makeSummaryReadsConditions

#!/usr/bin/env ruby

require 'optparse'
require 'ostruct'
require 'rubygems'
require 'csv'
require 'bio'
require 'ZFile'
require 'Stats'

opt = OpenStruct.new
opt.sizes = false
o = OptionParser.new
o.banner << " csv file [fasta...fasta...]"
o.on("-s", "--size", "include read sizes") {opt.sizes = true}
begin
  o.parse!
rescue
  STDERR << $!.message << "\n"
  STDERR << o
  exit(1)
end
if (ARGV.size < 1)
  STDERR << o
  exit(1)
end

csv = ARGV.shift

reads = Hash.new
isogroups = Hash.new
contigs = Hash.new
conditions = nil 
assembly = File.basename(csv, ".csv").split("_isotigs").first
greads = Hash.new
greadMed = Hash.new
greadMean = Hash.new 
 
CSV.foreach(csv, :headers => true, :converters => :numeric) do |row|
  contig = row["Contigs"]
  isogroup = row["Isogroup"]
  conditions = row.headers.grep(/Normalized/).collect{|x| x.split(" ").first} if (!conditions)
  conditions.each do |condition|
    if (!greads[condition])
      greads[condition] = 0
      greadMean[condition] = 0
      greadMed[condition] = 0
      if (opt.sizes)
        lens = []
        STDERR.printf("Counting reads for %s...\n", condition)
        Bio::FlatFile.new(Bio::FastaFormat, ZFile.new(condition + ".fna.bz2")).each do |read|
          greads[condition] += 1
          lens.push(read.length)
        end
        greadMean[condition] = lens.median.to_i
        greadMed[condition] = lens.average.to_i
      end
    end
    reads[condition] = 0 if (!reads[condition])
    contigs[condition] = Hash.new if (!contigs[condition])
    isogroups[condition] = Hash.new if (!isogroups[condition])
    reads[condition] += row[condition]
    contigs[condition][contig] = true if (row[condition] > 0)
    isogroups[condition][isogroup] = true if (row[condition] > 0)
  end
end

headers = ["Conditions", "Reads in Assembly", "Reads Generated", "Mean Read Len", "Median Read Len", 
  "Assembly", "Isogroups", "Contigs"]

print headers.to_csv
conditions.each do |condition|
  print [condition, reads[condition], greads[condition], greadMean[condition], greadMed[condition],
    assembly, isogroups[condition].keys.size, contigs[condition].keys.size].to_csv
end