hi,
I am a baby at perl so pls be gentle.
I am tring to read and write to a file at the same time. for now I have separated them (read from TEMPFILE and write to DBFILE).
what I need to do is add to the end of each line in the temp file the value $sequenceValue.
another problem Im having is althogh I use "seek" when reding the file I get the second line and not the first. thanks. 
print "what length?\n";
$sequenceLength = getc;
$fileName =  $sequenceLength . "temp.txt";

open(TEMPFILE,"+>".$fileName) or die "Can't open output.txt: $!";


sub builed_list{
  my($length, $seq)=@_;

  if($length == 1)
  {
    print TEMPFILE $seq;
    print TEMPFILE "\n";
    return;
  }

  $length--;
  $sequenceA = $seq ."A";
  builed_list($length, $sequenceA);
  $sequenceC = $seq ."C";
  builed_list($length, $sequenceC);
  $sequenceG = $seq ."G";
  builed_list($length, $sequenceG);
  $sequenceT = $seq ."T";
  builed_list($length, $sequenceT);
}
$sequence = "A";
&builed_list($sequenceLength,$sequence);
$sequence = "C";
&builed_list($sequenceLength,$sequence);
$sequence = "G";
&builed_list($sequenceLength,$sequence);
$sequence = "T";
&builed_list($sequenceLength,$sequence);

$seekGood = seek TEMPFILE, 0, 0; #go to the begining of the file
if($seekGood == 0)
{
  die "can't seek\n";
}
$fileName =  $sequenceLength . "DB.txt";
open(DBFILE,"+>".$fileName) or die "Can't open output.txt: $!";

while(<TEMPFILE>)
{
  read TEMPFILE, $sequence, $sequenceLength;
  $sequenceValue = 0;

  for ($i=0; $i<$sequenceLength; $i++)
  {
    $base = substr $sequence, $i, 1;
    $addValue = 0;
    if($base eq "C")
    {
      $addValue += 1;
    }
    elsif($base eq "G")
    {
      $addValue += 2;
    }
    elsif($base eq "T")
    {
      $addValue += 3;
    }

    for($j=$i+1; $j<$sequenceLength; $j++)
    {
      $addValue *= 10;
    }
    $sequenceValue += $addValue;

  }
  print DBFILE "$sequence $sequenceValue";
  
  print DBFILE "\n";
  printf("%s %d\n",$sequence,  $sequenceValue);
}

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In reply to how to read and write at the same time + a problem with seek by wolffm

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