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#declare all filenames
$filename1 = 'one.txt';
$filename2 = 'two.txt';
$filename3 = 'three.txt';

#open text file 1

open (FILE1, $filename1) or die "Unable to open $filename1 because $!\
+n";

# Store the contents of the first file into $hash{col1_col2}

...
    $hash{$key1}++;
};
close FILE1;

while ($line = <FILE2>) {
    chomp ($line);
...
    $hash{key2}++
}
};

while ($line = <FILE2>) {
    chomp ($line);
...
        $hash{key2}++
    }
};

open (FILE2, $filename2) or die "Unable to open $filename2 because $!\
+n";

...
}
};
close FILE2;

sub process_file {
    my $filename = shift or die "Missing filename!";
...
    }
    close FILE;
}

process_file($filename2);
process_file($filename3);