#!/usr/bin/env ruby
=begin
------------------------------------------------------------------
  doVelvet.rb
------------------------------------------------------------------
  for executing velvet for 50 simulated circular read data
------------------------------------------------------------------
  all rights reserved to TOQUE
------------------------------------------------------------------
  started on 03 Mar. 2020
------------------------------------------------------------------
  This script assumes that you have velvet files in
  /Volumes/comp1/GenomeSeq/velvet.  
  After 'chmod +x,' execute the following commands.
------------------------------------------------------------------
  cd [your_path]/circular20/contigs/
  mkdir velvet
  cd velvet
  ../../rbsCir/doVelvet.rb
------------------------------------------------------------------
=end

seeds = Array.new
File.open("../../rbsRing/rseeds.txt"){|fh|
  fh.each{|line|
    line.chomp.split(",").each{|rs|
      seeds << rs.to_i
    }
  }
}

seeds.each{|seed|  
  command = "../../../software/velvet/velveth vlvt#{seed} 61 -shortPaired -fastq -separate ../../ringReads/r#{seed}/sim90i200c20_?.fq -shortPaired -fastq -separate ../../ringReads/r#{seed}/sim90i500c20_?.fq; ../../../software/velvet/velvetg vlvt#{seed} -ins_length auto -exp_cov auto -cov_cutoff auto; mv vlvt#{seed}/contigs.fa r#{seed}.fa; rm -rf vlvt#{seed}"
  system(command)
}