The perl code is calling out to the shell with the system command. It's using interpolation to inject the value of the perl variables $label, $apex, $reference, and $name into the string that will be executed by the shell.

The output of the awk command will be captured in a file named temp_marker_$name, where $name is first expanded to whatever is held in that perl variable

The purpose of the the backslashes in the string is to ensure that the following character is passed literally to the shell. For example, this prevents perl from treating constructs such as "$3" as a perl variables.

\ is being used as an escape character, the variables are being used insert values within parts of the strings (see String_interpolation). Basically the program is building a command which gets called by system. You can output the command to screen easily by replacing the system call with a print, like so

print "awk \'\$1 == \"$label\" && \$3 <= $apex && \$4 >= $apex\{print\
+}\' $reference >temp_marker_$name";
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Using Perl instead of awk you would do:

use strict; 
use warnings;
my $label     = "some string";
my $apex      = 10; # some number
my $reference = "somefile.txt";
my $name      = "out.txt";

open IN, "<", $reference or die "Cannot open file $reference.\n";
open OUT, ">", "temp_marker_$name" or die "Cannot open file temp_marke
+r_$name.\n";
while(<IN>) {
    my @fields = split; # cannot remember what awk splits on by defaul
+t
    if( $fields[0] eq $label
    and $fields[2] <= $apex
    and $fields[3] >= $apex ) {
        print OUT $_;
    }
}
close OUT;
close IN;
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So basically its a loop? Is the comparison being done on every line in reference, a single line, or some other part?

Pretty much. Awk works a lot like "perl -ane", looping over lines in a file and splitting them into fields. An awk command is of the form "TEST { ACTION }", where TEST controls whether ACTION is performed. It's more involved than that, but since I learned Perl first, I rarely use awk. You might try feeding the awk command to a2p to get a perl equivalent of what it does.