#!/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;