) ? "'red'" : (@o[:color] ? "clr[#{c.ord-64}]" : "'black'"))}.join(',')
+	 data.rrun "rect((1:#{data.aln.cols-1})-0.5, rep(#{i}, #{data.aln.cols-1}), (1:#{data.aln.cols-1})+0.5, rep(#{i+1}, #{data.aln.cols-1}), col=c(#{color}), border=NA);"
+	 i += 1
+      end
+
+      puts "Plotting statistics." unless @o[:q]
+      data.rrun "par(mar=c(5,4,0,0.5)+.1);"
+      unless @o[:q] or not some_thr
+	 puts "  * sensitivity: #{data.rrun "100*sum(w$tp)/(sum(w$tp)+sum(w$fn))", :float}%"
+	 puts "  * specificity: #{data.rrun "100*sum(w$tn)/(sum(w$fp)+sum(w$tn))", :float}%"
+	 puts "  * accuracy: #{data.rrun "100*(sum(w$tp)+sum(w$tn))/(sum(w$p)+sum(w$n))", :float}%"
+      end
+      data.rrun "plot(1, t='n', xlim=c(0,#{data.aln.cols}),ylim=c(50,100),xlab='Alignment position (amino acids)',ylab='Precision',xaxs='i');"
+      if some_thr
+	 data.rrun "pos <- (w$V1+w$V2)/2"
+	 data.rrun "lines(pos[!is.na(w$specificity)], w$specificity[!is.na(w$specificity)], col='darkred', lwd=2, t='o', cex=1/3, pch=19);"
+	 data.rrun "lines(pos[!is.na(w$sensitivity)], w$sensitivity[!is.na(w$sensitivity)], col='darkgreen', lwd=2, t='o', cex=1/3, pch=19);"
+	 data.rrun "lines(pos[!is.na(w$accuracy)], w$accuracy[!is.na(w$accuracy)], col='darkblue', lwd=2, t='o', cex=1/3, pch=19);"
+	 #data.rrun "lines(pos[!is.na(w$precision)], w$precision[!is.na(w$precision)], col='purple', lwd=2, t='o', cex=1/3, pch=19);"
+      end
+      data.rrun "legend('bottomright',legend=c('Specificity','Sensitivity','Accuracy'),lwd=2,col=c('darkred','darkgreen','darkblue'),ncol=3,bty='n')"
+      data.rrun "dev.off();"
+   end # plot!
+
+   #================================[ Utilities ]
+   def blast2table(blast_f, table_f, aln, minscore)
+      ifh = File.open(blast_f, "r")
+      ofh = File.open(table_f, "w")
+      while ln = ifh.gets
+	 bh = BlastHit.new(ln, aln)
+	 ofh.print bh.to_s if bh.bits >= minscore
+      end
+      ifh.close
+      ofh.close
+   end
+   def genes2genomes(gis, nucl=false)
+      genomes = []
+      ids = Array.new(gis)
+      while ids.size>0
+	 doc = Nokogiri::XML( elink({:dbfrom=>(nucl ? 'nuccore' : 'protein'), :db=>'nuccore', :id=>ids.shift(200).join(',')}) )
+	 genomes += doc.xpath('/eLinkResult/LinkSet/LinkSetDb/Link/Id').map{ |id| id.content }
+      end
+      genomes.uniq
+   end
+   def eutils(script, params={}, outfile=nil)
+      response = RestClient.get "#{ROCker.eutils}/#{script}", {:params=>params}
+      raise "Unable to reach NCBI EUtils, error code #{response.code}." unless response.code == 200
+      unless outfile.nil?
+	 ohf = File.open(outfile, 'w')
+	 ohf.print response.to_s
+	 ohf.close
+      end
+      response.to_s
+   end
+   def efetch(*etc) self.eutils 'efetch.fcgi', *etc end
+   def elink(*etc) self.eutils 'elink.fcgi', *etc end
+   def bash(cmd, err_msg=nil)
+      o = `#{cmd} 2>&1 && echo '{'`
+      raise (err_msg.nil? ? "Error executing: #{cmd}\n\n#{o}" : err_msg) unless o[-2]=='{'
+      true
+   end
+end
+
+#================================[ Extensions ]
+class Numeric
+   def ordinalize
+      n= self.to_s
+      s= n[-2]=='1' ? 'th' :
+	 n[-1]=='1' ? 'st' :
+	 n[-1]=='2' ? 'nd' :
+	 n[-1]=='3' ? 'rd' : 'th'
+      n + s
+   end
+end
+

data/lib/rocker/alignment.rb

@@ -0,0 +1,63 @@
+#
+# @author Luis M. Rodriguez-R <lmrodriguezr at gmail dot com>
+# @author Luis (Coto) Orellana
+# @license artistic license 2.0
+# @update Jan-22-2015
+#
+
+require 'rocker/sequence'
+
+
+class Alignment
+   attr_reader :seqs, :cols
+   def initialize
+      @seqs = {}
+   end
+   def read_fasta(file) self.read_file(file, false) end
+   def read_rocker(file) self.read_file(file, true) end
+   def read_file(file, is_rocker)
+      f = File.open(file, 'r')
+      id = nil
+      sq = ""
+      while ln = f.gets
+	 if is_rocker
+	    next if /^#:(.*)/.match(ln).nil?
+	    ln = $1
+	 end
+	 m = /^>(\S+)/.match(ln)
+	 if m.nil?
+	    sq += ln
+	 else
+	    self << Sequence.new(id, sq) unless id.nil?
+	    id = m[1]
+	    sq = ""
+	 end
+      end
+      self << Sequence.new(id, sq) unless id.nil?
+   end
+   def <<(seq)
+      @seqs[seq.id] = seq
+      @cols = seq.cols if self.cols.nil?
+      raise "Aligned sequence #{seq.id} has a different length (#{seq.cols} vs #{self.cols})" unless seq.cols == self.cols
+   end
+   def get_gis
+      regexps = [/^gi\|(\d+)\|/, /^(\d+)\|/, /^(\d+)$/, /^gi\|(\d+)$/, /\|gi\|(\d+)\|/, /\|gi\|(\d+)$/]
+      gis = []
+      self.seqs.keys.each do |id|
+	 gi = nil
+	 regexps.each do |regexp|
+	    unless regexp.match(id).nil?
+	       gi = $1
+	       break
+	    end
+	 end
+	 gis << gi unless gi.nil?
+      end
+      gis
+   end
+   def seq(id) @seqs[id] end
+   def size() self.seqs.size end
+   def to_seq_s() self.seqs.values.map{|s| s.to_seq_s}.join + "\n" end
+   def to_s() self.seqs.values.map{|s| s.to_s}.join + "\n" end
+end
+

data/lib/rocker/blasthit.rb

@@ -0,0 +1,39 @@
+#
+# @author Luis M. Rodriguez-R <lmrodriguezr at gmail dot com>
+# @author Luis (Coto) Orellana
+# @license artistic license 2.0
+# @update Jan-22-2015
+#
+
+class BlastHit
+   attr_reader :sbj, :sfrom, :sto, :bits, :istrue, :midpoint
+   # Initialize from BLAST using new(ln,aln), initialize from TABLE using new(ln)
+   def initialize(ln, aln=nil)
+      l = ln.chomp.split(/\t/)
+      if aln.nil?
+	 @sbj	= l[0]
+	 @sfrom	= l[1].to_i
+	 @sto	= l[2].to_i
+	 @bits	= l[3].to_f
+	 @istrue = l[4]=='1'
+	 @midpoint = l[5].to_i
+      else
+	 s = aln.seq(l[1])
+	 return nil if s.nil?
+	 @sbj	= s.id
+	 a	= s.pos2col(l[8].to_i)
+	 b 	= s.pos2col(l[9].to_i)
+	 @sfrom	= [a,b].min
+	 @sto	= [a,b].max
+	 @bits	= l[11].to_f
+	 @istrue = ! /@%/.match(l[0]).nil?
+	 @midpoint = s.pos2col(((l[8].to_f+l[9].to_f)/2).ceil)
+      end
+   end
+   def to_s
+      self.sbj.nil? ? "" :
+	 [self.sbj, self.sfrom.to_s, self.sto.to_s, self.bits.to_s,
+	    self.istrue ? '1' : '0', self.midpoint].join("\t") + "\n"
+   end
+end
+

data/lib/rocker/rinterface.rb

@@ -0,0 +1,39 @@
+#
+# @author Luis M. Rodriguez-R <lmrodriguezr at gmail dot com>
+# @author Luis (Coto) Orellana
+# @license artistic license 2.0
+# @update Jan-22-2015
+#
+
+class RInterface
+   @@R_BIN = "R"
+   def RInterface.R_BIN=(rbin) @@R_BIN=rbin end
+   attr_reader :handler
+   def initialize
+      @handler = IO.popen("#{@@R_BIN} --slave 2>&1", "w+")
+   end
+   def run(cmd, type=nil)
+      @handler.puts cmd
+      @handler.puts "cat('---FIN---\n')"
+      o = ""
+      while true
+         l = @handler.gets
+	 raise "R failed on command:\n#{cmd}\n\nError:\n#{o}" if l.nil?
+	 break unless /^---FIN---/.match(l).nil?
+	 o += l
+      end
+      o.chomp!
+      case type
+      when :float
+	 /^\s*\[1\]\s+([0-9\.Ee+-]+|Inf).*/.match(o).nil? and raise "R error: expecting float, got #{o}"
+	 return Float::INFINITY if $1=='Inf'
+	 return $1.to_f
+      when :int
+	 /^\s*\[1\]\s+([0-9\.Ee+-]+).*/.match(o).nil? and raise "R error: expecting integer, got #{o}"
+	 return $1.to_i
+      else
+	 return o
+      end
+   end
+end
+

data/lib/rocker/rocdata.rb

@@ -0,0 +1,124 @@
+#
+# @author Luis M. Rodriguez-R <lmrodriguezr at gmail dot com>
+# @author Luis (Coto) Orellana
+# @license artistic license 2.0
+# @update Jan-22-2015
+#
+
+require 'rocker/rinterface'
+require 'rocker/rocwindow'
+require 'rocker/alignment'
+require 'tmpdir'
+
+class ROCData
+   attr_reader :aln, :windows, :r
+   # Use ROCData.new(table,aln,window) to re-compute from table, use ROCData.new(data) to load
+   def initialize(val, aln=nil, window=nil)
+      @r = RInterface.new
+      @nucl = false
+      if not aln.nil?
+	 @aln = aln
+	 self.rrun "library('pROC');"
+	 self.rrun "x <- read.table('#{val}', sep='\\t', h=F);"
+	 self.init_windows! window
+      else
+	 f = File.open(val, "r")
+	 @windows = []
+	 while ln = f.gets
+	    break unless /^#:/.match(ln).nil?
+	    @windows << ROCWindow.new(self, ln)
+	 end
+	 f.close
+	 @aln = Alignment.new
+	 @aln.read_rocker(val)
+      end
+   end
+   def win_at_col(col) self.windows.select{|w| (w.from<=col) and (w.to>=col)}.first end
+   def in_nucl?() @nucl end
+   def nucl=(nucl) @nucl=nucl end
+   def refine! table
+      while true
+	 return false unless self.load_table! table
+	 break if self._refine_iter(table)==0
+      end
+      return true
+   end
+   def _refine_iter table
+      to_refine = []
+      self.windows.each do |w|
+	 next if w.almost_empty or w.length <= 5
+	 self.rrun "acc <- w$accuracy[w$V1==#{w.from}];"
+	 to_refine << w if self.rrun("ifelse(is.na(acc), 100, acc)", :float) < 95.0
+      end
+      n = to_refine.size
+      return 0 unless n > 0
+      to_refine.each do |w|
+	 w1 = ROCWindow.new(self, w.from, (w.from+w.to)/2)
+	 w2 = ROCWindow.new(self, (w.from+w.to)/2, w.to)
+	 if w1.almost_empty or w2.almost_empty
+	    n -= 1
+	 else
+	    @windows << w1
+	    @windows << w2
+	    @windows.delete w
+	 end
+      end
+      @windows.sort!{ |x,y| x.from <=> y.from }
+      n
+   end
+   def load_table! table, sbj=[], min_score=0
+      self.rrun "x <- read.table('#{table}', sep='\\t', h=F);"
+      self.rrun "x <- x[x$V1 %in% c('#{sbj.join("','")}'),];" if sbj.size > 0
+      self.rrun "x <- x[x$V4 >= #{minscore.to_s},];" if min_score > 0
+      Dir.mktmpdir do |dir|
+         self.save(dir + "/rocker")
+	 self.rrun "w <- read.table('#{dir}/rocker', sep='\\t', h=F);"
+      end
+      self.rrun "w <- w[!is.na(w$V5),];"
+      if self.rrun("nrow(w)", :int)==0
+         warn "\nWARNING: Insufficient windows with estimated thresholds.\n\n"
+         return false
+      end
+      self.rrun <<-EOC
+	 w$tp<-0; w$fp<-0; w$tn<-0; w$fn<-0;
+	 for(i in 1:nrow(x)){
+	    m <- x$V6[i];
+	    win <- which( (m>=w$V1) & (m<=w$V2))[1];
+	    if(!is.na(win)){
+	       if(x$V4[i] >= w$V5[win]){
+		  if(x$V5[i]==1){ w$tp[win] <- w$tp[win]+1 }else{ w$fp[win] <- w$fp[win]+1 };
+	       }else{
+		  if(x$V5[i]==1){ w$fn[win] <- w$fn[win]+1 }else{ w$tn[win] <- w$tn[win]+1 };
+	       }
+	    }
+	 }
+      EOC
+      r.run <<-EOC
+	 w$p <- w$tp + w$fp;
+	 w$n <- w$tn + w$fn;
+	 w$sensitivity <- 100*w$tp/(w$tp+w$fn);
+	 w$specificity <- 100*w$tn/(w$fp+w$tn);
+	 w$accuracy <- 100*(w$tp+w$tn)/(w$p+w$n);
+	 w$precision <- 100*w$tp/(w$tp+w$fp);
+      EOC
+      
+      return true
+   end
+   def init_windows!(size)
+      @windows = []
+      1.step(self.aln.cols,size).each { |a| @windows << ROCWindow.new(self, a, a+size-1) }
+   end
+   def rrun(cmd, type=nil) self.r.run cmd, type end
+   def save(file)
+      f = File.open(file, "w")
+      f.print self.to_s
+      f.close
+   end
+   def to_s
+      o = ''
+      self.windows.each{|w| o += w.to_s}
+      o += self.aln.to_s
+      return o
+   end
+end
+

data/lib/rocker/rocwindow.rb

@@ -0,0 +1,63 @@
+#
+# @author Luis M. Rodriguez-R <lmrodriguezr at gmail dot com>
+# @author Luis (Coto) Orellana
+# @license artistic license 2.0
+# @update Jan-22-2015
+#
+
+class ROCWindow
+   attr_reader :data, :from, :to, :hits, :tps, :thr
+   def initialize(data, from=nil, to=nil)
+      @data = data
+      if from.is_a? String
+	 r = from.split(/\t/)
+	 @from	= r[0].to_i
+	 @to	= r[1].to_i
+	 @hits	= r[2].to_i
+	 @tps	= r[3].to_i
+	 @thr	= r[4].to_f
+      else
+	 a = from.nil? ? 1 : [from,1].max
+	 b = to.nil? ? data.aln.cols : [to,data.aln.cols].min
+	 @from = [a,b].min
+	 @to = [a,b].max
+	 @thr = nil
+	 self.compute!
+      end
+   end
+   def compute!
+      self.load_hits
+      @hits = self.rrun "nrow(y);", :int
+      @tps = self.rrun "sum(y$V5);", :int
+      unless self.almost_empty
+	 self.rrun "rocobj <- roc(y$V5, y$V4);"
+	 thr = self.rrun 'coords(rocobj, "best", ret="threshold", best.method="youden", best.weights=c(0.5, sum(y$V5)/nrow(y)))[1];', :float
+	 @thr = thr.to_f
+	 @thr = nil if @thr==0.0 or @thr.infinite?
+      end
+   end
+   def around_thr
+      a = self.previous
+      b = self.next
+      while not a.nil? and a.thr.nil?
+	 a = a.previous
+      end
+      while not b.nil? and b.thr.nil?
+	 b = b.next
+      end
+      return nil if a.nil? and b.nil?
+      return a.thr if b.nil?
+      return b.thr if a.nil?
+      return (b.thr*(self.from-a.from) - a.thr*(self.from-b.from))/(b.from-a.from)
+   end
+   def load_hits() self.rrun "y <- x[x$V6>=#{self.from} & x$V6<=#{self.to},];" end
+   def previous() (self.from == 1) ? nil : self.data.win_at_col(self.from - 1) end
+   def next() (self.to == self.data.aln.cols) ? nil : self.data.win_at_col(self.to + 1) end
+   def thr_notnil() (@thr.nil? or @thr.infinite?) ? self.around_thr : @thr end
+   def fps() self.hits - self.tps end
+   def almost_empty() self.fps < 3 or self.tps < 3 end
+   def length() self.to - self.from + 1 end
+   def rrun(cmd, type=nil) self.data.rrun cmd, type end
+   def to_s() [self.from, self.to, self.hits, self.tps, self.thr_notnil].join("\t") + "\n" end
+end
+

data/lib/rocker/sequence.rb

@@ -0,0 +1,38 @@
+#
+# @author Luis M. Rodriguez-R <lmrodriguezr at gmail dot com>
+# @author Luis (Coto) Orellana
+# @license artistic license 2.0
+# @update Jan-22-2015
+#
+
+class Sequence
+   attr_reader :id, :seq, :aln
+   def initialize(id, aln)
+      @id = id
+      @aln = aln.gsub(/[-\.]/,'-').gsub(/[^A-Za-z-]/, '').upcase
+      @seq = aln.gsub(/[^A-Za-z]/, '').upcase
+   end
+   def pos2col(pos)
+      col = 0
+      self.aln.split(//).each do |c|
+	 col+=1
+	 pos-=1 unless c=='-'
+	 return col if pos==0
+      end
+      col
+   end
+   def col2pos(col)
+      pos = 1
+      self.aln.split(//).each do |c|
+         col-=1
+	 pos+=1 unless c=='-'
+	 return pos if col==0
+      end
+      pos
+   end
+   def cols() self.aln.length end
+   def length() self.seq.length end
+   def to_seq_s() ">#{self.id}\n#{self.seq}\n" end
+   def to_s() "#:>#{self.id}\n#:#{self.aln}\n" end
+end
+

metadata

@@ -0,0 +1,54 @@
+--- !ruby/object:Gem::Specification
+name: bio-rocker
+version: !ruby/object:Gem::Version
+  version: 0.1.0
+platform: ruby
+authors:
+- Luis (Coto) Orellana
+- Luis M. Rodriguez-R
+autorequire: 
+bindir: bin
+cert_chain: []
+date: 2015-01-20 00:00:00.000000000 Z
+dependencies: []
+description: Detecting and quantifying functional genes in short-read metagenomic
+  datasets
+email: lhorellana@gatech.edu
+executables:
+- ROCker
+extensions: []
+extra_rdoc_files: []
+files:
+- lib/rocker.rb
+- lib/rocker/sequence.rb
+- lib/rocker/alignment.rb
+- lib/rocker/blasthit.rb
+- lib/rocker/rocwindow.rb
+- lib/rocker/rocdata.rb
+- lib/rocker/rinterface.rb
+- bin/ROCker
+homepage: http://enve-omics.ce.gatech.edu/rocker
+licenses:
+- artistic 2.0
+metadata: {}
+post_install_message: 
+rdoc_options: []
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - '>='
+    - !ruby/object:Gem::Version
+      version: '0'
+required_rubygems_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - '>='
+    - !ruby/object:Gem::Version
+      version: '0'
+requirements: []
+rubyforge_project: 
+rubygems_version: 2.0.14
+signing_key: 
+specification_version: 4
+summary: ROCker
+test_files: []