require POSIX;


open(FILE, ">ighv-refdir-aligned.phy");



open(REFDIR, "ighv-refdir-aligned.txt");

my($i) = 0;
my(@names) = ();
my(@sequences) = ();
while (<REFDIR>) {
  my(@regions) = split(/\s+/);
  $names[$i] = $regions[0];
  $sequences[$i] = $regions[1];
  $sequences[$i] .= $regions[3];
  $sequences[$i] .= $regions[5];
  
  print $names[$i];
  if (length($names[$i]) > 15) {
    print "\t"; 
  } else {
    print "\t\t"; 
  }
  print $sequences[$i] . "\n";
  $i++;
}


my($cnt) = 0;
#for ($cnt=0; $cnt<50; $cnt++) #length($sequences[0])) {
  #for ($j=0; $j<=$#names; $j++) {
printf FILE "\t" . scalar @names . "\t" . length($sequences[0]) . "\n";
for ($i=0; $i<@names; $i++) {
  print FILE substr($names[$i], 0, 6);
  print FILE "     ";
  for ($cnt=0; $cnt<50; $cnt++) {
    print FILE substr($sequences[$i], $cnt, 1);
    if ((($cnt+1) % 10) == 0) {
      print FILE " ";
    }
  }
  print FILE "\n";
}

printf FILE "\n";
        
$kmax = length($sequences[0]) / 50; $kmax = POSIX::floor($kmax);
$k = 1;
$mult = 50;
$multx = 0;

while ($k <= $kmax) {
    if ($k == $kmax) {
        $multx = length($sequences[0]) - $kmax * 50;
    } else
    {
        $multx = 50;
    }

    for ($i=0; $i<@sequences; $i++) {
      printf  FILE "           ";
      for ($j=$k * $mult; $j<($k * $mult + $multx); $j++) {
        printf FILE substr($sequences[$i], $j, 1);
        if ((($j+1) % 10) == 0) {
          printf FILE " ";
        }
      }
      printf FILE "\n";
    }
    printf FILE "\n";
    $k++;
  }