Hi rashichauhan,

Code is not working.A new file is genertaed but consist of only last element of first file.Plz help me in this regard.

Use an hash and cut the chase on using for loops.
Open the first file and read line by line, then on each line split on space, use those as your key/value of the hash.Then open the second file, step through it, one after the other, splitting on each line too. Then use the word to check if such exist in your hash, if so print it to the file you want and if not print it to another one.

Something like this will do.

#!/usr/bin/perl -l
use warnings;
use strict;

use Inline::Files;

my %file1;

while (<FILE1>) {
    next if /^\s+$/;
    my ( $key, $value ) = split;
    $file1{$key} = $value;
}
my $str_union;
my $str_inter;

while (<FILE2>) {
    next if /^\s+$/;
    my ( $key, $value ) = split;
    if ( $file1{$key} ) {
        $str_union .= $_;
    }
    else {
        $str_inter .= $_;
    }
}

print "This goes to File 3\n", $str_union,
  "\nThis goes to File 4\n", $str_inter;

__FILE1__
EC:1.1.1.42    isocitratedehydrogenase
EC:1.1.1.44    6-phosphogluconatedehydrogenase
EC:1.1.1.49    glucose-6-phosphate1-dehydrogenase

__FILE2__
EC:1.1.1.42    isocitratedehydrogenase
EC:1.1.1.44    6-phosphogluconatedehydrogenase
EC:1.1.1.49    glucose-6-phosphate1-dehydrogenase

EC:1.11.1.9    glutathioneperoxidase
EC:2.5.1.16    spermidinesynthase

EC:6.3.1.8    glutathionesynthase
[download]

Note: Though this code works, but it just to show the concept am describing. On a 'good' day since the two while loops "smell" the same one can 'string' them together in a way to avoid DRY
Hope this helps.