#!/usr/bin/env ruby

=begin
collect_varFilter_results.rb
06 November 2010

Read in varFilter output files from a folder tree.

/projects/mirna/MX/TCGA/LAML/*/*/snv/*.varFilter

=end
basedir = "/projects/mirna/MX/TCGA/LAML"

Dir.chdir(basedir)
#Dir.chdir("/Users/grobertson/GENEREG/ChIP/CHIP_SEQ/SOLEXA/TCGA/AML/data/genomic_wash-u/test")

samples = Dir.glob("MX*")

i = 0
samples.each do |sample|
   i += 1
   puts "#{i}: #{sample}"

   subdir = File.join( basedir, sample )
   Dir.chdir(subdir)

   features = Dir.glob("MX*features")
   i = 0
   features.each do |feature|
      i += 1
      puts " #{i}: #{feature}"


      snvdir = File.join( feature, "snv" )
      Dir.chdir(snvdir)
         # MX0062_ATTGGC_mirna.minSNVQ20.varFilter
         varfilter = Dir.glob("*.varFilter")
         puts "  #{varfilter}"

         #in_rh = File.open( varfilter, 'r' )




   end

end


puts "\ndone!"