G'day agnes00,

The following reads through the input file twice: once to gather information; a second time to generate the output. The data that's collected is small; there's no reproduction of the data already in the input file. There are no nested loops. The only regex is the /;/ in the split statement.

You only showed two lines of sample data: this code will exclude the record with the two instances of 'SU LI IR ST' regardless of the order in which it appears. I've added other test data: I've no idea whether that's representative of your real data.

#!/usr/bin/env perl

use strict;
use warnings;
use autodie ':all';
use constant {
    MATCH => 0,
    CHECK1 => 2,
    CHECK2 => 4,
    FLAG => 'SU LI IR ST',
    RECORD => 0,
    EXCLUDE => 1,
};

my $backup = 'pm_11115310_lines_BU.txt';
my $temp = 'pm_11115310_lines_TMP.txt';
my $input = 'pm_11115310_lines.txt';

`cp $backup $input`;

_print_data($input);

my (%seen, %exclude);

{
    open my $fh, '<', $input;

    while (<$fh>) {
        chomp;
        ++$exclude{$.} and next unless length;
        my @parts = split /;/, $_, 6;
        my $possible_exclude
            = $parts[CHECK1] eq FLAG && $parts[CHECK2] eq FLAG;

        if (exists $seen{$parts[MATCH]}) {
            if ($possible_exclude) {
                ++$exclude{$.};
            }
            else {
                if ($seen{$parts[MATCH]}[EXCLUDE]) {
                    ++$exclude{$seen{$parts[MATCH]}[RECORD]};
                    $seen{$parts[MATCH]}= [$., 0];
                }
            }
        }
        else {
            $seen{$parts[MATCH]} = [$., $possible_exclude];
        }
    }

    seek $fh, 0, 0;
    $. = 0;
    open my $tmp, '>', $temp;

    while (<$fh>) {
        next if $exclude{$.};
        print $tmp $_;
    }
}

`cp $temp $input`;

_print_data($input);

sub _print_data {
    my ($file) = @_;
    print '-' x 20, " $file ", '-' x 20, "\n";
    system cat => $file;
    print '-' x (42 + length $file), "\n";
}
[download]

Output:

-------------------- pm_11115310_lines.txt --------------------

S_FER_SCAM1_ARRESTO;ARRESTO;ST;0;ST;1;0;TS;0;0


S_FER_SCAM1_ARRESTO;ARRESTO;SU LI IR ST;0;SU LI IR ST;1;0;TS;0;0

S_FER_SCAM2_ARRESTO;ARRESTO;ST;0;ST;1;0;TS;0;0
S_FER_SCAM2_ARRESTO;ARRESTO;SU LI IR ST;0;SU LI IR ST;1;0;TS;0;0
S_FER_SCAM2_ARRESTO;ARRESTO;XU LI IR ST;0;SU LI IR ST;1;0;TS;0;0
S_FER_SCAM2_ARRESTO;ARRESTO;SU LI IR ST;0;XU LI IR ST;1;0;TS;0;0
S_FER_SCAM2_ARRESTO;ARRESTO;XU LI IR ST;0;XU LI IR ST;1;0;TS;0;0

S_FER_SCAM3_ARRESTO;ARRESTO;ST;0;ST;1;0;TS;0;0

S_FER_SCAM4_ARRESTO;ARRESTO;SU LI IR ST;0;SU LI IR ST;1;0;TS;0;0

S_FER_SCAM5_ARRESTO;ARRESTO;SU LI IR ST;0;SU LI IR ST;1;0;TS;0;0
S_FER_SCAM5_ARRESTO;ARRESTO;ST;0;ST;1;0;TS;0;0

---------------------------------------------------------------
-------------------- pm_11115310_lines.txt --------------------
S_FER_SCAM1_ARRESTO;ARRESTO;ST;0;ST;1;0;TS;0;0
S_FER_SCAM2_ARRESTO;ARRESTO;ST;0;ST;1;0;TS;0;0
S_FER_SCAM2_ARRESTO;ARRESTO;XU LI IR ST;0;SU LI IR ST;1;0;TS;0;0
S_FER_SCAM2_ARRESTO;ARRESTO;SU LI IR ST;0;XU LI IR ST;1;0;TS;0;0
S_FER_SCAM2_ARRESTO;ARRESTO;XU LI IR ST;0;XU LI IR ST;1;0;TS;0;0
S_FER_SCAM3_ARRESTO;ARRESTO;ST;0;ST;1;0;TS;0;0
S_FER_SCAM4_ARRESTO;ARRESTO;SU LI IR ST;0;SU LI IR ST;1;0;TS;0;0
S_FER_SCAM5_ARRESTO;ARRESTO;ST;0;ST;1;0;TS;0;0
---------------------------------------------------------------
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Do note my use of a backup file. Simply overwriting your input data is not a good move at all!