Here's a quick intro.

In your case you would not have any values in the hash, just keys. You'd read the smaller file and add the lines to a hash as keys (the values are irrelevant, use 1 for example). Then as you would read the other file you'd just check whether exists $hash{$line} and you'd know right away whether such line was in the first file or not.

How do I then, get the data i want into the array?

use Modern::Perl
open trained , 'D://ARP//libsvm-3.12//families//antioxidant//independe
+nt.scale';
open predict , 'D://ARP//libsvm-3.12//families//antioxidant//testing.s
+cale';
my $counter =  0;
my $lol = 0;
select trained;
my @train = $_;
while (<predict>) {
    #print $_;
    
    my $predict = $_;
    if (exists $train{$predict} {
    print $predict;
    $counter = $counter + 1
}
}
print $counter;
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like this?

First by reading some docs. Random typing will not work!

What's the $lol variable for? Why do you select() a filehandle opened for reading? What do you think will be in $_ on line 7? You declare array @train, but later on attempt to use hash %train!

Jenda
Enoch was right!
Enjoy the last years of Rome.