Assuming you need to compare only the three last fields of your input files and that these three fields define a unique key for comparison, you could:
  1. read file 1 and store the 3 fields of interest into a hash (the three fields concatenated as a key, with a value of, say, 1);
  2. close file 1;
  3. read file 2, grab the three fields and check if that key exists in the hash.
Update:

The following is Perl pseudo-code to do that: 

my %hash;
# first open file1
while (my $line1 = <$file1>) {
    my $key = join ";", (split /,/, $line1)[1..3];
    $hash{$key} = 1;
}
close $file1;
open my $file2, "<", "file2.txt" of die "could not open file2.txt $!";
while (my $line2 = <$file1>) {
    my $key = join ";", (split /,/, $line2)[1..3];
    if (exists $hash{$key}) {
        # do something
    } else {
        # do something else
    }
}

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In reply to Re: Comparing specific columns from 2 files by Laurent_R
in thread Comparing specific columns from 2 files by arunsriniv

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