#!/usr/bin/env ruby 

require 'optimist'
require 'csv'

ARGV.push("--help") if ARGV.empty?
opts = Optimist::options do
  banner File.basename($0)
  opt :input, "input file(s)", :required=>true, :type=>:strings
  opt :metadata, "metadata.tsv", :required=>true, :type=>:string
  opt :num, "normalizing number", :default=>100000
  opt :csv, "output standard normalized csv"
end

samples = Hash.new
CSV.foreach(opts.metadata, options={:col_sep=>"\t", :headers=>true}) do |row|
  samples[row["Analysis_Id"]]=row["Sample"]
end

counts = Hash.new
levs = Hash.new
usedSamples = Hash.new
opts.input.each do |file|
  if File::Stat.new(file).size > 50
    name = File.basename(file, "_metaphlan.complex.trimmed.fasta.metaphlan")
    sample = samples[name]
    usedSamples[sample] = true if sample !~/VALIDATION/
    File.new(file).each do |line|
      if line =~/__/
        taxon, per = line.chomp.split("\t")
        count = (per.to_f*opts.num/100.0).to_i
        lev = taxon.split("|").last
        counts[lev] = Hash.new if ! counts[lev]
        counts[lev][sample] = count
      end
    end
  end
end


if opts.csv
  header = ["Sample", "Patient", "Sample_Type", "Library_Type"]
  header += counts.keys.sort
  print header.to_csv
  usedSamples.keys.sort.each do |key|
    row = [key] + key.split("_")
    row += counts.keys.sort.collect{|x| counts[x][key].to_i}
    print row.to_csv
  end
else
  header = ["taxlevel"," rankID", " taxon", " daughterlevels", " total"]
  header += usedSamples.keys.sort
  print header.to_csv(:col_sep=>"\t")
  counts.keys.sort.each do |key|
    lcounts = usedSamples.keys.sort.collect{|x|counts[key][x].to_i}
    row=["","",key,"", lcounts.reduce(:+)]
    row += lcounts
    print row.to_csv(:col_sep=>"\t")
  end
end