find_pvalue.rb in macroape-3.3.0

- old
+ new

@@ -22,11 +22,13 @@
   type motifs/KLF4.pat | ruby find_pvalue.rb .stdin 7.32 4.31 5.42
            or in linux
   cat motifs/KLF4.pat | ruby find_pvalue.rb .stdin 7.32 4.31 5.42
 }
 
+$:.unshift File.join(File.dirname(__FILE__),'./../../')
 require 'macroape'
+require 'bioinform'
 
 if ARGV.empty? or ARGV.include? '-h' or ARGV.include? '-help' or ARGV.include? '--help' or ARGV.include? '--h'
   STDERR.puts help_string
   exit
 end
@@ -54,25 +56,25 @@
       when '-b'
         background = ARGV.shift(4).map(&:to_f)
       when '-d'
         discretization = ARGV.shift.to_f
       when '-m'
-        PWM::MaxHashSize = ARGV.shift.to_f
+        Macroape::MaxHashSizeSingle = ARGV.shift.to_f
     end
   end
-  PWM::MaxHashSize = 1000000 unless defined? PWM::MaxHashSize
+  Macroape::MaxHashSizeSingle = 1000000 unless defined? Macroape::MaxHashSizeSingle
   
   
   if filename == '.stdin'
-    pwm = PWM::SingleMatrix.load_from_stdin(STDIN)
+#  TODO
   else
     raise "Error! File #{filename} doesn't exist" unless File.exist?(filename)
-    pwm = PWM::SingleMatrix.load_pat(filename)
+    pwm = Bioinform::PWM.new( File.read(filename) )
   end
-  pwm = pwm.with_background(background)
+  pwm.background(background)
 
   counts = pwm.discrete(discretization).counts_by_thresholds(* thresholds.map{|count| count * discretization})
-  pvalues = counts.map{|count| count.to_f / pwm.number_of_words}
+  pvalues = counts.map{|count| count.to_f / pwm.vocabulary_volume}
   pvalues.zip(thresholds,counts).each{|pvalue,threshold,count|
     puts "#{threshold}\t#{count}\t#{pvalue}"
   }
 rescue => err
   STDERR.puts "\n#{err}\n#{err.backtrace.first(5).join("\n")}\n\nUse -help option for help\n"
\ No newline at end of file