bio-rocker 1.0.0 → 1.1.9

data/lib/rocker/step/compile.rb

@@ -2,7 +2,7 @@
 # @author Luis M. Rodriguez-R <lmrodriguezr at gmail dot com>
 # @author Luis (Coto) Orellana
 # @license artistic license 2.0
-# @update Jun-05-2015
+# @update Sep-07-2015
 #
 
 class ROCker
@@ -14,17 +14,21 @@ class ROCker
       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? or not File.exist? @o[:blast]
+	 raise "-T/--table is mandatory unless -b is provided." if
+	    @o[:blast].nil? or not File.exist? @o[:blast]
 	 @o[:table] = "#{@o[:blast]}.table"
       else
 	 @o[:reuse] = true
       end
-      raise "-b/--blast is mandatory unless -t exists." if @o[:blast].nil? and not File.exist? @o[:table]
+      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."
+      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]
@@ -44,7 +48,8 @@ class ROCker
       data.nucl = @o[:nucl]
       if @o[:refine]
 	 puts "  * refining windows." unless @o[:q]
-	 warn "Insufficient hits to refine results." unless data.refine! @o[:table]
+	 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]

data/lib/rocker/step/filter.rb

@@ -2,7 +2,7 @@
 # @author Luis M. Rodriguez-R <lmrodriguezr at gmail dot com>
 # @author Luis (Coto) Orellana
 # @license artistic license 2.0
-# @update Jun-04-2015
+# @update Jun-08-2015
 #
 
 class ROCker
@@ -10,17 +10,21 @@ class ROCker
    #@@DEFAULTS.merge!({  })
    
    #================================[ Filter ]
-   def filter!
+   def filter!(data=nil)
       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]
+      # Read ROCker file
+      if data.nil?
+	 puts "Loading ROCker file: #{@o[:rocker]}." unless @o[:q]
+	 data = ROCData.new @o[:rocker]
+      end
 
-      puts "Filtering BLAST." unless @o[:q]
-      ih = File.open(@o[:qblast], 'r')
-      oh = File.open(@o[:oblast], 'w')
+      # Filter similarity search
+      puts "Filtering similarity search: #{@o[:qblast]}." 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

data/lib/rocker/step/plot.rb

@@ -2,25 +2,32 @@
 # @author Luis M. Rodriguez-R <lmrodriguezr at gmail dot com>
 # @author Luis (Coto) Orellana
 # @license artistic license 2.0
-# @update Jun-04-2015
+# @update Sep-09-2015
 #
 
 class ROCker
    #================================[ Class ]
-   @@DEFAULTS.merge!({:color=>false, :gformat=>'pdf', :width=>9, :height=>9, :impact=>false, :transparency=>true, :sbj=>[]})
+   @@DEFAULTS.merge!({
+      color:false, gformat:"pdf", width:9, height:9, impact:false,
+      transparency:true, sbj:[], tag_negatives:false
+   })
    
    #================================[ Search ]
    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?
+	 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 "-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?"
+      bash "echo '' | #{@o[:r]} --vanilla", "-r/--path-to-r must be " +
+	 "executable. Is R installed?"
 
+      # Source files
       puts "Reading files." unless @o[:q]
       puts "  * loding ROCker file: #{@o[:rocker]}." unless @o[:q]
       data = ROCData.new @o[:rocker]
@@ -31,40 +38,71 @@ class ROCker
 	 blast2table(@o[:blast], @o[:table], data.aln, @o[:minscore])
       end
 
+      # Matches (middle panel)
       puts "Plotting matches." unless @o[:q]
-      extra = @o[:gformat]=='pdf' ? "" : ", units='in', res=300"
+      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 "#{@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 "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,#{@o[:transparency] ? ".2" : "1"}), rgb(.5,0,0,#{@o[:transparency] ? ".2" : "1"})), length=0);"
-      data.rrun "points(x$V6, x$V4+noise, col=ifelse(x$V5==1, rgb(0,0,.5,#{@o[:transparency] ? ".5" : "1"}), rgb(.5,0,0,#{@o[:transparency] ? ".5" : "1"})), pch=19, cex=1/4);"
-
+      data.rrun "hit.col <- ifelse(x$V5==1, " +
+	 "rgb(0,0,.5,#{@o[:transparency] ? ".2" : "1"}), " +
+	 "rgb(.5,0,0,#{@o[:transparency] ? ".2" : "1"}))"
+      data.rrun "hit.col[ x$V5==-1 ] <- " +
+	 "rgb(0.722,0.722,0,#{@o[:transparency] ? ".2" : "1"})" if
+	 @o[:tag_negatives]
+      data.rrun "arrows(x0=x$V2, x1=x$V3, y0=x$V4+noise, lty=1, col=hit.col, " +
+	 "length=0);"
+      data.rrun "points(x$V6, x$V4+noise, col=hit.col, pch=19, cex=1/4);"
+      
+      # Windows (middle panel)
       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$V5[-1], lwd=2, length=0)"
+	 data.rrun "arrows(x0=w$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('Match span','Match 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')"
+      data.rrun "legend('bottomright', legend=c('Match span'," +
+	 "'Match mid-point','Reference (+)'," +
+	 "#{"'Reference (-)'," if @o[:tag_negatives]}'Non-reference'), " +
+	 "lwd=c(1,NA,1,1,1), pch=c(NA,19,19,19,19), ncol=5, bty='n', " +
+	 "col=c('black','black','darkblue'," +
+	 "#{"rgb(.722,.722,0)," if @o[:tag_negatives]}'darkred'))"
 
+      # Alignment (top panel)
       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');"
+      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);"
+         color = (s.aln.split(//).map do |c|
+	    c=="-" ? "'grey80'" :
+	       (@o[:sbj].include?(s.id) ? "'red'" :
+	       (@o[:color] ? "clr[#{c.ord-64}]" :
+	       "'black'"))
+	 end.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
 
+      # Statistics (bottom panel)
       puts "Plotting statistics." unless @o[:q]
       data.rrun "par(mar=c(5,4,0,0.5)+.1);"
-      data.rrun "plot(1, t='n', xlim=c(0,#{data.aln.cols}),ylim=c(#{@o[:ylim].nil? ? (@o[:impact] ? "-2,.1" : "50,100") : @o[:ylim]}),xlab='Alignment position (amino acids)',ylab='Precision',xaxs='i');"
+      data.rrun "plot(1, t='n', xlim=c(0,#{data.aln.cols}), " +
+	 "ylim=c(#{@o[:ylim].nil? ? (@o[:impact] ? "-2,.1" : "50,100") :
+	    @o[:ylim]}), xlab='Alignment position (amino acids)', " +
+	 "ylab='Precision',xaxs='i');"
       if some_thr
 	 sn = data.rrun "100*sum(w$tp)/(sum(w$tp)+sum(w$fn))", :float
 	 sp = data.rrun "100*sum(w$tn)/(sum(w$fp)+sum(w$tn))", :float
@@ -76,17 +114,33 @@ class ROCker
 	 end
 	 data.rrun "pos <- (w$V1+w$V2)/2"
 	 if @o[:impact]
-	    data.rrun "lines(pos[!is.na(w$specificity)], (w$specificity[!is.na(w$specificity)]-#{sp})*w$tp[!is.na(w$specificity)]/sum(w$tp), col='darkred', lwd=2, t='o', cex=1/3, pch=19);"
-	    data.rrun "lines(pos[!is.na(w$sensitivity)], (w$sensitivity[!is.na(w$sensitivity)]-#{sn})*w$tn[!is.na(w$sensitivity)]/sum(w$tn), col='darkgreen', lwd=2, t='o', cex=1/3, pch=19);"
-	    data.rrun "lines(pos[!is.na(w$accuracy)], (w$accuracy[!is.na(w$accuracy)]-#{ac})*(w$tp+w$tn)[!is.na(w$accuracy)]/sum(c(w$tp, w$tn)), col='darkblue', lwd=2, t='o', cex=1/3, pch=19);"
+	    data.rrun "lines(pos[!is.na(w$specificity)], " +
+	       "(w$specificity[!is.na(w$specificity)]-#{sp})*" +
+		  "w$tp[!is.na(w$specificity)]/sum(w$tp), " +
+	       "col='darkred', lwd=2, t='o', cex=1/3, pch=19);"
+	    data.rrun "lines(pos[!is.na(w$sensitivity)], " +
+	       "(w$sensitivity[!is.na(w$sensitivity)]-#{sn})*" +
+		  "w$tn[!is.na(w$sensitivity)]/sum(w$tn), " +
+	       "col='darkgreen', lwd=2, t='o', cex=1/3, pch=19);"
+	    data.rrun "lines(pos[!is.na(w$accuracy)], " +
+	       "(w$accuracy[!is.na(w$accuracy)]-#{ac})*" +
+		  "(w$tp+w$tn)[!is.na(w$accuracy)]/sum(c(w$tp, w$tn)), " +
+	       "col='darkblue', lwd=2, t='o', cex=1/3, pch=19);"
 	 else
-	    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$accuracy)], col='darkblue', lwd=2, t='o', cex=1/3, pch=19);"
+	    data.rrun "lines(pos[!is.na(w$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);"
 	 end
-	 #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 "legend('bottomright', " +
+	 "legend=c('Specificity','Sensitivity','Accuracy'), lwd=2, " +
+	 "col=c('darkred','darkgreen','darkblue'), ncol=3, bty='n')"
       data.rrun "dev.off();"
    end # plot!
 end # ROCker

data/lib/rocker/step/search.rb

@@ -2,9 +2,11 @@
 # @author Luis M. Rodriguez-R <lmrodriguezr at gmail dot com>
 # @author Luis (Coto) Orellana
 # @license artistic license 2.0
-# @update Jun-04-2015
+# @update Jun-08-2015
 #
 
+require 'tmpdir'
+
 class ROCker
    #================================[ Class ]
    #@@DEFAULTS.merge!({  })
@@ -12,9 +14,30 @@ class ROCker
    #================================[ Search ]
    def search!
       raise "-k/--rocker is mandatory." if @o[:rocker].nil?
-      raise "Code Under development..."
-      # ToDo
-      # [ ... ]
+      raise "-i/--query is mandatory." if @o[:query].nil?
+
+      # Check requirements
+      puts "Testing environment." unless @o[:q]
+      @o[:searchcmd] = @o[:searchcmd][@o[:search]] if @o[:searchcmd].is_a? Hash
+      @o[:makedbcmd] = @o[:makedbcmd][@o[:search]] if @o[:makedbcmd].is_a? Hash
+      self.bash "#{@o[:searchbins]}makeblastdb -version", "--search-bins must contain executables. Is BLAST+ installed?" if @o[:search]==:blast
+      self.bash "#{@o[:searchbins]}diamond --help", "--search-bins must contain executables. Is DIAMOND installed?" if @o[:search]==:diamond
+
+      # Run similarity search
+      Dir.mktmpdir do |dir|
+	 @o[:qblast] ||= "#{dir}/blast"
+	 puts "Loading ROCker file: #{@o[:rocker]}." unless @o[:q]
+	 data = ROCData.new @o[:rocker]
+	 puts "Running similarity search." unless @o[:q]
+	 puts "  * preparing database." unless @o[:q]
+	 ofh = File.new("#{dir}/ref.fasta", "w")
+	 ofh.print data.aln.to_seq_s
+	 ofh.close
+	 bash sprintf(@o[:makedbcmd], @o[:searchbins], 'prot', "#{dir}/ref.fasta", "#{dir}/ref")
+	 puts "  * running similarity search." unless @o[:q]
+	 bash sprintf(@o[:searchcmd], @o[:searchbins], 'blastx', @o[:query], "#{dir}/ref", @o[:qblast], @o[:thr])
+	 self.filter! data
+      end
    end # search!
 end # ROCker
 

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: bio-rocker
 version: !ruby/object:Gem::Version
-  version: 1.0.0
+  version: 1.1.9
 platform: ruby
 authors:
 - Luis (Coto) Orellana
@@ -9,34 +9,34 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2015-06-05 00:00:00.000000000 Z
+date: 2015-07-02 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rest-client
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - ">="
       - !ruby/object:Gem::Version
         version: 1.7.3
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - ">="
       - !ruby/object:Gem::Version
         version: 1.7.3
 - !ruby/object:Gem::Dependency
   name: json
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - ">="
       - !ruby/object:Gem::Version
         version: 1.8.1
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - ">="
       - !ruby/object:Gem::Version
         version: 1.8.1
 description: Detecting and quantifying functional genes in short-read metagenomic
@@ -47,19 +47,21 @@ executables:
 extensions: []
 extra_rdoc_files: []
 files:
+- bin/ROCker
 - 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/genome-set.rb
+- lib/rocker/protein-set.rb
 - lib/rocker/rinterface.rb
+- lib/rocker/rocdata.rb
+- lib/rocker/rocwindow.rb
+- lib/rocker/sequence.rb
 - lib/rocker/step/build.rb
 - lib/rocker/step/compile.rb
-- lib/rocker/step/search.rb
 - lib/rocker/step/filter.rb
 - lib/rocker/step/plot.rb
-- bin/ROCker
+- lib/rocker/step/search.rb
 homepage: http://enve-omics.ce.gatech.edu/rocker
 licenses:
 - artistic 2.0
@@ -70,17 +72,17 @@ require_paths:
 - lib
 required_ruby_version: !ruby/object:Gem::Requirement
   requirements:
-  - - ~>
+  - - ">="
     - !ruby/object:Gem::Version
       version: '2.0'
 required_rubygems_version: !ruby/object:Gem::Requirement
   requirements:
-  - - '>='
+  - - ">="
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 2.0.14
+rubygems_version: 2.4.5.1
 signing_key: 
 specification_version: 4
 summary: ROCker