Paste left read and right read from Illumina into a single megaread

mergePairedReads.rb

#!/usr/bin/env ruby
# (copy) Yannick Wurm - google me.
# All right reserved. 

help = "Usage: \n" + 
       "      #{$0} MySequences_R1.fastq MySequences_R2.fastq > MySequences_R1R2pasted.fastq\n" + 
       "Joins two paired reads into a single megaread. Can be helpful for deduplication.\n" +
       "The two fastq files must have reads in the same order. Some error checking is performed.\n"


##require 'bio-faster' # not used because I can only read one at a time. (there is no "next_entry" method)
##require 'bio'        # not used because I couldnt easily create a new fastq with pasted quality scores

if ARGV.length != 2 then
  warn help
  exit
end


fastq_R1, fastq_R2 = ARGV[0], ARGV[1]
[fastq_R1, fastq_R2].each do |file|
  raise IOError "Cannot find: #{file}" unless File.exists?(file)
  raise IOError "Empty file:  #{file}" if     File.zero?(file)
end


fastq_R1_stream = File.open(fastq_R1, 'r')
fastq_R2_stream = File.open(fastq_R2, 'r')

warn "Will merge #{fastq_R1} and #{fastq_R2}. If something crashes there is a problem with your fastq files"

while TRUE
  r1_id_line = fastq_R1_stream.gets
  r2_id_line = fastq_R2_stream.gets

  if r1_id_line.nil? and r2_id_line.nil? 
    warn "Reached end of both files. Done."
    exit 
  end
  if r1_id_line.nil? or r2_id_line.nil? 
    warn "ERROR: End of one file but not the other"
    warn "#{fastq_R1} contains: #{r1_id_line}"
    warn "#{fastq_R2} contains: #{r2_id_line}"
    warn "Prematurely stopping here"
  end

  r1_id    = r1_id_line.split(' ')[0]   #only id before space      
  r1_seq   = fastq_R1_stream.gets.chomp
  fastq_R1_stream.gets  # skip the line starting with "+"
  r1_quals = fastq_R1_stream.gets.chomp


  
  r2_id    = r2_id_line.split(' ')[0]
  r2_seq   = fastq_R2_stream.gets.chomp
  fastq_R2_stream.gets.chomp
  r2_quals = fastq_R2_stream.gets.chomp

  
  raise IOError, "Different ids in both files: first: #{r1_id}, second: #{r2_id}" if r1_id != r2_id

  puts [r1_id, 
        r1_seq + r2_seq,
        '+',
        r1_quals + r2_quals
       ].join("\n")
end
warn "Done."