Class: ROCData

Inherits:
Object
  • Object
show all
Defined in:
lib/rocker/rocdata.rb

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(val, aln = nil, window = nil) ⇒ ROCData

Use ROCData.new(table,aln,window) to re-compute from table, use ROCData.new(data) to load



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# File 'lib/rocker/rocdata.rb', line 17

def initialize(val, aln = nil, window = nil)
   @r = RInterface.new
   @nucl = false
   @refined = false
   if not aln.nil?
	 @aln = aln
      @signatures = { v: "ROCker #{ROCker.VERSION}", d: Time.now.to_s }
	 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 = []
      @signatures = {}
	 while ln = f.gets
         break unless /^#:/.match(ln).nil?
         if ln =~ /^#(\S+) (.*)/
            @signatures[$1.to_sym] = $2
         else
            @windows << ROCWindow.new(self, ln)
         end
	 end
	 f.close
	 @aln = Alignment.new
	 @aln.read_rocker(val)
   end
end

Instance Attribute Details

#aln ⇒ Object (readonly)

Returns the value of attribute aln.



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# File 'lib/rocker/rocdata.rb', line 14

def aln
  @aln
end

#r ⇒ Object (readonly)

Returns the value of attribute r.



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# File 'lib/rocker/rocdata.rb', line 14

def r
  @r
end

#refined ⇒ Object (readonly)

Returns the value of attribute refined.



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# File 'lib/rocker/rocdata.rb', line 14

def refined
  @refined
end

#signatures ⇒ Object (readonly)

Returns the value of attribute signatures.



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# File 'lib/rocker/rocdata.rb', line 14

def signatures
  @signatures
end

#windows ⇒ Object (readonly)

Returns the value of attribute windows.



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# File 'lib/rocker/rocdata.rb', line 14

def windows
  @windows
end

Instance Method Details

#_refine_iter(table) ⇒ Object 



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# File 'lib/rocker/rocdata.rb', line 58

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

#in_nucl? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/rocker/rocdata.rb', line 47

def in_nucl?() @nucl end

#init_windows!(size) ⇒ Object 



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# File 'lib/rocker/rocdata.rb', line 128

def init_windows!(size)
   @windows = []
   1.step(self.aln.cols,size).each do |a|
	 @windows << ROCWindow.new(self, a, a+size-1)
   end
end

#is_refined? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/rocker/rocdata.rb', line 57

def is_refined? ; @refined ; end

#load_table!(table, sbj = [], min_score = 0) ⇒ Object 



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# File 'lib/rocker/rocdata.rb', line 82

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

#nucl=(nucl) ⇒ Object 



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# File 'lib/rocker/rocdata.rb', line 48

def nucl=(nucl) @nucl=nucl end

#refine!(table) ⇒ Object 



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# File 'lib/rocker/rocdata.rb', line 49

def refine! table
   while true
	 return false unless self.load_table! table
	 break if self._refine_iter(table)==0
   end
   @refined = true
   return true
end

#rrun(cmd, type = nil) ⇒ Object 



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# File 'lib/rocker/rocdata.rb', line 134

def rrun(cmd, type=nil) self.r.run cmd, type end

#save(file, sign = {}) ⇒ Object 



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# File 'lib/rocker/rocdata.rb', line 135

def save(file, sign = {})
  @signatures.merge! sign
  File.open(file, 'w') { |fh| fh.print self.to_s }
end

#to_s ⇒ Object 



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# File 'lib/rocker/rocdata.rb', line 139

def to_s
  o = signatures.map{ |k,v| "##{k} #{v}\n" }.join
  self.windows.each{ |w| o += w.to_s }
  o += self.aln.to_s
  return o
end

#win_at_col(col) ⇒ Object 



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# File 'lib/rocker/rocdata.rb', line 44

def win_at_col(col)
   self.windows.select{|w| (w.from<=col) and (w.to>=col)}.first
end