====== COGclass2018.pl ======
written by Haeyoung Jeong.

  #!/usr/bin/perl
  # $ARGV[0]: GenQuery.COG.csv.bestHit;
  
  $fun = '/data/Utilities/DB/COG/COG2014/fun2003-2014.tab';
  $name = '/data/Utilities/DB/COG/COG2014/cognames2003-2014.tab';
  
  open FUN, $fun;
  while (<FUN>) {
      chomp;
      next if /^#/;
      my @temp = split /\t/, $_;
      $code2fun{$temp[0]} = $temp[1];
      push @oneLetter, $temp[0];
  }
  close FUN,
  
  open NAME, $name;
  while (<NAME>) {
      chomp;
      next if /^#/;
      my @temp = split /\t/, $_;
      if (length($temp[1]) > 1) {
          my @tmp = split //, $temp[1];
          $item = $tmp[ rand @tmp ];
          $cog2code{$temp[0]} = $item;
          print STDERR "$temp[0] $temp[1] (random selection) ===> $item\n";
      } else {
          $cog2code{$temp[0]} = $temp[1];
      }
      $cog2name{$temp[0]} = $temp[2];
  }
  
  open COG, $ARGV[0]; # GenQuery.COG.csv.bestHit
  while (<COG>) {
      chomp;
      my @temp = split /,/, $_;
      if ($temp[5] == -1) {
          $notAssigned++;
          $num++;
      
      } else {
          $codeNum{$cog2code{$temp[5]}}++;
          $num++;
      }
      print $_, ',', $cog2code{$temp[5]}, ',' . $cog2name{$temp[5]} . "\n"; 
      $lines++;
  } 
  
  print "#--------------------------------------------\n";
  foreach (@oneLetter) {
      $codeNum{$_} = 0 unless exists $codeNum{$_};
      print join "\t", '#', $code2fun{$_}, $codeNum{$_} . "\n";
  }
  print join "\t", '#', 'Not assigned', $notAssigned ."\n";
  print "#--------------------------------------------\n";
  print "#total: $num (line numbers of $ARGV[0] file: $lines)\n";