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!

In reply to Re^4: General program and related problems by micky744monk
in thread General program and related problems by micky744monk

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