====== post_phylosift.pl ======

  #!/usr/bin/perl
  #
  # argument 1: phylosift output directory (PS_temp)
  # argument 2: marker ID (DNGNG...)
  
  if (scalar @ARGV < 2) {
      print STDERR "You didn's speficied enough arguments!\n";
      exit;
  }
  
  $outdir = $ARGV[0] or 'PS_temp';
  opendir OUTDIR, $outdir;
  
  @org_dir = grep { not /^\./ } readdir OUTDIR;
  print STDERR "Organisms detected: @org_dir"\n;
  closedir OUTDIR;
  $final = "$ARGV[1].fsa";
  unlink $final if -f $final;
  open ALIGN, ">>$final";
  
  foreach my $org (sort @org_dir) {
      my @t = split /\./, $org;
      pop @t;
      $seq_id = join '.', @t;
  #    print "Seq ID: $seq_id\n";
      $fasta = "$ARGV[0]/$org/alignDir/$ARGV[1].codon.updated.1.fasta";
      $fasta = "$ARGV[0]/$org/alignDir/$ARGV[1].long.1.fasta" if $ARGV[1] =~ /16s_reps_bac/;
      open RESULT, $fasta or print STDERR "Can't open file $fasta for reading!\n";
      while (<RESULT>) {
          chomp;
          if (/^>(\S+)/) {
              print ALIGN ">$seq_id $1\n";
          } else {
              print ALIGN $_, "\n";
          }
      }
      close RESULT; 
  }