#!/usr/bin/perl -w
use strict;
my$line;
my@fields;
my@output;
open (FILE1, 'snp2.txt') or die "can't open the file: $!";
open (FILE2,'chr22.txt') or die "can't open the file: $!";
open (FD, '>test.txt') or die "can't open the file: $!";
my $position = tell(FILE2);
my %rs;
while ($line=<FILE2>) {
  my ($key)= $line=~/^(rs\d{5,})\b/;
  if (defined $key) {
  $rs{$key}= $position;
  }
  $position=tell(FILE2);
}
while (defined ($line= <FILE1>)) {
    my@fields= split (/\s+/ ,$line);
    my@output = grep /^rs\d{5,}\b/ ,@fields;
}
        foreach (@output) {
              if (exists $rs{$_}) {
                seek(FILE2,$rs{$_},0);
                my $line= <FILE2>;
    print FD $line;

    }
}
Close FILE1;
Close FILE2;
Close FD;
[download]

Did you see that your program is producing an error message? It should be 'close', not 'Close' at the end

Some words on debugging. If you don't know what your program does, insert print statements to find out (or use Data::Dumper).

For example a simple print @output; before the foreach loop would have told you that @output is empty.

Then you could have looked at the previous loop where @output should have been filled. A print join('|',@fields),"\n"; or even better print Dumper(\@fields); (you also need a line use Data::Dumper for this) and print Dumper(\@output); at the end of the loop would have given you surprising results. If you want to learn something, please do the above, look at the result and think about it. If you don't find the solution, read the spoiler below.

<Reveal this spoiler or all spoilers in this node or all in this thread>

After you solved the first problem you will see that there is a further problem, you are getting only the result of the last line in file1. The ouput of the prints or Dumper lines should give you a clue again, if not read the next spoiler

<Reveal this spoiler>

Thank you again for the time you are spending with me....I understood the other problems, whilst the push @array is not really a problem since even with this code printing the @output list I have all the rs from file 1. The code is still not working, but trying to run the code and checking the output I noticed that the first code had an empty hash. Now I tried to play a bit with hash definition (and what I did could be completely wrong) but now the array is giving me the file1 together with a number that could be the position, so I guess the code is treating the file like only one string....I do not know it should be something wrong on the first block and on the hash definition....if you could point me in the right direction, I could keep going on the debugging....

#!/usr/bin/perl -w
use strict;
my$line;
my@fields;
my@output;
my$position;
my%rs;
open (FILE1, 'snp.txt') or die "can't open the file: $!";
open (FILE2,'chr22.txt') or die "can't open the file: $!";
open (FD, '>test.txt') or die "can't open the file: $!";
while ($line=<FILE2>) {
      $line=~/^(rs\d{5,})\b/;
      $position = tell( FILE2 );
          if (defined $line) {
          $rs{$line}= $position;
      }
}
print %rs;

while (defined ($line= <FILE1>)) {
    my@fields= split (/\s+/ ,$line);
    @output=grep /^rs\d{5,}\b/ ,@fields;
}

foreach (@output) {
              if (exists $rs{$_}) {
                seek(FILE2,$rs{$_},0);
                my $line= <FILE2>;
    print FD $line;

    }
}
close FILE1;
close FILE2;
close FD;
[download]

The output file is empty to be precise Cheers again!