blastLocalAllVsAll

#!/usr/bin/env ruby

require 'ostruct'
require 'optparse'

opt = OpenStruct.new
opt.btab = false
opt.evalue = 1e-9
opt.maxHits = 50
$VERBOSE = nil
opt.blast = "blastp"


ARGV.options {|opts|
  opts.banner << " fasta [fasta...fasta...]"
  begin
    opts.on("-b ", "--blast ", String, 
    "blast to use (default #{opt.blast})") {|t| opt.blast = t}
    opts.on("-e", "--evalue ", Float, 
            "set BLASTP evalue (default #{opt.evalue})") {|t| opt.evalue = t}
    opts.on("-m ", "--maxHits ", Integer, 
          "max number of BLAST hits (default #{opt.maxHits})") {|t| opt.maxHits = t}
    opts.on("-x", "--btab", "run btab (default #{opt.btab})") {|t| opt.btab = t}
    opts.parse!
  rescue
    STDERR.puts $!.message
    STDERR.puts opts
    exit(1)
  end
  if (ARGV.size < 1)
    STDERR.puts opts
    exit(1)
  end
}

ARGV.each {|pep1|
  ARGV.each {|pep2|
    if (pep1 != pep2)
      if (Dir.glob("#{pep2}_vs_#{pep1}*").empty?)
        system("blastall -p  #{opt.blast} -e #{opt.evalue} -b #{opt.maxHits} -v #{opt.maxHits} -d #{pep1} -i #{pep2} > #{pep2}_vs_#{pep1}.blastp")
        system("btab #{pep2}_vs_#{pep1}.blastp") if opt.btab
      else
        STDERR.printf("Skipping #{pep1}_vs_#{pep2} due to existing results...\n")
      end
    end
  }
}