First of all sugar++ for giving us sample input and reference output as well as a clear description of what your problem is.

In addition to what the others have said: You build a fairly large regex from @dels, which might slow down things (if the number of items is in the millions).

I'd suggest to use a hash instead of @dels: 

#!/usr/bin/perl
use strict;
use warnings;
my $prev1=0;my $prev2=0;my @dels;
open my $file, '<', 'data.txt' or die "Can't open file: $!@";

my %dels;
while (<$file>) {
    # the \. prevents . from matching any character
    my @spl = split(/\.[fr]/, $_);
    if($prev1 eq $spl[0] && $prev2 eq $spl[1]){
        $dels{$spl[0]} = 1;
    }
    $prev1=$spl[0];$prev2=$spl[1];
}

# reset the file cursor, read from the beginning again
seek $file, 0, 0;
while (<$file>) {
    my @spl = split(/\.[fr]/, $_);
    print unless $dels{$spl[0]};
}
close $file;

[download]

This version gets rid of @arr entirely, and replaced the regex and @dels with %dels.

In reply to Re: to delete a set of specific lines in a file by moritz
in thread to delete a set of specific lines in a file by sugar

Title:
Use:  <p> text here (a paragraph) </p>
and:  <code> code here </code>
to format your post, it's "PerlMonks-approved HTML":


  • Posts are HTML formatted. Put <p> </p> tags around your paragraphs. Put <code> </code> tags around your code and data!
  • Titles consisting of a single word are discouraged, and in most cases are disallowed outright.
  • Read Where should I post X? if you're not absolutely sure you're posting in the right place.
  • Please read these before you post! —
  • Posts may use any of the Perl Monks Approved HTML tags:
    a, abbr, b, big, blockquote, br, caption, center, col, colgroup, dd, del, details, div, dl, dt, em, font, h1, h2, h3, h4, h5, h6, hr, i, ins, li, ol, p, pre, readmore, small, span, spoiler, strike, strong, sub, summary, sup, table, tbody, td, tfoot, th, thead, tr, tt, u, ul, wbr
  • You may need to use entities for some characters, as follows. (Exception: Within code tags, you can put the characters literally.)
            For:     Use:
    & &amp;
    < &lt;
    > &gt;
    [ &#91;
    ] &#93;
  • Link using PerlMonks shortcuts! What shortcuts can I use for linking?
  • See Writeup Formatting Tips and other pages linked from there for more info.